bluuebunny/crossref_metadata_2025 huggingface dataset:
Why respiratory viruses or bacteria have the highest probability to be deposited in the respiratory tract in flu seasons
Authors: Ishmatov Aleksandr N
Published: January 2018

Marc Lipsitch and Cécile Viboud (2009) (Lipsitch and Viboud, 2009): “Seasonal variation in the incidence of communicable diseases is among the oldest observations in population biology, dating back at least to ancient Greece, yet our understanding of the mechanisms underlying this phenomenon remains hazy at best.”

The latest researches show the infected people when breathing generate the infectious aerosols with particles below 1 µm. The airborne transmission of these particles is effective but the deposition of submicron particles in the respiratory tract (RT) has very low probability.

Here I investigated the processes in RT when breathing cold air and its role in the delivery of viruses and bacteria of submicron and ultrafine sizes in RT.

The original hypothesis of the highest probability of delivery and deposition of viruses or bacteria from inhaled air in the respiratory tract during flu seasons in different climatic conditions was investigated.

On the basis of estimation I have originally shown: Breathing cool air leads to the supersaturation of air in RT; the air supersaturation leads to the intensive condensational growth(CG) of inhaled viruses or bacteria in RT; CG leads to the intensive and dramatically growth of deposition rate of viruses or bacteria in RT.

Under normal conditions of inhaled air (T>20˚C; RH=60%) there is no transition in oversaturated condition in RT (CG is insignificant and probability of virus deposition on epithelium of RT is low – no more than 20%).

But with an increase in RH of inhaled air the oversaturation in RT occurs even at warm temperature of inhaled air. For inhaled air of T=20°C, RH>70% the local supersaturation in the airways occurs: the concentration of liquid water in the mixed air in RT (СLiq) is СLiq<2·4g/kg and for T=25°C; RH>90% СLiq<1·2g/kg.

The estimation also shown that for conditions of breathing cold air of T [-15..+15]˚C and Relatively Humidity (RH) of [30..60]% the supersaturation in the airways occurs: the concentration of liquid water in the mixed air in RT (СLiq) is [0·2..12·1]g/kg.

Under these conditions the growth of inhaled particles by condensation in RT is significant. It lead to the dramatically growth of deposition rate of the viruses and bacteria in RT (up to 97%).

These results correspond to influenza and seasonal respiratory infections in temperate and tropical climates and indicate the high probability of virus deposition on epithelium of RT.

It may be the key to ‘the age-old epidemiologic mystery of influenza seasonality in the different climatic conditions’.
Why respiratory viruses or bacteria have the highest probability to be deposited in the respiratory tract in flu seasons
Authors: Ishmatov Aleksandr N
Published: January 2018

Objective:

In this study the main aspects of influenza transmission via fine and ultrafine bioaerosols were considered. Here, we aimed to estimate the impact of the different environment conditions on the deposition rate of the infectious bioaerosols in the respiratory tract (RT).

Background:

The latest researches show the infected people generate the fine and ultrafine infectious bioaerosols with submicron particles/droplets (size below 1 µm). The airborne transmission of these particles/droplets in the environment is effective. It is considered the deposition of submicron particles in RT has very low probability. But most studies examined the deposition of the particles in RT under normal environmental conditions and did not paid attention to the different environmental factors.

Methods:

We review the problems of epidemiology of respiratory infections and aspects of airborne transmission/spread of infectious agents. We contrast these approaches with known data from next area: inhalation toxicology, respiratory drug delivery and physics of heat and mass transfer in the airways.

Results:

On the basis of these analyses, we propose the next main concepts:

1 Breathing cool air leads to the supersaturation of air in RT;

2 the air supersaturation leads to the intensive condensational growth(CG) of inhaled viruses or bacteria in RT;

3 CG leads to the intensive and dramatically growth of deposition rate of viruses or bacteria in RT.

We have shown:

a) Under normal conditions of inhaled air (T>20˚C; Relatively Humidity, RH=60%) there is no transition in supersaturated condition in RT and CG is insignificant and probability of virus deposition on epithelium of RT is low – no more than 20%.

b) Breathing cool/cold air of T<+15˚C and RH of [30..60]% leads to the supersaturation in the airways and it can dramatically increase the deposition rate of inhaled bioaerosols in RT(up to 96%).

c) With an increase in RH of inhaled air the supersaturation in RT occurs even at warm temperature of inhaled air (for inhaled air of T<20°C and RH>70% ; T<25°C and RH>90%). It also indicates the high deposition rate of bioaerosols in RT.

Conclusion:

Under specific environmental conditions (when flu seasons) the processes of supersaturation in the RT can be observed. These results indicate the high probability of virus deposition on epithelium of RT and correspond to influenza and seasonal respiratory infections in temperate and tropical climates.

We believe the effect of supersaturation in the lungs can be the key to understanding of ‘the age-old epidemiologic mystery of influenza seasonality in the different climatic conditions.’
Implementing an open source spatio-temporal search platform for Spatial Data Infrastructures
Authors: Corti Paolo , Lewis Benjamin , Kralidis Tom , Mwenda Jude
Published: January 2018

A Spatial Database Infrastructure (SDI) is a framework of geospatial data, metadata, users and tools intended to provide the most efficient and flexible way to use spatial information. One of the key software component of a SDI is the catalogue service, needed to discover, query and manage the metadata. Catalogue services in a SDI are typically based on the Open Geospatial Consortium (OGC) Catalogue Service for the Web (CSW) standard, that defines common interfaces to access the metadata information.

A search engine is a software system able to perform very fast and reliable search, with features such as full text search, natural language processing, weighted results, fuzzy tolerance results, faceting, hit highlighting and many others.

The Centre of Geographic Analysis (CGA) at Harvard University is trying to integrate within its public domain SDI (named WorldMap), the benefits of both worlds (OGC catalogs and search engines).

Harvard Hypermap (HHypermap) is a component that will be part of WorldMap, totally built on an open source stack, implementing an OGC catalog, based on pycsw, to provide access to metadata in a standard way, and a search engine, based on Solr/Lucene, to provide the advanced search features typically found in search engines.
Open source tools to support Integrated Coastal Management and Maritime Spatial Planning
Authors: Menegon Stefano , Sarretta Alessandro , Barbanti Andrea , Gissi Elena , Venier Chiara
Published: January 2018

This paper describes an open source suite of libraries and tools to support research activities on marine and coastal environment. The suite was initially implemented for the ADRIPLAN portal, an integrated web platform aimed at supporting Maritime Spatial Planning (MSP) activities and other activities concerning the managing of marine environment for the Adriatic-Ionian region. The main elements of the implemented solutions are: i) a GeoNode implementation for sharing geospatial datasets and maps; ii) a new python library (RectifiedGrid) that facilitates the work with geographical grid data; iii) a new python library (Tools4MSP) to perform spatial analysis and assessment of human uses, pressures and the potential impact of maritime and coastal activities on the environment; iv) a new GeoNode plugin (called GeoNode-Tools4MSP) that provides interactive widgets to set up the analyses and to visualize and explore the results. The Tools4MSP and the developed software have been released as FOSS under the GPL3 license and are currently under further development.
Integrating GIScience and Crop Science datasets: a study involving genetic, geographic and environmental data
Authors: Santos Roberto , Algar Adam , Field Richard , Mayes Sean
Published: January 2018

Sharing and reusing data in research is a welcome and encouraged practice since it maximises the scientific outcomes given limited financial, material and human resources. Interdisciplinary research is usually benefitted from this practice, reuniting researchers and data from two or more disciplines to advance fundamental understanding or tackle problems whose solution is beyond the limit of an individual body of knowledge. In this work, we discuss the challenges of associating localisation with other data types, particularly genetic data, in a project involving Crop Science and Geospatial Information Science disciplines that aim to improve the understanding of how geographical, environmental and anthropocentric factors affect the genetic variation in a neglected and underutilised crop called Bambara groundnut.
De novo assembly of Chinese forest musk deer (Moschus berezovskii) transcriptome from Next-Generation mRNA Sequencing
Authors: Xu Zhongxian , Jie Hang , Chen Binlong , Gaur Uma , Yang Mingyao , Wu Nan , Gao Jian , Li Pinming , Zhao Guijun , Zeng Dejun , Li Diyan
Published: January 2018

Musk secretion in male musk deer is regarded as a propitious mode of sexual election to attract a greater number of females. However, the genetic mechanisms of musk secretion are still poorly understood and unresolved making it necessary to elucidate the possible genetic mechanisms of musk formation. In the present study, we used heart and musk gland tissues from a male musk deer for next-generation mRNA sequencing, integrated with de novo assembly, unigenes annotation and differentially expressed genes analysis. A total of 239,383 transcripts and 208,730 unigenes were obtained from 2 pooled RNA samples. Annotated analysis indicated steroid compound metabolism (steroid biosynthesis, steroid hormone biosynthesis, aldosterone-regulated sodium reabsorption, terpenoid backbone biosynthesis) related to musk formation were annotated to many pathways; relevant genes were identified as well. In addition, 8,986 differentially expressed genes (6,068 up- and 2,198 down-regulated) between heart and musk gland were identified, among them, steroid component metabolism were abundant. Further exploration of functional enrichment analysis showed that pathways involved in musk secretion were up-regulated in musk gland compared with heart, especially steroid biosynthesis and terpenoid backbone biosynthesis whose metabolic productions were key components of musk. We identified several candidate genes such as DHCR7, DHCR24, NSDHL, CYP3A5, FDFT1, FDPS and HMGCL which were closely involved in metabolism of steroid, terpenoid and ketone bodies. Our data are expected to represent the most comprehensive sequence resource available for the forest musk deer so far, and provide a basis for further research on molecular genetics and functional genomics of musk secretion.
From photo-geology to 3D geological models. An open source approach
Authors: Santangelo Michele , Marchesini Ivan , Mirabella Francesco , Bucci Francesco , Cardinali Mauro , Guzzetti Fausto
Published: January 2018

Three-dimensional modeling of geological bodies is a useful tool for multiple applications. Such tasks are usually accomplished starting from field-collected data, which typically suffer from intrinsic limitations such as accessibility constraints and punctuality of data collected. In this work, we explore the reliability of photo-geological mapping from interpretation of aerial photographs in providing data useful to build up 3D geological models. The test was conducted in a 15 km2 in Umbria, central Italy. The three-steps open source GIS procedure that outputs 3D models from photo-geological data was developed using python in GRASS GIS environment and GNU-Linux OS. We maintain that this procedure can have potential broad applications in Earth Sciences, including geological and structural analyses, up to the preliminary evaluation of potential reservoirs.
Open source GIS for geological field mapping: research and teaching experience
Authors: De Donatis Mauro , Alberti Mauro , Cesarini Carlo , Menichetti Marco , Susini Sara
Published: January 2018

The journey to digital field mapping in the geosciences academic world is far from ending. When it started some years ago, many geoscientists were skeptical about the use of digital tools in the field. Nowadays, the work done in this decade shows clearly that this will be the way of working in the future. The traditional way of mapping can be incorporated and improved in the digital survey. Many of the previously existing limitations have been surmounted. Part of this process is possible thanks to the choice of open source tools.
Open source geoprocessing tools and meteorological satellite data for crop risk zones monitoring in Sub-Saharan Africa
Authors: De Filippis Tiziana , Rocchi Leandro , Vignaroli Patrizio , Bacci Maurizio , Tarchiani Vieri , Rapisardi Elena
Published: January 2018

In Sub-Saharan Africa analysis tools and models based on meteorological satellites data have been developed within different national and international cooperation initiatives, with the aim of allowing a better monitoring of the cropping season. In most cases, the software was a stand-alone application and the upgrade, in terms of analysis functions, database and hardware maintenance, was difficult for National Meteorological Services (NMSs) in charge of the agro-hydro-meteorological monitoring. The web based solution proposed in this work intends to improve and ensure the sustainability of applications so to support national Early Warning Systems (EWSs) for food security. The Crop Risk Zones (CRZ) model for Niger and Mali, integrated in a web-based open source framework, has been implemented using PL/pgSQL & PostGIS functions to process different meteorological data set: a) the rainfall precipitation forecast images from Global Forecast System (GFS) b) the Climate Prediction Center (CPC) Rainfall Estimator (RFE) for Africa c) MSG images from EUMETSAT Earth Observation Portal d) the MOD 16 Global Terrestrial Evapotranspiration Data Set. Restful Web Services uploads raster images into the PostGIS spatial database for PostgreSQL and PL/pgSQL functions were employed to run CRZ model to identify for the main crops of the Region, the installation phases, the crops phenological phases and risk production zones images. This model is focused on the early identification of risks and the production of information for food security within the time prescribed for decision-making. The challenge and the objective of this work is to set up an open access monitoring system, based on meteorological open data providers, targeting NMSs and any other local decision makers for drought risk reduction and resilience improvement.
Psychometric properties of the perceived stress scale (PSS): measurement invariance between athletes and non-athletes and construct validity
Authors: Chiu Yi-Hsiang , Lu Frank Jing-Horng , Lin Ju-Han , Nien Chiao-Lin , Hsu Ya-Wen , Liu Hong-Yu
Published: January 2018

Background: Although Perceived Stress Scale (PSS, Cohen, Kamarack, Mermelstein, 1983) has been validated and widely used in many domains, there is still no validation in sports by comparing athletes and non-athletes and examining related psychometric indices. Purpose: The purpose of this study was to examine the measurement invariance of PSS between athletes and non-athletes, and examine construct validity and reliability in the sports contexts. Methods: Study 1 sampled 359 college student-athletes (males = 233; females = 126) and 242 non-athletes (males=124; females=118) and examined factorial structure, measurement invariance and internal consistency. Study 2 sampled 196 student-athletes (males = 139, females = 57, Mage =19.88 yrs, SD = 1.35) and examined discriminant validity and convergent validity of PSS. Study 3 sampled 37 student-athletes to assess test-retest reliability of PSS. Results: Results found that 2-factor PSS-10 fitted the model the best and had appropriate reliability. Also, there was a measurement invariance between athletes and non-athletes; and PSS positively correlated with athletic burnout and life stress but negatively correlated with coping efficacy provided evidence of discriminant validity and convergent validity. Further, the test-retest reliability for PSS subscales was significant (r=.66 and r=.50). Discussion: It is suggested that 2-factor PSS-10 can be a useful tool in assessing perceived stress either in sports or non-sports settings. We suggest future study may use 2-factor PSS-10 in examining the effects of stress on the athletic injury, burnout, and psychiatry disorders.
Exploiting freely available imagery to improve land cover characterization and shallow landslide detection
Authors: Crema Stefano , Cavalli Marco , Bossi Giulia , Schenato Luca , Marchi Lorenzo
Published: January 2018

Natural hazards and land management issues can benefit nowadays from the increasing availability of free, high-resolution satellite imagery that opens the way to fine scale detailed investigations. In high elevation catchments the analysis of vegetation dynamics deserves particular attention since little climatic modifications can be amplified in such fragile systems. For the same reasons, the dynamic of instability phenomena as response to an input hydrological forcing, requires a meticulous spatial representation in order to better represent the active processes at catchment scale. The present work focuses on the analysis of high-resolution freely available imagery (Microsoft® Bing Maps™ Platform) that enables the characterization of vegetation cover and the automatic mapping of shallow landslides in an alpine catchment. Semi-automatic detection of vegetation is carried out at the fine scale using both orthophotos and freely available satellite imagery. The analysis based on the satellite imagery showed a better accuracy in respect to the one based on the orthophotos. In particular, satellite imagery analysis showed high sensitivity and high specificity even in low illumination conditions, while, for the same circumstances, orthophotos-based analysis shows a significant wrong detection rate. In the framework of a long term, multi-temporal and high-resolution characterization of vegetation cover and for a rapid mapping of shallow instability phenomena, the effectiveness of the proposed approach can speed up the representation of the local conditions towards an improvement of land management strategies and hazard and risk assessment.
Identification of “on-off residues” in rat Cav1.2 α1C subunit channel using in silico analysis and docking simulation
Authors: Trezza Alfonso , Bernini Andrea , Spiga Ottavia
Published: January 2018

Introduction

Voltage-dependent calcium channels (VSCC) is involved in important biological function as calcium ion transmembrane transport and cardiac contraction. VSCC is a multi-pass membrane protein, made up from α-1, α-2, β and δ subunits. α-1 subunit regulates the entry of ion calcium. Voltage-dependent L-type calcium channel subunit alpha-1C (Cav1.2 α1C subunit channel) is an isoform of VSCC, and is characterized from an high-voltage activation. Previous study have shown that class of molecules as benzothiazepines (Tikhonov D. et al, 2008), are able to block the alpha-1C subunit. Recent works have demonstrated that molecules belonged at the flavonoid class are able to inhibit or to raise channel activity (Saponara S. et al, 2011). In this work, we reported the sensing- residues that could play a key role in Cav1.2 α1C activity. Furthermore, we proposed a potential mechanism of action inside Cav1.2 α1C binding-site with differences between inhibitors and stimulants. Our work has clarifiedas the ligands operate on Cav1.2 α1C, this information could be useful in order to improve their usefulness.

Methods

The 3D structure of Cav1.2 α1C subunit channel was obtained on basis of previous work (Saponara S. et al, 2015). The structure of flavons were downloaded from Pubchem(Kim S. et al, 2015). Docking simulation was carried out through Autodock/Vina v.1.1.2 (O.Trott et al, 2010). PDBePISAwas used in order to evaluate buried surface area values (B.S.A). Protein-ligand interactions were obtained using protein–ligand interaction profiler (P.L.I.P)(Salentin S. et al, 2015). Pymol was used as molecular graphics system (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.).

Results and discussion

I­­­­­n vitro analysis on rat Cav1.2 L-type channel of 20 flavonoids have shown stimulatory and inhibitory activities (Saponara S. et al, 2015).The 11 inhibitors and 8 stimulators derivatives are positioned in their corresponding binding-sites with peculiar sensing-residues interactions (shown in figure 1). Analyzing the network of interactions among the two classes of flavonoids we have observed hydrogen bonds, hydrophobic interactions and π–π stacking bonds characterizing their activities that could differently promote pore open/closed conformation and decreasing voltage-sensitive calcium channel activity (Tikhonov D. et al, 2009). Furthermore, on the basis of the selectivity filters model, we have evaluated B.S.A residues values present in the­­­ binding-sites, we have observed that B.S.A of some residues dramatically decrease, showing that these residues play a key role in the pore stabilization. The different mechanism of action of these molecules can be attributed to their chemical-physical proprieties as steric hindrance and different positions of hydroxyl groups.
Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals
Authors: Raina Jean-Baptiste , Tapiolas Dianne , Motti Cherie A , Foret Sylvain , Seemann Torsten , Tebben Jan , Willis Bette L , Bourne David G
Published: January 2018

Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities by Pseudovibrio sp., and prevented the growth of two previously identified coral pathogens, Vibrio coralliilyticus and V. owensii, at very low concentrations (0.5 µg/mL) in agar diffusion assays. Genome sequencing of Pseudovibrio sp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention.
The GEOBASI (Geochemical Database of Tuscany) open source tools
Authors: Corongiu Manuela , Raco Brunella , Buccianti Antonella , Macera Patrizia , Mari Riccardo , Romanelli Stefano , Nisi Barbara , Menichetti Stefano
Published: January 2018

The tools implemented for the new Regional Geochemical Database, called GEOBASI, are hereafter presented. The database has permitted the construction of a repository where the geochemical information (compositional and isotopic) has been stored in a structured way so that it can be available for different groups of users (e.g. institutional, public and private companies). The information contained in the database can in fact be downloaded freely and queried to correlate geochemistry to other non compositional variables. The repository has been aimed at promoting the use of the geochemical data already available from previous investigations through a powerful Web-GIS interface. The resulting graphical-numerical tools in such a complex database have been developed to: 1) analyse the spatial variability of the investigated context, 2) highlight the geographic location of data pertaining to classes of values or single cases, 3) compare the results of different analytical methodologies applied to the determination of the same element and/or chemical species, 4) extract the geochemical data related to specific monitoring plans and/or geographical areas, and finally 5) recover information about data below the detection limit to understand their impact on the behaviour of the investigated variable.
Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies
Authors: Cabau Cédric , Escudié Frédéric , Djari Anis , Guiguen Yann , Bobe Julien , Klopp Christophe
Published: January 2018

Background

De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved.

Results

We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1,3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts.

Conclusion

Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an ease to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available at http://www.sigenae.org/drap .
Feasibility of using dried plant specimens for DNA barcoding. A case study of the Juncaceae
Authors: Do Danka , Záveská Drábková Lenka
Published: January 2018

Background. Phylogenetic and barcoding studies usually employ fresh parts of plants as the source of DNA. Successful DNA amplification has been achieved in such investigations for different regions. However, there is need for the utilization of dried samples, due to frequent inaccessibility of fresh precious plants or their parts for genetic analyses or barcoding studies. Difficulties in obtaining amplifiable DNA have appeared as one of the major pitfalls that resulted in slowdown of the use of herbarium specimens for DNA analyses. Methods. Recent study highlights the crucial issues that are being faced by comparison of herbarium and fresh plants for barcoding purposes. We analyzed the performance of samples from herbarium specimens of different age and fresh plants in PCR reaction and sequencing of seven regions (cpDNA: rbcL, rpoC1, trnL-F intergenic spacer, trnL intron, psbA-trnH, mtDNA: atp1 and nrDNA: ITS1-5.8S-ITS2) with a combination of twenty-eight primers. Conclusions. We show that herbarium specimens may be successfully applied both for phylogenetic as well as for barcoding purposes. In comparison with fresh samples, working with dried herbarium specimens is more complicated, but may lead to amplification and sequencing success in almost all cases when appropriate internal primers are designed or optimization methods are used. Both attempts are useful for this aim: using the set of universal primers recommended by CBOL and design specific primers for a particular group of interest. We found limited detrimental effect of specimen age and length of the amplicon on the amplification success in most of the tested regions in the Juncaceae.
Redescription of Arundel formation Ornithomimosaur material and a reinterpretation of Nedcolbertia justinhofmanni as an “Ostrich Dinosaur”: Biogeographic implications
Authors: Brownstein Chase Doran
Published: January 2018

The fossil record of dinosaurs from the Early Cretaceous of eastern North America is scant, and only a few sediments to the east of the continent are fossiliferous. Among them is the Arundel Formation of the east coast of the United States, which has produced among the best dinosaur faunas known from the Early Cretaceous of eastern North America. The diverse dinosaur fauna of this formation has been thoroughly discussed previously, but few of the dinosaur species originally described from the Arundel are still regarded as valid genera. Much of the Arundel material is in need of review and redescription. Among the fossils of dinosaurs from this formation are those referred to ornithomimosaurs. Here, I redescribe ornithomimosaur remains from the Arundel Formation which may warrant the naming of a new taxon of dinosaur. These remains provide key information on the theropods of the Early Cretaceous of Eastern North America. The description of the Arundel material herein along with recent discoveries of basal ornithomimosaurs in the past 15 years has allowed for comparisons with the coelurosaur Nedcolbertia justinhofmanni, suggesting the latter animal was a basal ornithomimosaurian dinosaur rather than a “generalized” coelurosaur. Comparisons between the Arundel ornithomimosaur and similar southeast Asian ornithomimosaurian material as well as ornithomimosaur remains from western North America suggest that a lineage of ornithomimosaurs with a metatarsal condition intermediate between that of basal and derived ornithomimosaurs was present through southeast Asia into North America, in turn suggesting that such animals coexisted with genera having a more primitive metatarsal morphology as seen in N. justinhofmanni.
Aspects of gorgonopsian paleobiology and evolution: insights from the basicranium, occiput, osseous labyrinth, vasculature, and neuroanatomy
Authors: Araujo Ricardo M , Fernandez Vincent , Polcyn Michael J , Fröbisch Jörg , Martins Rui M.S.
Published: January 2018

Synapsida, the clade including therapsids and thus also mammals, is one of the two major branches of amniotes. Organismal design, with modularity as a concept, offers insights into the evolution of therapsids, a group that experienced profound anatomical transformations throughout the past 270Ma, eventually leading to the evolution of the mammalian bauplan. However, the anatomy of some therapsid groups remains obscure. Gorgonopsian braincase anatomy is poorly known and many anatomical aspects of the brain, cranial nerves, vasculature, and osseous labyrinth, remain unclear. We analyzed two gorgonopsian specimens, GPIT/RE/7124 and GPIT/RE/7119, using propagation phase contrast synchrotron micro-computed tomography. The lack of fusion between many basicranial and occipital bones in the immature specimen GPIT/RE/7124 allowed us to reconstruct its anatomy and ontogenetic sequence in comparison with the mature GPIT/RE/7119. We examined the braincase and rendered various skull cavities. Notably, there is a separate ossification between what was previously referred to as the “parasphenoid” and the basioccipital. We reinterpreted this element as a posterior ossification of the basisphenoid: the basipostsphenoid. Moreover, the “parasphenoid” is a co-ossification of the dermal parasphenoid and the endochondral basipresphenoid. Our detailed examination of the osseous labyrinth reveals a unique discoid, rather than toroidal, morphology of the horizontal semicircular canal that probably results from architectural constraints of the opisthotic and supraoccipital ossifications. In addition, the orientation of the horizontal semicircular canal suggests that gorgonopsians had an anteriorly tilted alert head posture. The morphology of the brain endocast is in accordance with the more reptilian endocast shape of other non-mammaliaform neotherapsids.
Meditation and auditory attention: An ERP study of meditators and non-meditators
Authors: Biedermann Britta , de Lissa Peter , Mahajan Yatin , Polito Vince , Badcock Nicholas A , Connors Michael H , Quinto Lena , Larsen Linda , McArthur Genevieve M
Published: January 2018

A recent meta-analysis emphasises that meditation can improve attention in healthy adults (Sedlmeier et al., 2012). The findings of a study by Cahn and Polich (2009) suggests that there is an effect of a meditative state on three event-related potential (ERP) brain markers of low-level auditory attention in expert meditators: the N1, the P2, and the P3a. The current study built on these findings by examining the trait and state effects of meditation on the passive auditory mismatch negativity (MMN), N1, and P2 ERPs. We found that the MMN was significantly larger in meditators than non-meditators regardless of whether they were meditating or not (a trait effect), and that the N1 was significantly attenuated during meditation in non-meditators but not meditators (an interaction between trait and state). These outcomes suggest that low-level attention is superior in long-term meditators in general. In contrast, low-level attention is reduced in non-meditators when they are asked to meditate for the first time, possibly due to cognitive overload.
Angiosperm phylogeny poster (APP) – Flowering plant systematics
Authors: Cole Theodor C H , Hilger Hartmut H , Stevens Peter F
Published: January 2018

The "Angiosperm Phylogeny Poster – Flowering Plant Systematics" is an educational tool presenting an overview of the evolutionary relationships among flowering plants according to APG IV and APweb as of 2016. The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher levels within the tree. The intuitive color-coding facilitates memorization and teaching.

Translations of the poster by internationally renown botanists are now available in 18 languages. Hyperlinks to APweb (Peter F. Stevens, Missouri Botanical Garden) are provided for the orders and higher ranks.

This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
Angiosperm phylogeny poster (APP) – Flowering plant systematics, 2017
Authors: Cole Theodor C H , Hilger Hartmut H , Stevens Peter F
Published: January 2018

The "Angiosperm Phylogeny Poster – Flowering Plant Systematics" is an educational tool presenting an overview of the evolutionary relationships among flowering plants according to APG IV and APweb as of 2016. The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher levels within the tree. The intuitive color-coding facilitates memorization and teaching.

Translations of the poster by internationally renown botanists are now available in 18 languages. Hyperlinks to APweb (Peter F. Stevens, Missouri Botanical Garden) are provided for the orders and higher ranks.

This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
Angiosperm phylogeny poster (APP) – Flowering plant systematics, 2017
Authors: Cole Theodor C H , Hilger Hartmut H , Stevens Peter F
Published: January 2018

The "Angiosperm Phylogeny Poster – Flowering Plant Systematics" is an educational tool presenting an overview of the evolutionary relationships among flowering plants according to APG IV and APweb as of 2016. The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher levels within the tree. The intuitive color-coding facilitates memorization and teaching.

Translations of the poster by internationally renown botanists are now available in 20 languages. Hyperlinks to APweb (Peter F. Stevens, Missouri Botanical Garden) are provided for the orders and higher ranks.

This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
Whole-brain ex-vivo quantitative MRI of the cuprizone mouse
Authors: Wood Tobias C , Simmons Camilla , Hurley Samuel A , Vernon Anthony C , Torres Joel , Dell'Acqua Flavio , Williams Steve C R , Cash Diana
Published: January 2018

Myelin is a critical component of the nervous system and a major contributor to contrast in Magnetic Resonance (MR) images. However the precise contribution of myelination to multiple MR modalities is still under debate. The cuprizone mouse is a well established model of demyelination that has been used in several MR studies, but these have often imaged only a single slice and analysed a small region of interest in the corpus callosum. We imaged and analyzed the whole brain of the cuprizone mouse ex-vivo using high-resolution quantitative MR methods (multi-component DESPOT, Diffusion Tensor Imaging and Tensor Based Morphometry) and found changes in multiple regions, including the corpus callosum, cerebellum, thalamus and hippocampus. However the presence of inflammation, confirmed with histology, presents difficulties in isolating the sensitivity and specificity of these MR methods to demyelination using this model.
Augmenting caregiver in-home safety practices via mHealth: A randomized controlled trial
Authors: L. Wilson Michael , Kigwangalla Hamisi A.
Published: January 2018

Unintentional injuries among under-fives represent an important cause of preventable morbidity in Dar es Salaam, Tanzania. In-home interventions targeting caregiver safety practices currently show promise in reducing household injury risks. Mobile health (mHealth) is emerging as a potentially cost effective platform for the delivery of critical health information in resource poor settings. The goal of this project is to introduce an mHealth intervention targeting risk factors for child burn injuries in Dar es Salaam.
Testing the link between genome size and growth rate in maize
Authors: Tenaillon Maud I , Manicacci Domenica , Nicolas Stéphane D , Tardieu Francois , Welcker Claude
Published: January 2018

Little is known about the factors driving within species Genome Size (GS) variation. GS may be shaped indirectly by natural selection on development and adaptative traits. Because GS variation is particularly pronounced in maize, we have sampled 83 maize inbred lines from three well described genetic groups adapted to contrasted climate conditions: inbreds of tropical origin , Flint inbreds grown in temperate climates, and Dent inbreds distributed in the Corn Belt. As a proxy for growth rate, we measured the Leaf Elongation Rate maximum during nighttime (LERmax) as well as GS in all inbred lines. In addition we combined available and new nucleotide polymorphism data at 29,090 sites to characterize the genetic structure of our panel. We found significant variation for both LERmax and GS among groups defined by our genetic structuring. Tropicals displayed larger GS than Flints while Dents exhibited intermediate values. LERmax followed the opposite trend with greater growth rate in Flints than in Tropicals. In other words, LERmax and GS exhibited a significantly negative correlation (r=-0.27). However, this correlation was driven by among-group variation rather than within-group variation – it was no longer significant after controlling for structure and kinship among inbreds. Our results indicate that selection on GS may have accompanied ancient maize diffusion from its center of origin, with large DNA content excluded from temperate areas. Whether GS has been targeted by more intense selection during modern breeding within groups remains an open question.  
Common metabolic constraints on dive duration in endothermic and ectothermic vertebrates
Authors: Hayward April , Pajuelo Mariela , Haase Catherine G. , Anderson David M. , Gillooly James F.
Published: January 2018

Dive duration in air-breathing vertebrates is thought to be constrained by the volume of oxygen stored in the body and the rate at which it is consumed (i.e., “o xygen store/usage hypothesis” ). The body mass-dependence of dive duration among endothermic vertebrates is largely supportive of this model, but previous analyses of ectothermic vertebrates show no such body mass-dependence. Here we show that dive duration in both endotherms and ectotherms largely support the oxygen store/usage hypothesis after accounting for the well-established effects of temperature on oxygen consumption rates. Analyses of the body mass and temperature dependence of dive duration in 181 species of endothermic vertebrates and 29 species of ectothermic vertebrates show that dive duration increases as a power law with body mass, and decreases exponentially with increasing temperature. Thus, in the case of ectothermic vertebrates, changes in environmental temperature will likely impact the foraging ecology of divers.
Bovine tuberculosis in cattle from 1986 to 2012 in and around badger-culled areas of the RBCT
Authors: Hendy David
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of a trial where badgers were culled between 1998 and 2005. This trial, known as the Randomised Badger Culling Trial (RBCT), was performed across 100 km2 (nominal) zones in the West of England. The results were based on a model of new herd incidence data. It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence in surrounding areas.

This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates the data. The Animal and Plant Health Agency supplied this data in March 2016. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.

Whilst the proactive culls substantially and sustainably reduced cattle TB in treated areas, such culls did not significantly increase TB in the surrounding areas. In fact New Herd Incidents (NHI’s) between 2006 and 2012 dropped by 28%, 1% and 18% in the treated, outer 2km ring, and combined areas respectively. Based on the number of NHI’s prevented since 1998, a break-even cost for a badger removal exercise was calculated to be £8,454 per km2. This figure may be under-estimated because it takes no account of any NHI’s prevented after 2012.

The more limited reactive culls were found to have no significant impact. This applied to both the treated area and outer 2km ring.

The data also showed that the culls only reduced confirmed TB with no significant impact on unconfirmed TB. This was also found by the ISG when they reported results in 2007.

Arguments surrounding badger culling in the UK have been poorly based due to incomplete data. In view of this and media hype, it should be emphasised that after the first year of substantial culling across the study area, 9 years of data were needed to clearly see the full extent by which TB dropped in the RBCT. This has implications for the culls which started in South West England in 2013. If the current reporting delay of 20 months persists, it may be the autumn of 2023 at the earliest before the impact of these culls becomes clear. Also, if culls stop after year four in each zone, this risks benefits falling short of those achieved in the RBCT.
Randomised Badger Culling Trial: Impact based on more extensive data
Authors: Hendy David
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of a trial where badgers were culled between 1998 and 2005. This trial, known as the Randomised Badger Culling Trial (RBCT), was performed across 100 km2 (nominal) zones in the West of England. The results were based on a model of new herd incidence data. It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence in surrounding areas.

This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates the data. The Animal and Plant Health Agency supplied this data in March 2016. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.

Whilst the proactive culls substantially and sustainably reduced cattle TB in treated areas, such culls did not significantly increase TB in the surrounding areas. In fact New Herd Incidents (NHI’s) between 2006 and 2012 dropped by 28%, 1% and 18% in the treated, outer 2km ring, and combined areas respectively. Based on the number of NHI’s prevented since 1998, a break-even cost to complete a badger removal exercise was calculated to be £8,454 per km2. This figure may be under-estimated because it takes no account of any NHI’s prevented after 2012.

The more limited reactive culls were found to have no significant impact. This applied to both the treated area and outer 2km ring.

The data also showed that the culls only reduced confirmed TB with no significant impact on unconfirmed TB. This was also found by the ISG when they reported results in 2007.

Conclusions in the RBCT final report were made based on incomplete data so are poorly grounded. In addition to this, many mass media outlets are already adversely reporting the impact for culls which started in South West England in 2013. In the RBCT, after the first year of substantial culling, 9 years of data were needed to clearly see the full extent by which TB dropped when the data was not time-shifted. It is likely that the impact of the 2013 culls will not become clear until sometime between 2020 and 2025.