bluuebunny/crossref_metadata_2025 huggingface dataset:
Large scale eucalypt plantations associated to increased fire risk
Authors: Cordero Rivera Adolfo
Published: January 2018

To satisfy the high timber demands of human society, forest plantations, especially with fast growing species like pines and eucalypts, are increasing worldwide. In some European countries, the number of wildfires has been augmenting since the second half of the XX century, in parallel with these tree plantations. The record for wildfires in Europe is paradoxically found in the NW of the Iberian Peninsula, a region where broadleaved Quercus forests are the potential climax vegetation, with a humid climate, unfavourable for fire occurrence. The ecological and forestry literature have analysed fire occurrence with complex models of fuel accumulation and vegetation structure, combined with no less complex climatic models to explain why this region has such a high fire occurrence. Economists have concentrated on the relationship between income and fire. Historians, sociologists and political scientists have long ago demonstrated that several conflicts over land use and property are behind most wildfires in this region, but there is little interaction between these fields. Here I use official statistics about fire frequency and wood production to test whether fire frequency is associated to the use of pyrophytic species. I found that fire frequency in NW Spain can be predicted by the amount of eucalypt biomass accumulated in forest plantations. I further explore the relationships between intensive sylviculture and fire risk at a regional scale (the North of the Iberian Peninsula) and a large scale, the Mediterranean countries. NW Iberia peasants have traditionally used fire to manage their common lands, and used the same techniques to oppose forest policies implemented by Franco’s dictatorship, which continued until now with little changes. The use of highly pyrophytic species like eucalypts and some pines has exacerbated this problem, as suggested by the positive correlation between eucalypt plantations and fire frequency at the local, regional and Mediterranean scales.
Effect of an oral dietary supplementation by a formulation based on silibinin-phosphatidylcholine complex in cats with liver diseases
Authors: Biasibetti Elena , Cocca Tiziana , Capucchio Maria Teresa , Togni Stefano , Giacomelli Luca , Giraudo Leonardo , Bigliati Mauro , Barbara Marco
Published: January 2018

Background: Liver pathology in cats represents a frequent clinical condition occurring in animals of any age. Dietary supplementation with hepatoprotective and antioxidant products could represent a beneficial strategy to prevent and treat these disorders. We evaluated the tolerability and efficacy of long-term treatment with a multi-component, dietary supplement containing functional natural ingredients with recognized hepatoprotective properties in cats suffering from liver diseases

Methods: 20 European domestic cats of either gender, 10 with hepatic lipidosis and 10 with cholangitis received for 180 consecutive days a multi-component formulation based on the silibinin-phosphatidylcholine complex as paste or tablet. Clinical assessment and blood and urine parameters were evaluated at T0 (inclusion time) and after 7, 28, 60, 90 and 180 days from the initiation of the study.

Results: The oral supplementation with the silibinin-phosphatidylcholine complex significantly reduced the activity of liver enzymes in serum (alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, γ -glutamyl transferase) and the content of total bilirubin, albumin, pre- and post- bile acids, in cats with hepatic lipidosis or cholangitis, normalizing their liver function parameters. Moreover, following the supplementation, the appetite was restored in all cats and the frequent episodes of diarrhea and vomit reported at inclusion almost disappeared.

Discussion: Dietary supplementation with the silibinin-phosphatidylcholine complex containing functional natural ingredients with recognized hepatoprotective and antioxidant actions might represent an effective strategy to improve the conditions of liver dysfunction, such as hepatitis lipidosis and cholangitis, in cats.
Social marketing interventions for neglected tropical diseases (NTDs): A systematic review protocol
Authors: Aya Pastrana Nathaly , Miranda J Jaime , Somerville Claire , Beran David , Suggs L Suzanne
Published: January 2018

Background. Social marketing influences behaviors to improve the health and wellbeing of individuals and society, and this approach could be used in the field of public health for the prevention and control Neglected Tropical Diseases (NTDs). NTDs are diseases of poverty that place a burden in individuals, communities and health systems, and that exacerbate the cycle of poverty. Differences in risk and socio-cultural factors make women and children differently vulnerable. Guided by the Hierarchical Model of Social Marketing, this systematic review will assess the breadth of coverage of social marketing interventions about the 17 World Health Organization’s priority NTDs. Additionally, it will use the WHO Gender Assessment Tool (GAT) to assess the gender responsiveness of the included interventions. Methods. This protocol follows the guidelines of the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P). Searches will be conducted in the databases of PubMed, EbscoHost, ProQuest, Web of Science (WOS), Global Index Medicus and Virtual Health Library (VHL) Regional Portal, and there will be no language restriction. Social marketing interventions implemented at the community, health facility and public policy settings will be included if they target an NTD; it applies at least 1 of the 4 core social marketing concepts, and 1 of the 5 social marketing techniques as described in the Hierarchical Model of Social Marketing. Data management of records will be done in Covidence, a Cochrane systematic review platform, and of data extracted in Excel. The QATSDD Critical Appraisal Tool will be used to assess the quality of individual studies in terms of how they report their research processes. Discussion. The results of this review will contribute to understand the social marketing concepts and techniques that have been used to address NTDs, and their behavioral determinants and behavioral outcomes. Furthermore, the results of this review will bring together the strengths from multidisciplinary fields by integrating gender, social marketing and NTDs in a systematic manner. Systematic review registration. PROSPERO CRD42017063858
Resounding failure to replicate links between developmental language disorder and cerebral lateralisation
Authors: Wilson Alexander C , Bishop Dorothy V M
Published: January 2018

Background. It has been suggested that failure to establish cerebral lateralisation may be related to developmental language disorder (DLD). There has been weak support for any link with handedness, but more consistent reports of associations with functional brain lateralisation for language. The consistency of lateralisation across different functions may also be important. We aimed to replicate previous findings of an association between DLD and reduced laterality on a quantitative measure of hand preference (reaching across the midline) and on language laterality assessed using functional transcranial Doppler ultrasound.

Methods. From a sample of twin children aged from 6 to 15 years, we identified 107 cases of DLD and 156 typically-developing (TD) comparison cases, all of whom had useable data from fTCD yielding a laterality index (LI), as well as measures of handedness.

Results. Indices of handedness and language laterality for this twin sample were similar to those previously reported with these measures for single-born children. There was no difference between the DLD and TD groups on quantitative measures of handedness or language lateralisation, or on a categorical measure of consistency of left hemisphere dominance. Contrary to prediction, there was a greater incidence of right lateralisation for language in the TD group (19.90%) than the DLD group (9.30%), confirming that atypical laterality is not inconsistent with typical language development. We also failed to replicate associations between language laterality and language test scores.

Discussion. Given the large sample studied here and the range of measures, we suggest that previous reports of atypical manual or language lateralisation in DLD may have been false positives.
Intraspecific functional and genetic diversity of Petriella setifera
Authors: Pertile Giorgia , Panek Jacek , Oszust Karolina , Siczek Anna , Frąc Magdalena
Published: January 2018

Petriella setifera is poorly-known species with only fragmentary information in literature and with published partial genome about the fungal species. Therefore, the aim of the study was an analysis of the intraspecific genetic and functional diversity of new isolated fungal species of P. setifera. From the molecular biological viewpoint, the intraspecific variability was found through the Amplified Fragment Length Polymorphism analysis (AFLP). The analysis showed a good variability among the analysed isolates, which was demonstrated by the clear subdivision of all the isolates into two clusters with 51% and 62% of similarity, respectively. For the metabolic diversity, the BIOLOG system was used and this analysis revealed clear different patterns on the carbon substrates utilization between the isolates bringing a clear separation of the five isolates into three clusters with 0%, 42% and 54% of similarity, respectively. These two techniques allowed estimation of the intraspecific variability within the five isolates of P. setifera strains. Both the methodologies are two easy and rapid techniques to indicate the genetic and functional variability at the intraspecific level within the species, especially, if a biological and functional information about the analysed fungal strains are limited.
umx: Twin and Path-based Structural Equation Modeling in R
Authors: Bates Timothy C , Maes Hermine H , Neale Michael C
Published: January 2018

Structural equation modeling (SEM) is an important research tool, both for path-based model specification, common in the social sciences, and also matrix-based models in heavy use in behavior genetics. We developed umx to give more immediate access, concise syntax and helpful defaults for users in these two broad disciplines. umx supports development, modification, and comparison of models, as well as both graphical and tabular output. The second major focus of umx, behavior genetic models, is supported via functions implementing standard multi-group twin models. These functions support raw and covariance data, including joint ordinal data, and give solutions for ACE models including support for covariates, common- and independent-Pathway models, and Gene \(\times\) Environment interaction models. A tutorial site and question forum are also available.
Sexually dimorphic venom proteins in long-jawed orb-weaving spiders (Tetragnatha) with potential roles in sexual interactions
Authors: Zobel-Thropp Pamela A , Bulger Emily A , Cordes Matthew H J , Binford Greta J , Gillespie Rosemary G , Brewer Michael S
Published: January 2018

Venom has been associated with the ecological success of many groups of organisms, most notably reptiles, gastropods, and arachnids. In some cases, diversification has been directly linked to tailoring of venoms for dietary specialization. Spiders in particular are known for their diverse venoms and wide range of predatory behaviors, although there is much to learn about scales of variation in venom composition and function. The current study focuses on venom characteristics in different sexes within a species of spider. We chose the genus Tetragnatha (Tetragnathidae) because of its unusual courtship behavior involving interlocking of the venom delivering chelicerae (i.e., the jaws), and several species in the genus are already known to have sexually dimorphic venoms. Here, we use transcriptome and proteome analyses to identify venom components that are dimorphic in Tetragnatha versicolor. We present cDNA sequences of unique high molecular weight proteins that are only present in males and that have remote, if any, detectable similarity to known venom components in spiders or other venomous lineages and several have no detectable homologs in existing databases. While the function of these proteins is not known, their presence in association with the cheliceral locking mechanism during mating together with the presence of prolonged male-male mating attempts in a related, cheliceral-locking species (Doryonychus raptor) lacking the dimorphism suggests potential for a role in sexual communication.
Four simple ways to increase power without increasing the sample size
Authors: Lazic Stanley E
Published: January 2018

Underpowered experiments have three problems: the probability of a false positive result is higher, true effects are harder to detect, and the true effects that are detected tend to have inflated effect sizes. Many biology experiments are underpowered and recent calls to change the traditional 0.05 significance threshold to a more stringent value of 0.005 will further reduce the power of the average experiment. Increasing power by increasing the sample size is often the only option considered, but more samples increases costs, makes the experiment harder to conduct, and is contrary to the 3Rs principles for animal research. We show how the design of an experiment and some analytical decisions can have a surprisingly large effect on power.
Advancing ecological restoration through experimental design on spatial and temporal scales relevant to wildlife
Authors: Dybala Kristen E , Dettling Mark D , Gardali Thomas , Grossman Judah D , Kelsey Rodd , Seavy Nathaniel E
Published: January 2018

Experimenting with new and unconventional restoration methods and designs is critical to advancing the field of ecological restoration. Conventional methods cannot be considered reliable in a future with climate change-induced shifts in weather conditions, species distributions, and ecosystem processes. It is crucial that researchers and practitioners collaborate to identify the most effective restoration methods, yet there remains a disturbing lack of restoration experiments at the spatial or temporal scales relevant for evaluating wildlife responses. We suspect that willingness to attempt such experiments is hampered by the perceived difficulty of conducting these experiments combined with a fear of failure. However, we argue that failure to experiment with new methods guarantees learning nothing new. Here, we address many of the major challenges of designing an experiment to evaluate wildlife responses to restoration, including (1) distinguishing between the goals and objectives of the restoration project and the key uncertainties the experiment will address, (2) designing the experiment itself, including optimizing plot size and replication, and (3) determining how and when the results will be evaluated. We then illustrate how we designed an experiment to evaluate riparian bird responses to restoration along the lower Cosumnes River in the Central Valley of California, USA. Researchers and practitioners working together from the start of the objectives-setting process, through experimental design, implementation, and evaluation can proactively address the challenges of conducting a restoration experiment and maximize the chances of successfully identifying effective restoration methods, adding to the practitioners’ toolbox, and accelerating the rate of successful habitat restoration.
Comparative description and ossification patterns of Dendropsophus labialis (Peters, 1863) and Scinax ruber (Laurenti, 1758)(Anura: Hylidae)
Authors: Arenas Rodríguez Angélica , Rubiano Juan Francisco , Hoyos Julio Mario
Published: January 2018

Although comparative studies of anuran ontogeny have provided new data on heterochrony in the life cycles of frogs, most of them have not included Colombian species. Using different staining techniques, we describe the cranial and poscranial elements development in two hylid species, Scinax ruber and Dendropsophus labialis, providing new data for more comprehensive ontogenetic studies in Neotropical frogs. We examined specimens from Gosner stages 25 to 45. We found differences in the infrarostral and suprarostral cartilages, optic foramen, planum ethmoidale, and the gill apparatus. In the ossification sequence, one of the first elements to ossify were the transverse process of spinal column and atlas in both species, and the parasphenoid in the skull. New descriptions of skeletal development and ossification sequences of larval stages of these two species, especially data concerning the postcranium, contribute with useful information for analysis of sequential heterochrony, because although the hylids are widely known, there are few works (15 of 700 species) about ossification sequence that include the whole skeleton.
Evolutionary Systems Biology integration of multi-level CTMC interaction models of biochemistry and cancer cell growth using Evolvix.
Authors: Meyer Jocelyn R , Alarid Elaine , Loewe Laurence
Published: January 2018

While biochemistry evidently affects the growth rate of cells, many biochemists routinely ignore population variation, just like population geneticists usually ignore causal details of biochemistry that underpin a change in growth rate caused by a mutation. A true EvoSysBio integration requires an explicit mechanism for how molecular reaction rates affect the reproduction rates that determine the fitness of an organism. Here we simulate a very simple and completely explicit Continuous-Time Markov Chain (CTMC) model of cancer cells whose growth rate is affected by the biochemical equilibrium between two molecular complexes. Approximately 70% of breast cancers are of a type that overexpress Estrogen Receptor-alpha (ERα). Cell growth in this type of cancer is inhibited by hormonal therapies that antagonize ERα function as a transcription factor. ERα is encoded by the ESR1 gene, which itself is a target of ERα mediated transcription. When activated by estrogen, ERα binds to the ESR1 promoter, repressing new synthesis of ERα protein. Estrogen binding also induces pathways that lead to degradation of ERα protein. This negative feedback loop is finely tuned to natural levels of estrogen and results in natural levels of growth. In breast cancer, the system is thrown off its natural course such that increased levels of ERα induce levels of cell growth that can lead to cancer. Thus, both genetic changes to the ESR1 promoter, ERα protein degradation, and biochemical changes in estrogen metabolism can effectively cause changes in cell growth rates, which can be seen as the ‘fitness’ of a cancer cell. Predicting cancer cell growth in this system raises a conceptual multi-level simulation problem, because the molecular aspects of this model need to compute the biochemistry in a way that influences growth rates at the cellular level, without resetting growth at each cell division. We present progress towards addressing this simulation challenge in pure mass-action models, which we implemented using the Evolvix model description language. We found that such models can be constructed in more than one way. We explored some candidate model properties that could aid efforts to develop abstractions for more efficiently simulating the common multi-level modeling problems behind many important biological questions. These efforts are ongoing and aim to find efficient ways of encoding and exploring such models in silico. In particular, we are investigating how architecting a new compiler for a general-purpose programming language for biology could improve the efficiency of analyzing the dynamic multi-level simulation scenarios that characterize many questions in EvoSysBio. Progress can be followed at http://evolvix.org.
Fluorescent organic exudates of corals and algae in tropical reefs are compositionally distinct and increase with nutrient enrichment
Authors: Quinlan Zachary A , Remple Kristina , Fox Michael D , Silbiger Nyssa J , Oliver Thomas A , Putnam Hollie M , Kelly Linda W , Carlson Craig A , Donahue Megan J , Nelson Craig E
Published: January 2018

Dissolved organic matter (DOM) composition is a key determinant of microbial community metabolism and trophic nutrient transfer. On coral reefs, four primary groups of benthic organisms dominate photosynthetic production: corals, macroalgae, microphytobenthos, and encrusting algae on rubble, all of which exude significant quantities of DOM. We conducted a mesocosm experiment to characterize and contrast DOM exudates from these four organismal groups under three levels of continuous inorganic nutrient enrichment. We measured bulk dissolved organic carbon and nitrogen and the multivariate spectral characteristics of fluorescent DOM (fDOM). Moderate nutrient enrichment enhanced DOM exudation by all producers. Corals exuded rapidly accumulating DOM with a markedly high concentration of aromatic amino acid-like fDOM components that clearly distinguishes them from algal exudates, which were dominated by humic-like fDOM components and did not accumulate significantly. Our results emphasize the differences between coral and algae in their potential to influence microbial communities and metabolism in reefs.
Geographical differences in the effects of age and height at peak height velocity on final body height: An analysis of a population-based cross-sectional growth curve in Japan
Authors: Yokoya Masana
Published: January 2018

Background. The aim of this study was to elucidate the effect of geographical differences in the age at peak height velocity (APHV) and height at peak height velocity (HPHV) on final height, at a prefectural level, and to evaluate the current average height status of 47 prefectures in Japan.

Methods. We elucidated the association between the geographical differences in a prefectural-level cross-sectional population-based infancy-childhood-puberty (ICP) growth curve, derived from prefectural mean height data (age: 5-17 years, 2006-2013), APHV and HPHV, for final height.

Results. The correlation between the APHV and final height was very weak; however, the results of a multiple regression analysis showed that the final height of each prefecture can be accurately predicted based on the APHV and HPHV. This result showed that the earlier the APHV and higher the HPHV, the higher the final height. An earlier APHV reduced the height gain in the puberty component; however, this did not reduce the final height.

Discussion. From the perspective of the average value of each prefecture, in the present situation, the effect of an earlier APHV in increasing the amount of growth of the childhood component exceeded its effect in reducing the growth of the puberty component. In short, the final height of the prefectures depends on how large the height growth is in the early stages of childhood. However, the HPHV tended to be region-specific, and it is unlikely that it can increase the average height in this population in the future.
If funders and libraries subscribed to open access: The case of eLife, PLOS, and BioOne
Authors: Willinsky John , Rusk Matthew
Published: January 2018

Following on recent initiatives in which funders and libraries directly fund open access publishing, this study works out the economics of systematically applying this approach to three biomedical and biology publishing entities by determining the publishing costs for the funders that sponsored the research, while assigning the costs for unsponsored articles to the libraries. The study draws its data from the non-profit biomedical publishers eLife and PLOS, and the nonprofit journal aggregator BioOne, with this sample representing a mix of publishing revenue models, including funder sponsorship, article processing charges (APC), and subscription fees. This funder-library open access subscription model is proposed as an alternative to both the closed-subscription model, which funders and libraries no longer favor, and the APC open access model, which has limited scalability across scholarly publishing domains. Utilizing PubMed filtering and manual-sampling strategies, as well as publicly available publisher revenue data, the study demonstrates that in 2015, 86 percent of the articles in eLife and PLOS acknowledged funder support, as did 76 percent of the articles in the largely subscription journals of BioOne. Twelve percent of the articles identified the NIH as a funder, 8 percent identifies other U.S. government agencies. Approximately half of the articles were funded by non-U.S. government agencies, including 1 percent by Wellcome Trust and 0.5 percent by Howard Hughes Medical Institute. For 17 percent of the articles, which lacked a funder, the study demonstrates how a collection of research libraries, similar to the one currently subscribing to BioOne, could cover publishing costs. The goal of the study is to inform stakeholder considerations of open access models that can work across the disciplines by (a) providing a cost breakdown for direct funder and library support for open access publishing; (b) positing the use of publishing data-management organizations (such as Crossref and ORCID) to facilitate per article open access support; and (c) proposing ways in which such a model offers a more efficient, equitable, and scalable approach to open access than the prevailing APC model, which originated with biomedical publishing.
Prolonged exposure to ethylene may provide Rhodococcus sp. the ability to delay the effects of ripening in several species of climacteric fruit.
Authors: Perry Guenevere
Published: January 2018

Post-harvest biotechnology is a growing industry. Many farmers are looking for economic and organic methods to preserve crops while effectively decreasing post-harvest losses. Previous studies suggested Rhodococcus rhodochrous DAP 96253 specifically cultured on cofactor enriched media (cofactors, cobalt and urea) enabled the bacteria to delay climacteric ripening in several species of fruit, (Pierce et al., 2008; Pierce et al., 2011).

However, Rhodococcus rhodochrous not cultured on enriched media, but induced with hydrocarbons were also enabled to delay fruit ripening. Hydrocarbon induction doubled NHase activity and significantly improved bacteria ability to delay the effects of fruit ripening on a molecular level. Bacteria reduced cyanide concentration released by plant tissue in the atmosphere by half, and decreased glucose concentration within plant tissue by 18g/L. Experimental results suggest that R. rhodochrous may use a novel pathway to that includes an inducible monooxygenase like enzyme that allows Rhodococcus rhodochrous cells the ability to delay ripening in various species of climacteric fruits.
Objective detection of auditory steady-state responses based on mutual information: Receiver operating characteristics and validation across modulation rates and levels
Authors: Bidelman Gavin M , McElwain Claire
Published: January 2018

Auditory steady-state responses (ASSRs) are sustained potentials used to assess the physiological integrity of the auditory pathway and objectively estimate hearing thresholds. ASSRs are typically analyzed using statistical procedures in order to remove the subjective bias of human operators. Knowing when to terminate signal averaging in ASSR testing is also critical for making efficient clinical decisions and obtaining high-quality data in empirical research. Here, we investigated a new detection metric for ASSRs based on mutual information (MI) [Bidelman, G. M. (2014). Objective information-theoretic algorithm for detecting brainstem evoked responses to complex stimuli. J. Am. Acad. Audiol., 25(8), 711-722], previously bench tested using only a single suprathreshold stimulus. ASSRs were measured in n=10 normal hearing listeners to various stimuli varying in modulation rate (40, 80 Hz) and level (80 – 20 dB SPL). MI-based classifiers applied to ASSRs recordings showed that accuracy of ASSR detection ranged from ~75 - 99% and was better for 40 compared to 80 Hz responses and for higher compared to lower stimulus levels. Detailed receiver operating characteristics (ROC) were used to establish normative ranges for MI for reliable ASSR detection across levels and rates (MI=0.9-1.6). Relative to current statistics for ASSR identification (F-test), MI was found to be a more efficient metric for determining the stopping criterion for signal averaging. Our new results confirm that MI can be applied across a broad range of ASSR stimuli and might offer improvements to conventional objective techniques for ASSR detection.
Tolerance in intergroup encounters: Payoffs and plasticity in non-human primates and humans
Authors: Pisor Anne C , Surbeck Martin
Published: January 2018

Primate individuals use a variety of strategies in intergroup encounters, from aggression to tolerance; however, despite the prevalence of tolerance in humans, recent focus on the evolution of intergroup contest has come at the cost of characterizing the role of tolerance in human sociality. Can we use the selection pressures hypothesized to favor tolerance in intergroup encounters in the non-great ape primates to explain the prevalence and plasticity of tolerance in humans and our closest living relatives? In the present paper, we review these candidate ecological and social factors and conclude that additional selection pressures are required to explain the prevalence of tolerance in human intergroup encounters; we nominate the need to access non-local resources in the human foraging ecology as a candidate pressure. To better evaluate existing hypotheses, additional, targeted data are needed to document the prevalence and plasticity of tolerance during intergroup encounters in some great ape species.
Cricket umpire assistance and ball tracking system using a single smartphone camera
Authors: Arora Udit , Verma Sohit , Sahni Sarthak , Sharma Tushar
Published: January 2018

Several ball tracking algorithms have been reported in literature. However, most of them use high-quality video and multiple cameras, and the emphasis has been on coordinating the cameras or visualizing the tracking results. This paper aims to develop a system for assisting the umpire in the sport of Cricket in making decisions like detection of no-balls, wide-balls, leg before wicket and bouncers, with the help of a single smartphone camera. It involves the implementation of Computer Vision algorithms for object detection and motion tracking, as well as the integration of machine learning algorithms to optimize the results.

Techniques like Histogram of Gradients (HOG) and Support Vector Machine (SVM) are used for object classification and recognition. Frame subtraction, minimum enclosing circle, and contour detection algorithms are optimized and used for the detection of a cricket ball. These algorithms are applied using the Open Source Python Library - OpenCV. Machine Learning techniques - Linear and Quadratic Regression are used to track and predict the motion of the ball. It also involves the use of open source Python library VPython for the visual representation of the results. The paper describes the design and structure for the approach undertaken in the system for analyzing and visualizing off-air low-quality cricket videos.
Longitudinal analysis of raccoon rabies in West Virginia, 2000-2015
Authors: Plants K. Bert , Wen Sijin , Wimsatt Jeffrey , Knox Sarah
Published: January 2018

Animal borne rabies is a source of infection in humans, and raccoons (Procyon lotor) are the primary terrestrial reservoir in West Virginia (WV). To assess the behavior and status of raccoon variant rabies virus (RRV) in WV, a longitudinal analysis for the period 2000-2015 was performed, using data provided by the state Bureau of Public Health. Analytic approaches included linear-mixed, Poisson, and zero inflated Poisson regressions. Each of these approaches indicated that there had been a reduction in numbers of RRV positive animals over the study period, predominantly due to a decrease in raccoon infections. Non-raccoon species did not appear to have a similar decline, however. This has implications for the preventive measures currently being implemented. Spatial analyses of RRV and further examination of the virus in non-raccoon species are warranted.
The performance of cleaner wrasse, Labroides dimidiatus, in a reversal learning task varies across experimental paradigms
Authors: Marcadier Fanny , Binning Sandra A , Wismer Sharon , Krattinger Océane , Quatttrini Fausto , Bshary Redouan , Gingins Simon
Published: January 2018

Testing cognitive performance in controlled laboratory experiments is a powerful tool for understanding the extent and evolution of cognitive abilities in non-human animals. However, cognitive testing is prone to a number of potential biases, which, if unnoticed or unaccounted for, may affect the conclusions drawn. We examined whether slight modifications to the experimental procedure and apparatus used in a spatial discrimination and reversal learning task affected performance outcomes in the bluestreak cleaner wrasse, Labroides dimidiatus (hereafter ‘cleaners’). Using two-alternative forced choice tests, fish had to learn to associate a food reward with a side (left or right) in their holding aquarium. Individuals were tested in one of four experimental treatments that differed slightly in procedure and/or physical set-up. Cleaners from all four treatment groups were equally able to solve the initial spatial discrimination test. However, groups differed in their ability to solve the reversal learning task: no individuals solved the reversal task when tested in small tanks with a transparent partition separating the two options, whereas over 50% of individuals solved the task when performed in a larger tank, or with an opaque partition. These results clearly show that seemingly insignificant details to the experimental set-up matter when testing cognitive performance, and might significantly influence the outcome of experiments. When designing the methodology for comparative cognitive tests, care should be taken to ensure that all groups understand and can respond to the relevant cue to avoid misinterpretations.
A blockchain solution to gun control
Authors: Heston Thomas F
Published: January 2018

Blockchain technology can be utilized to improve gun control without changing existing laws. Firearm related mortality is at epidemic levels in the United States and not only has a significant impact upon public health, it also creates a large financial burden. Suicide is the most common way guns kill. Through better gun tracking and improved screening of high risk individuals, this technological advance in distributed ledger technology will improve background checks on individuals and tracing of guns used in crimes.
Myelin can't change the basic mechanisms of axonal conduction
Authors: Morelli Alessandro M , Panfoli Isabella
Published: January 2018

We propose a new hypothesis about the physical-chemical mechanisms of nerve conduction in myelinated nerves, tending to bridge the theoretical gap existing to date between the basic neuronal activity and its adaptation to myelination. All the considerations imply a simplification of the underlying theories, identifying a precise role for myelin. The ATP-supplying energetic role for myelin allows to overcome the theories that have not yet found a physical-chemical solid confirmation. A radical simplification of nerve conduction mechanism is envisaged: it can be supposed that this mechanism remains unaltered in the passage from the unmyelinated to the myelinated conditions.
Assistive guidance system for the visually impaired
Authors: Takhar Rohit , Sharma Tushar , Arora Udit , Verma Sohit
Published: January 2018

In recent years, with the improvement in imaging technology, the quality of small cameras have significantly improved. Coupled with the introduction of credit-card sized single-board computers such as Raspberry Pi, it is now possible to integrate a small camera with a wearable computer. This paper aims to develop a low cost product, using a webcam and Raspberry Pi, for visually-impaired people, which can assist them in detecting and recognising pedestrian crosswalks and staircases. There are two steps involved in detection and recognition of the obstacles i.e pedestrian crosswalks and staircases. In detection algorithm, we extract Haar features from the video frames and push these features to our Haar classifier. In recognition algorithm, we first convert the RGB image to HSV and apply histogram equalization to make the pixel intensity uniform. This is followed by image segmentation and contour detection. These detected contours are passed through a pre-processor which extracts the region of interests (ROI). We applied different statistical methods on these ROI to differentiate between staircases and pedestrian crosswalks. The detection and recognition results on our datasets demonstrate the effectiveness of our system.
GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data
Authors: Chen Li , Reeve James , Zhang Lujun , Huang Shengbin , Chen Jun
Published: January 2018

Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome data, which contain a vast number of zeros due to the physical absence or under-sampling of the microbes. Normalization methods that specifically address the zero inflation remain largely undeveloped. Here we propose GMPR - a simple but effective normalization method - for zero-inflated sequencing data such as microbiome data. Simulation studies and real datasets analyses demonstrate that the proposed method is more robust than competing methods, leading to more powerful detection of differentially abundant taxa and higher reproducibility of the relative abundances of taxa.
GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data
Authors: Chen Li , Reeve James , Zhang Lujun , Huang Shengbing , Chen Jun
Published: January 2018

Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome data, which contain a vast number of zeros due to the physical absence or under-sampling of the microbes. Normalization methods that specifically address the zero inflation remain largely undeveloped. Here we propose GMPR - a simple but effective normalization method - for zero-inflated sequencing data such as microbiome data. Simulation studies and real datasets analyses demonstrate that the proposed method is more robust than competing methods, leading to more powerful detection of differentially abundant taxa and higher reproducibility of the relative abundances of taxa.
QCOBJ a Python package to handle quantity-aware configuration files
Authors: Vidmar Roberto , Creati Nicola
Published: January 2018

Configuration files are widely used by scientists and researchers to configure the parameters and initial settings for their computer programs. We present here a Python package that adds physical quantities to these parameters and validate them against user defined specifications to ensure that they are in the correct range and eventually converted to the requested unit of measurement. The package contains also a graphical user interface class to display and edit configuration file content and compare them side by side highlighting their differences.
Benthic macrofaunal structure and secondary production in tropical estuaries on the Eastern Marine Ecoregion of Brazil
Authors: Bissoli Lorena B , Bernardino Angelo F
Published: January 2018

Estuaries are highly productive and support diverse benthic assemblages, but few estimates of benthic production are available for most ecosystems. In tropical estuaries mangroves and tidal flats are typical habitats with high spatial heterogeneity of benthic macrofaunal assemblages. However, accessing differences and similarities of benthic assemblages within estuarine habitats and between regional ecosystems may provide scientific support to management of those ecosystems. Here we studied three tropical estuaries in the Eastern Marine Ecoregion of Brazil to assess the spatial variability of benthic assemblages from vegetated (mangroves) and unvegetated (tidal flats) habitats. A nested sampling design was used to determine spatial scales of variability in benthic macrofaunal density, biomass and secondary production. Habitat differences in benthic assemblage composition, biomass, density and secondary production were significant, but also varied between estuaries. Macrofaunal secondary production differed between estuaries and between tidal flat and mangrove habitats, and those differences were related to the composition of benthic assemblages. High benthic production were associated with tidal flats in estuaries with presumable less human impacts, although benthic assemblages from mangrove sediments had similar production irrespective of human disturbances. Given variable levels of human impacts and predicted climate change effects on tropical estuarine assemblages in Eastern Brazil, our data support the use of benthic secondary production to address long-term changes and improved management of estuaries in Eastern Brazil.
Knockout of c-mos gene does not affect tumor progression in murine models of lung and colorectal cancer
Authors: Chen Zhengxi , Qiao Ju , Chen Zhenqi , Xiao Qian
Published: January 2018

Background. The c-mos proto-oncogene was one of the first proto-oncogenes to be cloned. Apart from its role in meiosis, many efforts have been made to illuminate the mechanisms by which c-mos acts as an oncogene. c-mos or its coding messenger RNA have been confirmed in most somatic tissues at low levels. However, a detailed role of c-mos as an oncogene in somatic cells remains unknown.

Methods. In this study, we analyzed online databases to find out the correlation between Mos expression and poor survival rates in human cancer patients. Then, we investigated whether the involvement of c-mos in tumor progression via applying Apcmin intestinal cancer model and KrasG12D lung cancer model.

Results. First, we found the expression of Mos differed between human and mice, and a significant correlation between high Mos expression and poor survival rates in lung cancer patients. Interestingly, we tested that the effects of deficient c-mos in both Apcmin intestinal cancer model and KrasG12D lung cancer model. Despite the abovementioned significant correlation, the results did not show a strong inhibitory effect on murine models of lung and intestine tumors. We find no evidence of a direct role for c-mos in tumor progression in abovementioned mice models.

Discussion. It indicated that functions of c-mos gene might be species-specific and that c-mos involvement in tumor progression was circumstantial and it probably depended on other oncogene activation.

Keywords: c-mos, Kras, Apc, survival rate, murine model, lung cancer, colorectal cancer
Enhancing knowledge of head and neck anatomy in preclinical medical students using low fidelity simulation
Authors: St. Hilaire Rose Clarie , Buckley Lisa , Gilbert Gregory E. , Leighton Kim , Barremkala Mallikarjuna , Callender Diana , Pederson David
Published: January 2018

Background: Simulation-based medical education is more prevalent in undergraduate preclinical medical education and acts as a foundation for clinical learning in years three and four. Currently, there is a call to teach clinical application of basic science material in preclinical years one and two.

Methods: Two groups of students participated in this investigation; a historical control of 270 students from the 2010 matriculating class and students receiving the intervention (anatomy lecture plus airway management simulation) from the 2012 matriculating class (n=337). Descriptive statistics were calculated for demographic and academic performance variables. Unadjusted and adjusted odds of passage of mid-term and final assessment were calculated. The final assessment was defined as one correct, two correct, and all three questions correct.

Results: Adjusted odds of passage of mid-term exam for the control group were 3.9 (95% CI: 2.7-5.9), virtually unchanged from the unadjusted odds of passage. Control group results for final exam passage as defined as one correct increased from .7 to .9 when adjusted for variables (95% CI:.3-2.5). Odds of passage of final assessment, for the control group, for adjusted models for two or greater correct increased from 4.1 to 5.6 (95% CI:2.6-13.7) and from 34.1 to 44.0 (95% CI: 21.7-102.5) when three answers (or 100%) are needed for passage.

Conclusions: When passage criteria for the final exam were defined as one correct, addition of a simulation exercise to the anatomy lecture increased the rate of passage by 11% after adjusting for covariates. However, when passage criteria for the final exam was defined as two or three correct, addition of a simulation exercise to the anatomy lecture decreased the rate of passage.
Metabarcoding littoral hard-bottom communities: unexpected diversity and database gaps revealed by two molecular markers
Authors: Wangensteen Owen S , Palacín Creu , Guardiola Magdalena , Turon Xavier
Published: January 2018

We developed a metabarcoding method for biodiversity characterization of structurally complex natural marine hard-bottom communities. Novel primer sets for two different molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase, COI, and the V7 region of ribosomal RNA 18S were used to analyse eight different marine shallow benthic communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea). Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. We found unexpectedly high values for MOTU richness, suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignation of the detected sequences. Nevertheless, over 90% (in abundance) of the sequenced reads could be successfully assigned to phylum or lower taxonomical level. This identification rate might be significantly improved in the future, as reference databases are updated. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples, and emerges as a robust, fast, objective and affordable method for comprehensively characterizing the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans, allowing for standardized biomonitoring of these ecologically important communities. The new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.