bluuebunny/crossref_metadata_2025 huggingface dataset:
The dentary of Wareolestes rex and new fossil mammal material from the Middle Jurassic of Skye, Scotland
Authors: Panciroli Elsa , Benson Roger B. J. , Walsh Stig
Published: January 2018

The Middle Jurassic was a pivotal time for many vertebrate groups: recent research suggests mammals experienced a surge in ecological diversity at this time. However, vertebrate fossils from the Middle Jurassic are rare. Until now, Middle Jurassic mammals in the UK came almost exclusively from Bathonian deposits in England, while globally the most complete specimens are mainly found in China. Ongoing fieldwork on the Isle of Skye suggests this locality is of international significance for microvertebrate skeletal remains. So far, Skye has yielded skeletal associations and fragmentary material including early mammals, tritylodontids, salamanders and basal squamates.

We report the most complete specimen of the Middle Jurassic morganucodontan Wareolestes rex, from the Bathonian Kilmaluag Formation of Skye, Scotland. The specimen was digitally reconstructed using microCT scan data. It comprises a partial left dentary with two erupted molars, one unerupted molar, and three unerupted premolars. Empty alveoli for a canine, p1 and p3 are also present.

Wareolestes was previously known from four isolated molars from Kirtlington, England, and there was debate over the position of the holotype tooth as an upper or lower molar. Comparing our new material with the holotype, we support the original diagnosis of the holotype as a lower molar, most likely m1. In the Scottish specimen, unerupted and erupted premolars, and presence of permanent molars, supports diphyodonty in Wareolestes. This has previously been suggested for other morganucodontans. Damage to the dentary of Wareolestes means questions remain regarding the sequence of replacement along the tooth row in this genus.
What is the impact of regulatory guidance and expiry of drug patents on dementia drug prescriptions in England: a trend analysis in the Clinical Practice Research Datalink
Authors: Walker Venexia M , Davies Neil M , Kehoe Patrick G , Martin Richard M
Published: January 2018

Background: Drugs for dementia have been available in England from 1997. Since their launch, there have been several changes to national guidelines and initiatives that may have influenced prescribing. These include changes in National Institute for health and Care Excellence (NICE) guidance; several government dementia strategies; the addition of dementia to the Quality and Outcomes Framework (QOF); and the expiry of drug patents. Despite this, there has been little research into the effect of these events on prescribing. This paper examines prescribing trends in England using data from the UK Clinical Practice Research Datalink since the launch of drugs for dementia up to 1st January 2016.

Methods: We considered the monthly proportion of patients eligible for treatment, with a diagnosis of probable Alzheimer’s disease, receiving their first prescription for each drug class – namely acetylcholinesterase (AChE) inhibitors (donepezil, rivastigmine, galantamine) and N-Methyl-D-aspartate (NMDA) receptor antagonists (memantine). Trend analysis using joinpoint models was then applied to identify up to two trend changes per treatment of interest.

Results: The overall trend was for increasing prescriptions in each drug class over the period they were studied. This was indicated by the average monthly percentage change, which was 6.0% (95% CI: -6.4 to 19.9; June 1997 to December 2015) for AChE inhibitors and 15.4% (95% CI: -77.1 to 480.9; January 2003 to December 2015) for NMDA receptor antagonists. Prescriptions of AChE inhibitors increased at the end of 2012, probably in response to the patent expiry of these drugs earlier that year. The Prime Minister’s Dementia Challenge launched in May 2012 may also have contributed to the observed increase. However, neither this strategy nor patent expiry appeared to influence prescriptions of NMDA receptor antagonists. Instead trend changes in this drug class were driven by NICE guidance released in 2011 that allowed access to these drugs outside of clinical trials.

Conclusions: Dementia drug prescribing does not always respond to factors such as regulatory guidance, recommendations or patent expiry and, when it does, not necessarily in a predictable way. This suggests that improved communication with clinicians may be needed to improve the cost-effective use of drugs for dementia.
Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method
Authors: Amado Cattáneo Raúl , Diambra Luis , McCarthy Andrés Norman
Published: January 2018

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filter out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.
Pumpkin powdery mildew disease severity influences the fungal diversity of the phyllosphere
Authors: Zhang Zhuo , Luo Luyun , Tan Xinqiu , Kong Xiao , Yang Jianguo , Wang Duanhua , Zhang Deyong , Jin Decai , Liu Yong
Published: January 2018

Phyllosphere microbiota play a crucial role in plant-environment interactions and are influenced by biotic and abiotic factors. However, there is little research on how pathogen s affect the microbial community. In this study, we collected 16 pumpkin (Cucurbita moschata) leaf samples showing symptoms of powdery mildew disease with different disease severity levels ranging from L1 (least severe) to L4 (most severe). We examined the fungal community structure and diversity by Illumina MiSeq sequencing of the internal transcribed spacer (ITS) region of ribosomal RNA genes. The fungal communities were dominated by members of the Basidiomycota and Ascomycota. The dominant genus was Podosphaera on the diseased leaves, which was the key pathogen responsible for the pumpkin powdery mildew. Ascomycota and Podosphaera increased in abundance as disease severity increased from L1 to L4, and were significantly more abundant than other microorganisms at disease severity L4 (P<0.05). The richness and diversity of the fungal community increased from L1 to L2, and then declined from L2 to L4, likely due to the biotic pressure at disease severity L4. Maintaining species richness in the phyllosphere will be an important part of managing disease control in this agroecological system and an essential step toward predictable biocontrol of powdery mildew in pumpkin.
Procedure to integrate i2b2 and REDCap: a case study at ICSM
Authors: Tibollo Valentina , Bucalo Mauro , Vella Danila , Stuppia Morena , Barbarini Nicola , Bellazzi Riccardo
Published: January 2018

REDCap (Research Electronic Data Capture) is one of the most popular web-based applications to support data capture for research studies and registries. i2b2 (Informatics for Integrating Biology and the Bedside) is a widely adopted data warehouse to re-use clinical data for research purposes. A general procedure able to integrate these solutions could facilitate research activities in several institutions. Starting from the principles adopted by the SEINE approach, one of the most successful approach designed to i2b2-REDCap integration, we proposed a general and flexible ETL (Extract Transform and Load) procedure for synchronizing an i2b2 project with a REDCap study.
On the exponent in the von Bertalanffy growth model
Authors: Renner-Martin Katharina , Brunner Norbert , Kühleitner Manfred , Nowak Georg , Scheicher Klaus
Published: January 2018

Bertalanffy proposed the differential equation m´(t) = p × m (t) a –q × m (t) for the description of the mass growth of animals as a function m(t) of time t. He suggested that the solution using the metabolic scaling exponent a = 2/3 (von Bertalanffy growth function VBGF) would be universal for vertebrates. Several authors questioned universality, as for certain species other models would provide a better fit. This paper reconsiders this question. Using the Akaike information criterion it proposes a testable definition of ‘weak universality’ for a taxonomic group of species. (It roughly means that a model has an acceptable fit to most data sets of that group.) This definition was applied to 60 data sets from literature (37 about fish and 23 about non-fish species) and for each dataset an optimal metabolic scaling exponent 0 ≤ a opt < 1 was identified, where the model function m(t) achieved the best fit to the data. Although in general this optimal exponent differed widely from a = 2/3 of the VBGF, the VBGF was weakly universal for fish, but not for non-fish. This observation supported the conjecture that the pattern of growth for fish may be distinct. The paper discusses this conjecture.
Refining amino acid hydrophobicity for dynamics simulation of membrane proteins
Authors: Hills, Jr Ronald D
Published: January 2018

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.
Population structure and phenotypic variation of Sclerotinia sclerotiorum from dry bean in the United States
Authors: Kamvar Zhian N , Amaradasa Bimal S , Jhala Rachana , McCoy Serena , Steadman James R , Everhart Sydney E
Published: January 2018

The ascomycete pathogen Sclerotinia sclerotiorum is a necrotrophic pathogen on over 400 known host plants, and is the causal agent of white mold on dry bean. Currently, there are no known cultivars of dry bean with complete resistance to white mold. For more than 20 years, bean breeders have been using white mold screening nurseries with natural populations of S. sclerotiorum to screen new cultivars for resistance. It is thus important to know if the genetic diversity in populations of S. sclerotiorum within these nurseries a) reflect the genetic diversity of the populations in the surrounding region and b) are stable over time. Furthermore, previous studies have investigated the correlation between mycelial compatibility groups (MCG) and multilocus haplotypes (MLH), but none have formally tested these patterns. We genotyped 366 isolates of S. sclerotiorum from producer fields and white mold screening nurseries surveyed over 10 years in 2003–2012 representing 11 states, Mexico, France, and Australia at 11 microsatellite loci resulting in 165 MLHs. Populations were loosely structured over space and time based on analysis of molecular variance and discriminant analysis of principal components, but not by cultivar, aggressiveness, or field source. Of all the regions tested, only Mexico (n=18) shared no MLHs with any other region. Using a bipartite network-based approach, we found no evidence that the MCGs accurately represent MLHs. Our study suggests that breeders should continue to test dry bean lines in several white mold screening nurseries across the US to account for both the phenotypic and genotypic variation that exists across regions.
Subcutaneous microdialysis in the awake rat.
Authors: Risselada Marije , Messenger Kristen M
Published: January 2018

Background. Microdialysis is a valued method to study the pharmacokinetics of drug distribution from an injection site or to a tumor site. The objective of this study was to assess the feasibility of prolonged use of subcutaneously implanted microdialysis catheters to assess local retention and systemic uptake of carboplatin in rats post anesthetic recovery.

Methods. Twelve rats were used: one control rat and 11 treatment rats. The control rat was used to outline the surgical implantation technique of the microdialysis catheter. Treatment rats were administered 5mg carboplatin in poloxamer 407 and divided in two treatment cohorts. Microdialysis catheters were used in both cohorts to collect extracellular fluid. Placement technique was modified between the two cohorts. Treatment cohort 1 (n=6) had the microdialysis catheter implanted in the wound bed, sutured in place and tunneled subcutaneously along the dorsum to exit dorsally in the cervical area. The ends were secured to a Velcro strip sutured to the dorsal cervical skin to avoid trauma by the rat. Treatment cohort 2 (n=5) had the catheter looped around the right hind limb, with the functional part sutured in place in the wound bed, and tunneled through a subcutaneously implanted sterile intravenous line exiting dorsally in the cervical area. The ends were maintained within the IV line and held in place with wound clips. Results. All 11 microdialysis catheters in the treatment cohorts were functional immediately after implantation, but only one out of 11 microdialysis catheters in the treatment cohorts was functional at 24hrs, and none at 48hrs. Discussion. The results of this study suggest that microdialysis catheters cannot be maintained in unanesthetized rats without further modification of the implantation protocol.
Using iNaturalist observations to detect disease in Red Mangroves (Rhizophora mangle)
Authors: Rossi Ryann E
Published: January 2018

Detection of disease over broad spatial scales is important to managing the spread of many diseases. One way to do this is to work with citizen scientists to collect data over broad spatial and temporal scales. Citizen science observations are becoming more widely available through web and app interfaces such as iNaturalist.org. iNaturalist.org provides passive sampling of organisms through photographs with a geolocation. These observations are often used to examine biodiversity and species monitoring, but, disease detection is also possible. Here, I demonstrate the utility of using iNaturlist.org observations of red mangrove to detect foliar disease symptoms such as lesions. I downloaded observations of red mangrove from iNaturalist.org, filtered them and examined images for foliar disease symptoms. Out of 153 filtered images, I found that 42% showed no signs of foliar disease while 58% did show foliar disease symptoms. I also found that observations of red mangrove were recorded from 15 countries in total, with 11 countries having at least one observation with foliar disease symptoms present. While small, this study demonstrates the utility of using resources such as iNaturalist.org to obtain preliminary disease observations which can be used to further focus in person disease surveys and sampling.
A novel shiny platform for the geo-spatial analysis of large amount of patient data.
Authors: Guarino Francesco , Russo Mario Alessandro , Franzese Monica , Righelli Dario , Improta Giovanni , Angelini Claudia , Triassi Maria
Published: January 2018

It has been estimated that up to 80% of all data stored in health care databases may have spatial components. To fully exploit such components, there is a need of improving existing tools or developing novel spatio-temporal functionalities. Geographic information systems (GIS) as QuantumGis, SOLAP2, etc. are potential candidates to support decisional needs, but despite their capabilities, they are still scarcely employed in association within BI applications. For these reasons, we are developing a GIS user-friendly interface in R environment in order to dynamically and interactively visualize and analyze (within BI platforms) diverse informative data layers (e.g., pathology incidence data, environmental pollution, etc.). Although preliminary, we believe that this kind of tools could be suitable used for epidemiologic, environmental and economical studies by providing geographical maps and statistical data analyses of interest for different stakeholders.
The first report of the prevalence of Nosema ceranae in Bulgaria
Authors: Hristov Peter , Georgieva Any , Radoslavov Georgi , Sirakova Daniela , Dzhebir Gyulnas , Shumkova Rositsa , Neov Boiko , Bouga Maria
Published: January 2018

Nosema apis and Nosema ceranae are the two main microsporidian parasites causing nosematosis in honey bee Apis mellifera. The object of the present study is to investigate the presence of Nosema apis and Nosema ceranae in the Bulgarian honey bee. The 16S (SSU) rDNA gene region was chosen for analysis. A duplex PCR assay was performed on 108 honey bee samples from three different parts of the country (South, North and West Bulgaria). The results showed that the samples from the northern part of the country were with the highest rate of invasion (77.2%) for Nosema ceranae while those from the mountainous parts (the Rodopa Mountains, South Bulgaria) were with the lowest rate (13.9%). Infection with Nosema apis alone and co-infection N. apis/N. ceranae were not detected in any samples. These findings suggest that Nosema ceranae is the dominant species in the Bulgarian honey bee. It is not known when the introduction of Nosema ceranae in Bulgaria has occurred, but like in the rest of the world, this species has become the dominant one in Bulgarian Apis mellifera. In conclusion, this is the first report for molecular detection of Nosema infection in Bulgarian honey bee that confirms the worldwide dissemination and prevalence of Nosema ceranae.
Industry payments to physician journal editors
Authors: Wong Victoria S S , Avalos Lauro N , Callaham Michael L
Published: January 2018

Objective: To assess industry payments to physician journal editors, and determine how their financial conflict of interest rate compares to all physicians within the specialty.

Study Design and Setting: Open Payments is a United States federal program that mandates reporting of medical industry payments to physicians. We performed a retrospective analysis of prospectively collected data, reviewing August 1, 2013 to December 31, 2016 payments using the Open Payments search tool. We collected payments data on “top tier” US-based physician-editors of highly-cited medical journals including 1) total general payments from industry, 2) total “direct” research payments, and 3) associated “indirect” research funding. We compared payments to physician-editors and payments to physicians-by-specialty using existing published data.

Results: In 35 journals, 333 (74.5%) of 447 “top tier” editors met inclusion criteria as US-based physician-editors. Of these, 212 (63.7%) received any industry-associated payments in the study period. In an average year during the study period, 141 (42.3%) of physician-editors received any payments directed to themselves (rather than their institutions), 120 (36.0%) received payments >$50; 66 (19.8%) received payments >$5,000 (the threshold designated by the National Institutes of Health as a Significant Financial Interest); and 51 (15.3%) received payments >$10,000. Mean annual payment of "total general payments" was $55,157 (standard deviation 561,885, range 10-10,981,153) with median of $3,512. Median general industry payments to physician-editors were mostly higher compared to all physicians within their specialty.

Conclusions: A substantial minority of physician-editors receive direct payments from industry within any given year, though most editors received payment of some kind in the study period. There were significant outliers. More robust and specific editor financial COI declarations may be appropriate given the extent of editors’ influences on the medical literature.
Becoming more transparent: Collecting and presenting data on biomedical Ph.D. alumni
Authors: Pickett Christopher L , Tilghman Shirley
Published: January 2018

For more than 20 years, panels of experts have recommended that universities collect and publish data on the career outcomes of Ph.D. students. However, little progress has been made. Over the past few years, a handful of universities, including those in the National Institutes of Health’s Broadening Experiences in Scientific Training consortium, and organizations, including the Association of American Universities and the Association of American Medical Colleges, launched projects to collect and publish data on biomedical Ph.D. alumni. Here, we describe the outcome of a meeting, convened by Rescuing Biomedical Research, of universities and associations working to improve the transparency of career outcomes data. We were able to achieve consensus on a set of common methods for alumni data collection and a unified taxonomy to describe the career trajectories of biomedical Ph.D.s. These materials can be used by any institution, with little or no modification, to begin data collection efforts on their Ph.D. alumni. These efforts represent an important step forward in addressing a recommendation that has been made for decades that will improve the ability of trainees to better plan for their careers and for universities to better tailor their training programs.
Antimicrobial activity of extracts from exotic fruits and vegetables
Authors: Kirby-Lee Kendrick A
Published: January 2018

Novel sources of antimicrobial agents need to be identified to address the looming crisis of antimicrobial resistance. The overall goal of the described experiments was to determine whether extracts of exotic vegetables, mushrooms, and herbs have antimicrobial properties. Vegetable and herbal extracts were purchased from online supplier. Fresh vegetable roots and mushrooms were run through a commercially available juicer to obtain aqueous extracts. Extracts were spotted onto filter paper disks and activity assessed by measuring the zone of inhibition for both E. coli K-12 and B. subtilis as representative Gram-negative and Gram-positive organisms, respectively. Synergy testing was also performed by placing disks spotted with extracts in close proximity to one another. Amongst commercial extracts, prominent Gram-positive activity was found for Echinacea, grapefruit seed, olive leaf, and golden seal extracts; and prominent mixed Gram-negative and Gram-positive activity was found for clove extract. Amongst fresh vegetable and mushroom juicing extracts, Gram-positive activity was detected for celery root.
Designer food webs: from build-it-and-they-will-come to intentionality-in-design
Authors: Felson Alexander , Ellison Aaron M
Published: January 2018

Anthropogenic landscapes provide opportunities for ecologists to deliberately and intentionally design urban food webs. Ecologists working as full, collaborative partners with designers can construct functional food webs for urban environments that benefit society. As a first step, ecologists can learn to partner with designers by translating ecological knowledge at scales relevant to design strategies and decision-making. Building relationships at multiple intersections within a designed project is essential for fostering co-generated strategies to achieve functional food webs in a designed and aesthetic urban context. Designing diverse, self-sustaining, urban food webs will require testing, monitoring, and adaptive management. Here, we discuss relevant ecological theory and explore case studies illustrating aspects of the design process and opportunities for designing and constructing food webs.
Influence of alignment uncertainty on homology and phylogenetic modeling
Authors: Chang Jia-Ming , Notredame Cedric
Published: January 2018

Most evolutionary analyses or structure modeling are based upon pre-estimated multiple sequence alignment (MSA) models. From a computational point of view, it is too complex to estimate a correct alignment. Hence, increasing or identifying signal inside sequence alignment has intensified over the last few years. During the presentation, I would like to share two approaches, homology extension and sampling, on this topic.

The first part, transmembrane proteins (TMPs) constitute about 20~30% of all protein coding genes. The relative lack of experimental structure has so far made it hard to develop specific alignment methods and the current state of the art (PRALINE™) only manages to recapitulate 50% of the positions in the reference alignments available from the BAliBASE2-ref7. We show how homology extension can be adapted and combined with a consistency based approach in order to significantly improve the multiple sequence alignment of alpha-helical TMPs. TM-Coffee is a special mode of PSI-Coffee able to efficiently align TMPs, while using a reduced reference database for homology extension. Our benchmarking on BAliBASE2-ref7 alpha-helical TMPs shows a significant improvement over the most accurate methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™.

The second part, homology and evolutionary modeling are the most common applications of MSAs. In this work, we show how this problem can be partly overcome using the transitive consistency score (TCS), an extended version of the T-Coffee scoring scheme. Using this local evaluation function, we show that one can identify the most reliable portions of an MSA, as judged from BAliBASE and PREFAB structure-based reference alignments. We also show how this measure can be used to improve phylogenetic tree reconstruction using both an established simulated data set and a novel empirical yeast data set. Our approach relies on the T-Coffee framework; it uses libraries of pairwise alignments to evaluate any third party MSA. We compared TCS with Heads-or-Tails, GUIDANCE, Gblocks, and trimAl and found it to lead to significantly better estimates of structural accuracy and more accurate phylogenetic trees.

References:

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. Nucleic acids research 44, W339–343(2016).

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction. Nucleic acids research 43, W3–6 (2015).

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.Molecular biology and evolution 31, 1625–37 (2014).

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. Bmc Bioinformatics 13, S1 (2012).

Website:

PSI/TM-Coffee http://tcoffee.crg.cat/tmcoffee, TCS http://tcoffee.crg.cat/tcs
Six wedges to curing disease
Authors: Hochberg Michael E
Published: January 2018

One of the great challenges in ecology and evolutionary biology is to explain disease, whether caused by infectious agents such as parasites and pathogens, or by the deterioration or transformation of cellular behavior and function, a prime example of the latter being cancer. Decades of observation and research suggest that successfully treating disease requires insights into how the environment mediates the interactions between disease causing agents (DCAs) and diseased individuals. A major finding is that single factor, targeted therapies are not only likely to fail in controlling or eradicating many DCAs, but are also likely to select for resistance, reducing options for subsequent treatment attempts, and in cases of infectious DCAs, rendering therapeutic agents (e.g., antibiotics) obsolete. I argue that meeting the growing challenge of treating disease in agriculture and animal husbandry, in protected and domesticated species, wildlife, and in the human population will require a fundamental understanding of ecological interactions at sites of infection or disease. I discuss different ways in which components of such disease ecosystems mediate DCA and therapeutic dynamics and resistance evolution, and derive a very simple mathematical criterion for therapeutic success. I then touch on how fundamental insights as revealed by the processes of evolutionary rescue and competitive release can help understand why therapies succeed or fail. Finally, I present six “wedges” that can each contribute alone, or as part of multi-pronged approaches to successfully treating disease.
TED toolkit: a comprehensive approach for convenient transcriptomic profiling as a clinically-oriented application
Authors: Ali Thahmina , Kim Baekdoo , Lijeron Carlos , Ogunwobi Olorunseun O , Mazumder Raja , Krampis Konstantinos
Published: January 2018

In translational medicine, the technology of RNA sequencing (RNA-seq) continues to prove powerful, and transforming the RNA-seq data into biological insights has become increasingly imperative. We present the Transcriptomics profiler for Easy Discovery (TED) toolkit, a comprehensive approach to processing and analyzing RNA-seq data. TED is divided into three major modules: data quality control, transcriptome data analysis, and data discovery, with eleven pipelines in total. These pipelines perform the preliminary steps from assessing and correcting the quality of the RNA-seq data, to the simultaneous analysis of five transcriptomic features (differentially expressed coding, non-coding, novel isoform genes, gene fusions, alternative splicing events, genetic variants of somatic and germline mutations) and ultimately translating the RNA-seq analysis findings into actionable, clinically-relevant reports. TED was evaluated using previously published prostate cancer transcriptome data where we observed previously studied outcomes, and also created a knowledge database of highly-integrated, biologically relevant reports demonstrating that it is well-positioned for clinical applications. TED is implemented on an instance of the Galaxy platform (Galaxy page: http://galaxy.hunter.cuny.edu/u/bioitcore/p/transcriptomics-profiler-for-easy-discovery-ted-toolkit , Documentation Manual: http://ted.readthedocs.io/en/latest/index.html ) as intuitive and reproducible pipelines providing a manageable strategy for conducting substantial transcriptome analysis in a routine and sustainable fashion for bioinformatics researchers and clinicians alike.
Habitat use, preference and utilization distribution of two crane species (Genus: Grus) in Huize National Nature Reserve, Yunnan-Guizhou Plateau, China
Authors: Kong Dejun , Luo Weixiong , Huan Guoyue , Li Zhuoqing , Yang Xiaojun
Published: January 2018

Understanding habitat use and spatial distribution of wildlife could help conservationists determine high-priority areas and enhance conservation efforts. In this study, we studied habitat use, preference and utilization distribution of two Gruidae species (Black-necked Cranes Grus nigricollis and Eurasian Cranes G. grus) in Huize National Natural Reserve, Yunnan-Guizhou Plateau, SW China. Line transect method indicated that the anthropogenic habitat of farmland was utilized the most by these two species (>90% of flocks observed for both). But Black-necked Cranes preferred marsh to farmland and grassland while Eurasian Cranes favored grassland in our study. Nearly all the Black-necked Cranes (99.30% of the flocks observed) utilized habitats in the core area of the reserve, covering an area of 283.84 ha close to the common roost. Eurasian Cranes were mostly (55.39% of the flocks observed) distributed in the buffer zone with higher elevation and further distance to the roost, covering an area of 558.73 ha. We believe that our findings could help guide habitat management, functional zoning planning and adjustment in the future. According to our results, we recommended restoration of more wetlands, retain large areas of farmland, and protect the areas that cranes use most frequently.
A guide to Bayesian model checking for ecologists
Authors: Conn Paul , Johnson Devin , Williams Perry , Melin Sharon , Hooten Mevin
Published: January 2018

Checking that models adequately represent data is an essential component of applied statistical inference. Ecologists increasingly use hierarchical Bayesian statistical models in their research. The appeal of this modeling paradigm is undeniable, as researchers can build and fit models that embody complex ecological processes while simultaneously controlling observation error. However, ecologists tend to be less focused on checking model assumptions and assessing potential lack-of-fit when applying Bayesian methods than when applying more traditional modes of inference such as maximum likelihood. There are also multiple ways of assessing the fit of Bayesian models, each of which has strengths and weaknesses. For instance, Bayesian p-values are relatively easy to compute, but are well known to be conservative, producing p-values biased toward 0.5. Alternatively, lesser known approaches to model checking, such as prior predictive checks, cross-validation probability integral transforms, and pivot discrepancy measures may produce more accurate characterizations of goodness-of-fit but are not as well known to ecologists. In addition, a suite of visual and targeted diagnostics can be used to examine violations of different model assumptions and lack-of-fit at different levels of the modeling hierarchy, and to check for residual temporal or spatial autocorrelation. In this review, we synthesize existing literature to guide ecologists through the many available options for Bayesian model checking. We illustrate methods and procedures with several ecological case studies, including i) analysis of simulated spatio-temporal count data, (ii) N-mixture models for estimating abundance and detection probability of sea otters from an aircraft, and (iii) hidden Markov modeling to describe attendance patterns of California sea lion mothers on a rookery. We find that commonly used procedures based on posterior predictive p-values detect extreme model inadequacy, but often do not detect more subtle cases of lack of fit. Tests based on cross-validation and pivot discrepancy measures (including the ``sampled predictive p-value'') appear to be better suited to model checking and to have better overall statistical performance. We conclude that model checking is an essential component of scientific discovery and learning that should accompany most Bayesian analyses presented in the literature.
Key steps to avoiding artistry with significance tests
Authors: Doncaster C Patrick , Ezard Thomas H G
Published: January 2018

Statistical significance provides evidence for or against an explanation of a population of interest, not a description of data sampled from the population. This simple distinction gets ignored in hundreds of thousands of research publications yearly, which confuse statistical with biological significance by referring to hypothesis-testing analyses as demonstrating significant results. Here we identify three key steps to objective reporting of evidence-based analyses. Firstly, by interpreting P -values correctly as explanation not description, authors set their inferences in the context of the design of the study and its purpose to test for effects of biologically relevant size; nowhere in this process is it informative to use the word ‘significant’. Secondly, empirical effect sizes demand interpretation with respect to a size of relevance to the test hypothesis. Thirdly, even without an a priori expectation of biological relevance, authors can and should interpret significance tests with respect to effects of reliably detectable size.
Is habitat important? Morphology and genome size of Epipactis helleborine (L.) Crantz growing in anthropogenic and natural habitats
Authors: Rewicz Agnieszka , Rewers Monika , Jędrzejczyk Iwona , Rewicz Tomasz , Kołodziejek Jeremi
Published: January 2018

Background. The process of apophytism or spreading native species to human-made habitats is one of the main elements in the creation of plant cover in anthropogenic areas. Lately, an increase of anthropogenic localities with valuable flora (rare and law protected species) has been observed. Apophytes are also members of the family Orchidaceae, especially from the genus Epipactis. The aim of the study was to i) determine and compare the phenotypic variation of E. helleborine plants in anthropogenic and natural habitats, ii) compare the genome size estimation of plants growing in natural and anthropogenic habitats. The results reported in this study may indicate that a habitat influences morphological characteristics of plant species.

Methods. The research was carried out in Poland from 2011 to 2013. The study sites were located in three different geographical regions: from the Białowieża Primeval Forest, Northern East Poland, through Central Poland, to the Lower Silesia Province, Southern West Poland. We investigated eight populations of E. helleborine: four from natural habitats and four from anthropogenic habitats. Biometrical analyses were performed on shoots and flowers. The flowers were characterised by 25 biometric features and measured using a Nikon SMZ 800 binocular, microscopic Moticam-1SP cameras and the MIPlus07 program (Conbest Co.). The nuclear DNA content was determined in fresh and young leaves of E. helleborine, collected from eight populations.

Results. We observed that in anthropogenic populations: i) shoots were higher than shoots from natural populations, ii) flowers differed significantly in terms of ten biometric features between habitats, iii) the genome size differed significantly between the plants growing in natural and anthropogenic habitats.

Discussion. According to some researchers, the presence of phenotypic plasticity and the occurrence of ecotypes are adaptation strategies of plants to environmental changes. In our opinion, in the case of the studied anthropogenic habitats (roadside) in which the E. helleborine populations grew, we can talk about ecofen due to the often repeated set of characteristic features. i.e.: high shoots, long inflorescence and long, broad leaves. We agree, however, that it is difficult to isolate a taxonomic unit for ecofen due to the lack of experimental research.
Acoustic profiling of Orthoptera for species monitoring and discovery: present state and future needs
Authors: Riede Klaus
Published: January 2018

Background: Bioacoustic monitoring and classification of animal communication signals has developed into a powerful tool for measuring and monitoring species diversity within complex communities and habitats. The high number of stridulating species among Orthoptera allows their detection and classification in a non-invasive and economic way, particularly in habitats where visual observations are difficult or even impossible, such as tropical rainforests.

Methods: Major sound archives where queried for Orthoptera songs, with special emphasis on usability as reference training libraries for computer algorithms.

Results: Orthoptera songs are highly stereotyped, reliable taxonomic features. However, exploitation of songs for acoustic profiling is limited by the small number of reference recordings: existing song libraries represent only about 1,000 species, mainly from Europe and North America, covering less that 10% of extant stridulating Orthoptera species. Available databases are fragmented and lack tools for song annotation and efficient feature-based search. Results from recent bioacoustic surveys illustrate the potential of the method, but also challenges and bottlenecks impeding further progress. A major problem is time-consuming data analysis of recordings. Computer-aided identification software has been developed for classification and identification of cricket and grasshopper songs, but these tools are still far from practical field application.

Discussion: A framework for acoustic profiling of Orthoptera should consist of the following components:

(1) Protocols for standardised acoustic sampling, at species and community level, using acoustic data loggers for autonomous long-term recordings;

(2) Open access to and efficient management of song data and voucher specimens, involving the Orthoptera Species File (OSF) and Global Biodiversity Information Facility (GBIF);

(3) An infrastructure for automatised analysis and song classification;

(4) Complementation and improvement of Orthoptera sound libraries, using Orthoptera Species File as taxonomic backbone and repository for representative song recordings. Taxonomists should be encouraged to deposit original recordings, particularly if they form part of species descriptions or revisions.
A simple method for data partitioning based on relative evolutionary rates
Authors: Rota Jadranka , Malm Tobias , Wahlberg Niklas
Published: January 2018

Background. Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We applied this method to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths).

Methods. We used TIGER to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into bins based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k-means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder.

Results. In all eight datasets, partitioning using TIGER and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position.

Discussion. We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.
High quality draft genome of Brucella abortus strain Col-B012, isolated from a Holstein cattle in Nariño Colombia, brings new insights into the diagnosis and the epidemiology of biovar 4 strains
Authors: Pacheco-Montealegre Mauricio , Patiño Rocío E , Torres Ligia , Jiménez Sabrina , Rodriguez Jose Luís , Caro-Quintero Alejandro
Published: January 2018

Brucellosis is a commonly diagnosed zoonosis that causes infertility and abortion in cattle, it is acquired from handling of infected animals or consuming contaminated milk or milk products. In Colombia, it is classified as prevention and control disease, despite its relevance little is known about the origin, epidemiology and the genetic constituents of the strains circulating in dairy farms. Here we present the draft genome of B. abortus Col-B012, an isolate obtained from a female Holstein belonging to a dairy farm in Nariño, Colombia. This genome comprises 3,234,714 bp and 3,018 predicted protein-encoding genes. Using comparative genomics and phylogenetic analysis, we found that the strain Col-B012 clustered with known biovar 4 variants. The analysis of the core genes allowed the identification of polymorphisms only present in biovar 4 genomes, these alleles might be associated with the phenotypic and pathogenic characteristics of the group and are proposed as possible targets for identification by PCR. The sequencing of B. abortus Col-B012 genome provides important insights to improve the diagnosis and the epidemiology of this disease and represents the first report of the biovar 4 in Colombia.
Short-term gains in histology knowledge: A veterinary gaming application
Authors: Bauman Eric B. , Gilbert Gregory E , Vaughan Greg
Published: January 2018

Outcomes research exists incorporating non-digital games in veterinary education; however, little research examines outcomes from digital applications. Bauman’s Layered-Learning Model was applied to investigate whether a digital matching game produced short-term knowledge gains in veterinary students. Two groups of students (n1=67; n2=55) practiced the matching game for an hour. A Wilcoxon signed rank test tested for a statistically significant improvement in pre-test/post-test scores. All statistical analyses were done using R. Mean and median pre-test scores were 15 (SD=1.88; IQR: 2) and post-test scores 16 (SD=1.80; IQR: 2). Mean and median pre-test score for Group 2 were 13 (SD=2.30; IQR=2.5) and post-test scores 15 (SD=1.93; IQR=2.5). Both groups increased significantly in post-test scores (P value<.0001). Statistically significant short-term increases of marginal importance in histology knowledge was seen. A greater increase might be seen with quiz revision increasing difficulty and discrimination ability. Further directions should investigate long-term knowledge retention.