bluuebunny/crossref_metadata_2025 huggingface dataset:
Reducing bias in population and landscape genetic inferences: The effects of sampling related individuals and multiple life stages
Authors: Peterman William , Brocato Emily R , Semlitsch Raymond D , Eggert Lori S
Published: January 2018

In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. In this study, we sampled embryos, larvae, and adult Ambystoma maculatum from five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FST and DC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. Further, we found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when using DC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Our findings suggest that it may be possible to mix life stages to reach target sample size quotas, but researchers should nonetheless proceed with caution depending upon the goals and objectives of the study.
Recreational boating as a vector of spread of non-indigenous species around the Mediterranean Sea
Authors: Ulman Aylin , Marchini Agnese , Arvanitidis Christos , Occhipinti Anna
Published: January 2018

This study seeks to identify the hotspots for the secondary spread of non-indigenous species (NIS) resulting for recreational boating travel patterns across the Mediterranean Sea, and investigate the potential for internal spread within each study region. Three Mediterranean regions will be sampled for: 1) NIS richness in the marinas and NIS richness and abundance from recreational vessels; 2) biopollution level of transient recreational boats; 3) geographic range of NIS within each region; 4) hull cleaning and travel history of recreational boats. The results will then be tested with other abiotic factors to determine which factors are significant in contributing to making some marinas more high-risk for the presence and transfer of alien species. Finally, a spatial connectivity network analysis will be presented of the 30 sampled marinas by combining a risk-level for each marina along with recreational boating travel patterns. Marina selection is based on the busiest marinas for recreational boaters in each region in combination with securing permission and feasibility. Samples for Amathia verticillatum will be collected from each region and genetically tested to determine if they share the same initial or secondary source of invasion.
Architecture of the sperm whale forehead facilitates ramming combat
Authors: Panagiotopoulou Olga , Spyridis Panagiotis , Mehari Abraha Hyab , Carrier David R , Pataky Todd C
Published: January 2018

Herman Melville’s novel Moby Dick was inspired by historical instances in which large sperm whales (Physeter macrocephalus L.) sank 19th century whaling ships by ramming them with their foreheads. The immense forehead of sperm whales is possibly the largest, and one of the strangest, anatomical structures in the animal kingdom. It contains two large oil-filled compartments, known as the “spermaceti organ” and “junk”, that constitute up to one-quarter of body mass and extend one-third of the total length of the whale. Recognized as playing an important role in echolocation, previous studies have also attributed the complex structural configuration of the spermaceti organ and junk to acoustic sexual selection, acoustic prey debilitation, buoyancy control, and aggressive ramming. Of these additional suggested functions, ramming remains the most controversial, and the potential mechanical roles of the structural components of the spermaceti organ and junk in ramming remain untested. Here we explore the aggressive ramming hypothesis using a novel combination of structural engineering principles and probabilistic simulation to determine if the unique structure of the junk significantly reduces stress in the skull during quasi-static impact. Our analyses indicate that the connective tissue partitions within the junk reduce stress across the skull during impact; stress reduction is greatest in the anterior aspect of the skull; and removal of the connective tissue partitions increases stress concentrations on the tip of the skull, possibly making it prone to fracture. Although the unique structure of the junk certainly serves multiple functions, our results are consistent with the hypothesis that the structure also evolved to function as a massive battering ram during male-male competition.
The influence of mature oak stands and spruce plantations on soil-dwelling click beetles in lowland plantation forests
Authors: Loskotová Tereza , Horak Jakub
Published: January 2018

Most European forests have been converted into forest plantations that are managed for timber production. The main goal of this paper was to determine the difference between mature native sessile oak (Quercus petraea) stands and non-indigenous Norway spruce (Picea abies) plantations with respect to communities of Athous click beetles in approximately 6,500 ha of lowland plantation forest area in the Czech Republic. Athous subfuscus was the most abundant and widespread species, followed by A. zebei and A. haemorrhoidalis, while A. vittatus was considered rare. Spatial analysis of environmental variables inside studied patches showed that the species composition of Athous beetles best responded to a 20 m radius surrounding traps. Species’ responses to the environment showed that A. vittatus and A. haemorrhoidalis preferred oak stands, while A. zebei and A. subfuscus were associated with spruce plantations. In addition, oak stands showed higher diversity of beetle communities. The studied species are important for their ecosystem services (e.g. predation on pests or bioturbation) and seems to tolerate certain degrees of human disturbances, which is beneficial especially for forest plantations managed for timber production.
The dark cube: Dark and light character profiles
Authors: Garcia Danilo , Rosenberg Patricia
Published: January 2018

Background: Research addressing distinctions and similarities between people’s malevolent character traits (i.e., the Dark Triad: Machiavellianism, narcissism, and psychopathy) has detected mixed and inconsistent linear associations to temperament traits. On this basis, some researchers suggest that the dark traits are best represented as one global construct (i.e., the unification argument) rather than as ternary construct (i.e., the uniqueness argument). Here we put forward the dark cube (cf. Cloninger’s character cube) comprising eight dark profiles that can be used to compare individuals who differ in one dark character trait while holding the other two constant. Our aim was to investigate in which circumstances individuals who are high in each one of the dark character traits differ in Cloninger’s “light” character dimensions: self-directedness, cooperativeness, and self-transcendence. Additionally, we investigated if the people’s dark character profiles were associated to their light character profiles. Method: A total of 997 participants recruited from Amazon’s Mechanical Turk (MTurk) responded to the Short Dark Triad and the Short Character Inventory. Participants were allocated to eight different dark character profiles and eight light character profiles based on their scores in each of the traits and any possible combination of high and low scores. We used three-way interaction regression analyses and t-tests to investigate differences in Cloninger’s character dimensions between individuals with different dark profiles. As a second step, we compared the individuals’ dark profile with her/his character profile using an exact cell-wise analysis conducted in the ROPstat software ( http://www.ropstat.com ). Results: Individuals who expressed high levels of Machiavellianism and those who expressed high levels of psychopathy also expressed low self-directedness and low cooperativeness. Individuals with high levels of narcissism, in contrast, scored high in self-directedness. Moreover, individuals with a profile low in the dark traits were more likely to end up with a profile high in cooperativeness. The opposite was true for those individuals with a profile high in the dark traits. Conclusions: Our study suggests that individuals who are high in Machiavellianism and psychopathy share a unified non-agentic and uncooperative character (i.e., irresponsible, low in self-control, unempathetic, unhelpful, untolerant), while individuals high in narcissism have a more unique character configuration expressed as high in agency and, when the other dark traits are high, highly spiritual but uncooperative. In other words, based on differences in their associations to the light side of character, the Dark Triad seems to be a dyad rather than a triad.
Predicting the potential distributions of Senecio vulgaris L. in China
Authors: Cheng Dandan , Xu Lin
Published: January 2018

Predicting potential distribution for alien plants by species distribution model (SDM, or Ecological Niche Model) using occurrence data and habitat environmental variables plays an important role in management of the invasive risk by an alien plant. Common groundsels (Senecio vulgaris, Asteracea), native in Eurasia and North Africa, has been a cosmopolitan weed in temperature and also listed as one of invasive plants in China. We predict the potential distribution of this species in the world and in China particularly in Maxent (maximum entropy) models by using global occurrence records of S. vulgaris and the associated climate variables. The occurrence data were collected from the online databases, Global Biodiversity Information Facility database (GBIF), Chinese Virtual Herbarium database (CVH), and also from field work in China. The climate variables were download from WorldClim (http://www.worldclim.org). The occurrence records showed that S. vulgaris is present in 16 provinces or regions in north – eastern, south – western, central and north China, and almost not present in south – eastern, north – western China. The mapping of S. vulgaris potential distribution is diagonally across China, including the north – eastern, south – western China, and the cool area between the two regions. Analysis of the contribution and importance of climatic factors in the prediction model indicated that S. vulgaris adapts to the climate in humid and cool area in China (annual mean temperature ranges 2.4 ~ 17.5 ℃, and annual precipitation ranges 550 ~ 1500 mm). It is suggested that special attention should be paid to the plain in NE China and Shandong Peninsula, Yungui Plateau, the cool mountain area around Sichuan basin, in western Hubei, southern Shaanxi, Shanxi and around Beijing in order to manage the invasion risk by S. vulgaris. The better performance of the model built by using occurrence data in China than that by using the global data in relation the predict outcome in China imply that it is might be better to use regional data than the global data when predict potential distribution for an alien plant with long invasive history in study area.
Valproate antinociceptive and anti-inflammatory effect in female rodents
Authors: Figueiredo Karolinne S , Sales Maria LAO , Fontenele Juvenia B , Viana Glauce SB , Felix Francisco H
Published: January 2018

Valproate, an indirect γ-aminobutiric acid agonist has been successfully used in various painful conditions. Despite its frequent use, limited pre-clinical and clinical data exist about its analgesic effect. We tested valproate p.o. in increasing doses (10, 25, 50, 100 mg/kg) in acute nociception models in mice (writhing test and formalin licking-paw test) and in acute primary thermal hyperalgesia induced by carrageenan in rats, comparing its effects to a non-treated control and morphine (5 mg/kg), amitriptyline (10 mg/kg) or indomethacin (10 mg/kg). Valproate showed a statiscally significant (p<0.001) dose-response effect in these models, both in male and female mice and in female rats. Antihyperalgesic effect of valproate in the plantar model was not reverted by reserpine pre-treatment. Interestingly, the maximum effect of valproate on this model occurred at a dose of 50mg/kg and the higher dose of 100mg/kg showed a minor effect. Additionally, we demonstrated that valproate has anti-inflammatory effect in the carrageenan-induced oedema model in male and female mice. Valproate antinociceptive and anti-inflammatory effects seem not to be gender-specific in animal models.
On Machine Learning applications with algebraic geometry
Authors: Goteti Sasikanth
Published: January 2018

In this article, we briefly describe various tools and approaches that algebraic geometry has to offer to straighten bent objects. throughout this article we will consider a specific example of a bent or curved piece of paper which in our case acts very much like an elastica curve. We generalize this model to various shapes of paper which are stretched and bent and then finally implement it on a standard 80mg paper and see how the folds on paper can be completely removed using python and sage-math code. We conclude this article with a suggestion to algebraic geometry as a viable and fast performer alternative of neural networks in vision and machine learning.The purpose of this article is not to build a full blown framework but to show evidence or possibility of using algebraic geometry as an alternative to recognizing or extracting features on manifolds.
Phosphorus mobilizing consortium Mammoth P enhances plant growth
Authors: Baas Peter , Bell Colin , Mancini Lauren M , Lee Melanie N , Conant Richard T , Wallenstein Matthew D
Published: January 2018

Global agricultural productivity may be constrained by the finite and limited supply of phosphorus (P), adding to the challenges in meeting the projected needs of a growing human population in the coming decades. In addition, when P fertilizers are added to soils, they can become bound to soils resulting in low fertilizer efficiency. However, P-mobilizing bacteria could potentially liberate soil-bound P, resulting in a higher plant P uptake and increased yield. Bacteria can mobilize P through several mechanisms, suggesting that consortia of P-bacteria may be more effective than single species. Species diversity can have a synergistic, or non-additive, effect on ecosystem functioning (“the whole is more than the sum of its parts”) but rarely is the microbial community structure intentionally managed to improve plant nutrient uptake. We investigated whether inoculation of soils with a four-species bacterial community developed to mobilize soil P could increase plant productivity. In wheat and turf trials, we found that Mammoth P was able to deliver yields equivalent to those achieved using conventional fertilizer applications. Herbs and fruits showed that the combination of fertilizer with Mammoth P significantly increased productivity - in some cases productivity doubled. Metabolites produced by the Mammoth P consortium led to increased yields in some cases, suggesting that microbial products (produced in the absence of plants) played a role in enhancing plant productivity. Results from these trials indicate substantial potential of Mammoth P to enhance P supply to plants, improving P fertilizer use-efficiency and increasing agricultural productivity.
Sex expression and floral diversity in Jatropha curcas: A population study in its center of origin
Authors: Adriano-Anaya María de Lourdes , Pérez-Castillo Edilma , Salvador-Figueroa Miguel , Ruiz-González Sonia , Vázquez-Ovando José Alfredo , Grajales-Conesa Julieta J , Ovando-Medina Isidro
Published: January 2018

Sex expression and floral morphology studies are central to understand breeding behavior and to define the productive potential of plant genotypes. In particular, the new bioenergy crop Jatropha curcas L. has been classified as a monoecious species. Nonetheless, there is no information about its reproductive diversity in the Mesoamerican region, which is considered its center of origin and diversification. Thus, we determined sex expression and floral morphology in J. curcas populations from southern Mexico and Guatemala. Our results showed that most of J. curcas specimens had typical inflorescences separate sexes (monoecious), meanwhile the rest were atypical (gynoecious, androecious, andromonoecious, androgynomonoecious). The most important variables to group these populations, based on a discriminant analysis, were: male flower diameter, female petal length and male nectary length. From the southern Mexico "Guerrero" was the most diverse population and in Chiapas "Centro". On the other hand, a cluster analysis showed that the accessions from southern Mexico were grouped without showing any correlation with the geographical origin, while those accessions with atypical sexuality were grouped together. Additionally, a Mantel test showed a significant correlation between the distance matrix generated in this study and the genetic distance matrix (AFLP) previously reported for the same accessions. Our results contribute to design genetic improvement programs by using sexually and morphologically contrasting plants from the center of origin.
Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters
Authors: Khalili Samani Nima , Esa Yuzine , Amin S.M Nurul , Fatin Mohd Ikhsan Natrah
Published: January 2018

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental researches on biological characteristics of P.canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P.canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395 to 0.771 and 0.033 to 0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H0) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H0= 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940 at which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P.canius, and should be necessary highlighted for appropriate management and conservation of species. Though, further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.
­Immunohistochemistry for the detection of neural and inflammatory cells in equine brain tissue
Authors: Delcambre Gretchen H , Liu Junjie , Herrington Jenna M , Vallario Kelsey , Long Maureen T
Published: January 2018

Phenotypic characterization of cellular responses in equine infectious encephalitides has had limited description of both peripheral and resident cell populations in central nervous system (CNS) tissues due to limited species-specific reagents that react with formalin-fixed, paraffin embedded tissue (FFPE). This study identified a set of antibodies for investigating the immunopathology of infectious CNS diseases in horses. Multiple commercially available staining reagents and antibodies derived from antigens of various species for manual immunohistochemistry (IHC) were screened. Several techniques and reagents for heat-induced antigen retrieval, non-specific protein blocking, endogenous peroxidase blocking, and visualization-detection systems were tested during IHC protocol development. Boiling of slides in a low pH, citrate-based buffer solution in a double-boiler system was most consistent for epitope retrieval. Pressure-cooking, microwaving, high pH buffers, and proteinase K solutions often resulted in tissue disruption or no reactivity. Optimal blocking reagents and concentrations of each working antibody were determined. Ultimately, a set of monoclonal (mAb) and polyclonal antibodies (pAb) were identified for CD3+ (pAb A0452, Dako) T-lymphocytes, CD79αcy+ B-lymphocytes (mAb HM57, Dako), macrophages (mAb MAC387, Leica), NF-H+ neurons (mAb NAP4, EnCor Biotechnology), microglia/macrophage (pAb Iba-1, Wako), and GFAP+ astrocytes (mAb 5C10, EnCor Biotechnology). In paraffin embedded tissues, mAbs and pAbs derived from human and swine antigens were very successful at binding equine tissue targets. Individual, optimized protocols are provided for each positively reactive antibody for analyzing equine neuroinflammatory disease histopathology.
Improving the connection between data collection and decision making at US EPA and US DOE
Authors: Blacker Stanley
Published: January 2018

Solving an environmental problem requires stakeholder understanding and agreement. What appears to be simple problems to define become complex when data determine outcomes. This paper will describe the seven step decision logic developed for and used by US EPA to determine the problem and the decision rule for establishing compliance and acceptable uncertainty in the data used in informed decision making. Advances made in Kriging and Bayesian statistical inference tools to quantify estimates of data distributions and associated uncertainty will be described. But, making informed decisions pivot on tradeoff between cost of obtaining more information and cost of action. Raifa's foundational work on statistical decision theory is the basis for creating quantitative cost driven methodology directly applicable to cost-risk-benefit environmental decision making and actions. The paper presents various real world applications of these tools.
Putting the ghost in the machine: exploring human-machine hybrid virtual patient systems for health professional education
Authors: Topps David , Cullen Michelle L , Sharma Nishan , Ellaway Rachel H
Published: January 2018

Background: Virtual patient authoring tools provide a simple means of creating rich and complex online cases for health professional students to explore. However, the responses available to the learner are usually predefined, which limits the utility of virtual patients, both in terms of replayability and adaptability. Using artificial intelligence or natural language processing is expensive and hard to design. This project description lays out an alternative approach to making virtual patients more adaptable and interactive. Methods: Using OpenLabyrinth, an open-source educational research platform, we modified the interface and functionality to provide a human-computer hybrid interface, where a human facilitator can interact with learners from within the online case scenario. Using a design-based research approach, we have iteratively improved our case designs, workflows and scripts and interface designs. The next step is to robustly test this new functionality in action. This report describes the piloting and background as well as the rationale, objectives, software development implications, learning designs, and educational intervention designs for the planned study. Results: The costs and time required to modify the software were much lower than anticipated. Facilitators have been able to handle text input from multiple concurrent learners. Learners were not discouraged waiting for the facilitator to respond. Discussion: The implementation and use of this new technique seems very promising and there are a great many ways in which it might be used for training and assessment purposes. This report also explores the provisional implications arising from the study so far.
Urban park characteristics, genetic variation, and historical demography of white-footed mouse (Peromyscus leucopus) populations in New York City
Authors: Munshi-South Jason , Nagy Christopher
Published: January 2018

Severe fragmentation is a typical fate of native remnant habitats in cities, and urban wildlife with limited dispersal ability are predicted to lose genetic variation in isolated urban patches. However, little information exists on the characteristics of urban green spaces required to conserve genetic variation. In this study, we examine whether isolation in New York City (NYC) parks results in genetic bottlenecks in white-footed mice (Peromyscus leucopus), and test the hypotheses that park size and time since isolation are associated with genetic variability using nonlinear regression and information-theoretic model selection. White-footed mice have previously been documented to exhibit male-biased dispersal, which may create disparities in genetic variation between males and females in urban parks. We use genotypes of 18 neutral microsatellite data and four different statistical tests to assess this prediction. Given that sex-biased dispersal may create disparities between population genetic patterns inferred from bi- vs. uni-parentally inherited markers, we also sequenced a 324 bp segment of the mitochondrial D-loop for independent inferences of historical demography in urban P. leucopus. We report that isolation in urban parks does not necessarily result in genetic bottlenecks; only three out of 14 populations in NYC parks exhibited a signature of a recent bottleneck at 18 neutral microsatellite loci. Mouse populations in larger urban parks, or parks that have been isolated for shorter periods of time, also do not generally contain greater genetic variation than populations in smaller parks. These results suggest that even small networks of green spaces may be sufficient to maintain the evolutionary potential of native species with certain characteristics. We also found that isolation in urban parks results in weak to nonexistent sex-biased dispersal in a species known to exhibit male-biased dispersal in less fragmented environments. In contrast to nuclear loci, mitochondrial D-loop haplotypes exhibited a mutational pattern of demographic expansion after a recent bottleneck or selective sweep. Estimates of the timing of this expansion suggest that it occurred concurrent with urbanization of NYC over the last few dozens to hundreds of years. Given the general non-neutrality of mtDNA in many systems and evidence of selection on related coding sequences in urban P. leucopus, we argue that the P. leucopus mitochondrial genome experienced recent negative selection against haplotypes not favored in isolated urban parks. In general, rapid adaptive evolution driven by urbanization, global climate change, and other human-caused factors is underappreciated by evolutionary biologists, but many more cases will likely be documented in the near future.
De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease
Authors: Aggarwal Taruna , Westbrook Anthony , Broders Kirk , Woeste Keith , MacManes Matthew D
Published: January 2018

Geosmithia morbida is a filamentous ascomycete that causes Thousand Cankers Disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two known phytopathogens within the genus Geosmithia, and it is vectored into the host tree via the walnut twig beetle. We present the first de novo draft genome of G. morbida. It is 26.5 Mbp in length and contains less than 1% repetitive elements. The genome possesses an estimated 6,273 genes, 277 of which are predicted to encode proteins with unknown functions. Approximately 31.5% of the proteins in G. morbida are homologous to proteins involved in pathogenicity, and 5.6% of the proteins contain signal peptides that indicate these proteins are secreted. Several studies have investigated the evolution of pathogenicity in pathogens of agricultural crops; forest fungal pathogens are often neglected because research efforts are focused on food crops. G. morbida is one of the few tree phytopathogens to be sequenced, assembled and annotated. The first draft genome of G. morbida serves as a valuable tool for comprehending the underlying molecular and evolutionary mechanisms behind pathogenesis within the Geosmithia genus.

Keywords: de novo genome assembly, pathogenesis, forest pathogen, black walnut, walnut twig beetle.
Nutraceutical search through the pipeline of pharmacophore-based virtual screening
Authors: Dubey Amit , Del Prete Eugenio , Dotolo Serena , Gaeta Angelo , Marabotti Anna , Ramteke Pramod W , Facchiano Angelo
Published: January 2018

Nutraceuticals are food or their parts, present in conventional or non-conventional form, with verified safety and health benefits, beyond their nutritional value. In this work, we describe a novel pipeline for nutraceutical compounds research in the field of pharmacophore screening, providing a new idea for drug discovery. In the first step, to identify novel nutraceuticals potentially active as inhibitors of a given enzyme, a pharmacophore model is generated, with its key chemical features, starting from the experimental structure of the complex with known protein inhibitors, with pharmacophores ranking based on statistical values of sensitivity and specificity. After the validation step, this pharmacophore model is used for 3D structural screening and mapping against a subset of known nutraceutical compounds, generated through DrugBank or against special subsets from ZINC (ZINC Drug Database - Zdd and ZINC In Man - Zim). Moreover, molecular docking is performed to verify binding affinity of compounds. The hits with a good binding energy are then investigated in more details, compared with their pharmacophore features and analysed for their interacting residues. Then, to have an in silico interpretation of the potential activity of the compounds, an integrated investigation is performed, by mining literature reports about the effects of the specific compound (or food containing it) against human diseases, extracting expression data from omics repositories, in the view of integrating these information with molecular pathways and networks. Output of our pipeline are candidates for in vitro and in vivo experiments, to test the hypothesis and verify if they could become novel potential drugs.
Some technical and mechanical properties of mibuna (Brassica rapa var. Nipposinica) and mizuna (Brassica rapa var. Japonica)
Authors: Hasturk Sahin Fusun , Aktas Turkan , Eryilmaz Acikgoz Funda , Akcay Tamer
Published: January 2018

In this research, some physical (leaf area, leaf width, stalk width, plant mass, moisture) and mechanical properties (tear resistance, puncture resistance), color parameters (L*, a*, b*, YI) of Mibuna (Brassica rapavar. Nipposinica) and Mizuna (Brassica rapa var. Japonica) plants that are Far East Origin vegetables were determined and compared. Also respiratory rate and dry matter loss values just after harvesting and 1 week later harvesting were calculated and compared using measured CO2 concentration values. It was determined that the differences between mean values of physical properties of leaf and stalk parts of mizuna and mibuna plants were found to be statistically significant (P<0.05). CO2 measurements which were made just after harvesting and 1 week later harvesting showed that respiration rate and dry matter loss for mizuna was found faster than those values for mibuna plant. Also it was found that respiration rate and dry matter loss values determined just after harvesting was found higher than those values determined 1 week later harvesting.
A computational framework for colour metrics and colour space transforms
Authors: Farup Ivar
Published: January 2018

An object-oriented computational framework for the transformation of colour data and colour metric tensors is presented. The main idea of the design is to represent the transforms between spaces as compositions of objects from a class hierarchy providing the methods for both the transforms themselves and the corresponding Jacobian matrices. In this way, new colour spaces can be implemented on the fly by transforming from any existing colour space, and colour data in various formats as well as colour metric tensors and colour difference data can easily be transformed between the colour spaces. This reduces what normally requires several days of coding to a few lines of code without introducing a significant computational overhead. The framework is implemented in the Python programming language.
Maternal satisfaction about childhood immunization in primary health care center, Egypt
Authors: Abdo Hanan Abbas
Published: January 2018

Background: Childhood immunization is the most effective preventive services, and is critical to monitor and evaluate. A study reported an association between parental satisfactions with pediatric care and up-to-date immunization at 24 months independent of maternal age, race, and education. In addition to promoting utilization, satisfaction may increase involvement in the health care process. Health system factors included inconvenient clinic hours, dates or locations, waiting lines, and conflicting information. The inconvenience of clinic hours dates of immunization clinics, and locations of clinics were reported by 75% of parents. Objectives of the study: to determine the relationship between maternal knowledge about vaccination and satisfaction about vaccination program. Methods: A cross section study was conducted on three hundred and thirty five mothers chosen from PHCC participating in the study by providing information on satisfaction about the program and their knowledge about vaccination. Result: Inappropriate knowledge was reported by most of mothers (84.8%). Moreover, 95.2% of mothers were satisfied with childhood immunization services in primary healthcare center. Conclusion: The study shows that there was no statistically significant relation between maternal satisfaction with childhood immunization services and knowledge score, priorities from client's perspectives are changing, so on- going monitoring of client satisfaction is the cornerstone to improve quality of care.
Parents' phases and children's stages of HIV disclosure
Authors: Gachanja Grace , Burkholder Gary J , Ferraro Aimee
Published: January 2018

Background: HIV-positive parents are challenged with disclosure to their children. Some do not disclose at all, others disclose to some children, and many take years to fully disclose to all their children. Methods: This qualitative phenomenological study was conducted in Kenya to describe the lived experiences of HIV-positive parents and their children during the disclosure process. Sixteen HIV-positive parents were engaged in in-depth, semi-structured interviews. Interview data were analyzed using the modified Van Kaam method. Results: Parents had a total of 37 living children; 15 HIV-positive, 11 HIV-negative, and 11 of unknown HIV status. Parents went through four phases (secrecy, exploratory, readiness, full disclosure) of disclosure; most admitted needing healthcare professionals’ help to move their children through the three child stages (no, partial, full) of disclosure . Most parents were in between the exploratory and full disclosure phases but had taken years to navigate these phases. Twelve children (HIV-negative and unknown status) had full disclosure of their parents’ illnesses, nine HIV-positive children had full disclosure of their own and their parents’ illnesses, and 10 children (five HIV-positive, four unknown status, and one HIV-negative) had partial disclosure of their own and/or their parents’ illnesses. Parents had indefinite plans to disclose to the six children with no disclosure. Conclusion: Despite being challenged with disclosure, parents progressively navigated the disclosure phases and fully disclosed to the majority of their children. However, the creation of HIV disclosure guidelines, services, and programs would help hasten the time it takes for them to fully disclose to all their children.
The Adult ADHD Self-Report Scale: utility and reliability in college students with attention deficit hyperactivity disorder
Authors: Gray Sarah , Woltering Steven , Mawjee Karizma , Tannock Rosemary
Published: January 2018

Background. Attention Deficit Hyperactivity Disorder is a debilitating condition that often persists into adulthood. The past number of decades an increased number of adults with ADHD have gained entrance into the post-secondary education section and register with college or university Disability Service Offices. There is a need to explore utility of affordable materials to gain confidence in validating the original diagnoses and potentially detect feigning. Methods. 135 college students (mean age = 24, 42% males) with ADHD were recruited from post-secondary institutions. The freely available Adult ADHD Self-Report Scale (ASRS) self-report was utilized to assess current ADHD symptomatology. The ASRS was compared to an interview (over the phone) and other-report version (filled out by a significant other) that were directly derived from the original Self-report. Results. Results showed moderate levels of congruency between ASRS-Self and Other Report (correlation = .47). Furthermore, a robust relationship was shown between the ASRS-Self and the interview version (correlation = .66). Discussion. Current findings suggest the telephone-interview version of the ASRS may be an easy-to-use, reliable, and cost-effective supplement in gaining more confidence in determining ADHD in post-secondary education students. More research is required specifically testing its merits to detect feigning or support in diagnosis.
The sea urchin – the ultimate herbivore and biogeographic variability in its ability to deforest kelp ecosystems
Authors: Byrnes Jarrett E , Johnson Ladd E. , Connell Sean D. , Shears Nick T. , McMillan Selena M , Irving Andrew , Buschmann Alejandro H. , Graham Michael H. , Kinlan Brian P.
Published: January 2018

Barren rocky seafloor landscapes, denuded of almost all life by ravenous sea urchins, liberated from their predators, stands as one of the iconic images of trophic cascades in Ecology. While this paradigm has been cited in nearly every temperate rocky reef ecosystem across the globe, there is widespread disagreement as to its generality. Given their biology, sea urchins are clearly one of the ocean’s strongest herbivores in many systems, but where will their impact be strongest? Here we perform a global meta-analysis of sea urchin-kelp relationships in the field. We find that sea urchins appear to be able to control kelp abundances in any system where they can achieve high densities. Furthermore, their ability to create large-scale long-lasting barrens appears to be limited to biogeographic regions where they can achieve high consumptive potential. Based on the literature, we outline a conceptual model that examines when and where sea urchins should be able to have a strong regulating impact on kelp forest ecosystems. We suggest that many elements of global change may shift the balance of forces regulating sea urchin consumptive potential in these ecosystems. Given their ability to have strong impacts on temperate rocky reefs, these drivers need to be considered in concert with their effect on sea urchins when attempting to predict future change to marine ecosystems.
Crystal structure of the 3C protease from South African Territories type 2 foot-and-mouth disease virus
Authors: Yang Jingjie , Leen Eoin N , Maree Francois F , Curry Stephen
Published: January 2018

The replication of foot-and-mouth disease virus (FMDV) is dependent on the virus-encoded 3C protease (3Cpro). As in other picornaviruses, 3Cpro performs most of the proteolytic processing of the polyprotein expressed from the single open reading frame in the RNA genome of the virus. Previous work revealed that the 3Cpro from serotype A –one of the seven serotypes of FMDV – adopts a trypsin-like fold. Phylogenetically the FMDV serotypes are grouped into two clusters, with O, A, C, and Asia 1 in one, and the three South African Territories serotypes, (SAT-1, SAT-2 and SAT-3) in another. We report here the cloning, expression and purification of 3C proteases from four SAT serotype viruses (SAT2/GHA/8/91, SAT1/NIG/5/81, SAT1/UGA/1/97, and SAT2/ZIM/7/83) and the crystal structure at 3.2Å resolution of 3Cpro from SAT2/GHA/8/91).
Species presence frequency and diversity in different patch types along an altitudinal gradient: Larix chinensis Beissn in Qinling Mountains (China)
Authors: Huang Minyi , Duan Renyan , Wang Shixiong , Wang Zhigao , Fan Weiyi
Published: January 2018

Forest communities are mosaic systems composed of patches classified into four different developmental patch types: gap patch (G), building patch (B), mature patch (M) and degenerate patch (D). To study the mechanisms maintaining diversity in subalpine coniferous forests, species presence frequency and diversity in the four distinct patch types (G, B, M and D) of Larix chinensis conifer forests at three altitudinal gradients in the Qinling Mountains were analyzed. Our results were as follows: (1) Different species (or functional groups) had distinct presence frequencie s in the four different patch types along the altitudinal gradient. (2) Some species or functional groups (species groups sharing similar traits and response to environment) only occurred in some specific patches. For seed dispersal, species using wind mainly occurred in G and D, while species using small animals mainly occurred in B and M. (3) Species composition of adjacent patch types was more similar than non-adjacent patch types, based on the lower β diversity index of the former. (4) The maximum numbers of species and two diversity indices (D′ and H′) were found in the middle altitudes. Various gap-forming processes and dispersal limitation may be the two major mechanisms determining species diversity in Larix chinensis coniferous forests at the patch scale.
Pteridine levels and head weights are correlated with age and colony task in the honey bee, Apis mellifera
Authors: Rinkevich Frank D , Margotta Joseph W , Pittman Jean M , Ottea James A , Healy Kristen B
Published: January 2018

Background. The age of an insect strongly influences many aspects of behavior and reproduction. This interaction is epitomized in the temporal polyethism of honey bees in which young adult bees perform nurse and maintenance duties within the colony, while older bees forage for nectar and pollen. Task transition is dynamic and is driven by colony needs. However, an abundance of precocious foragers or overage nurses may have detrimental effects on the colony. Additionally, honey bee age affects insecticide sensitivity. Therefore, determining the age of an individual honey bee would be important to provide a measurement of colony health. Pteridines are purine-based pigment molecules found in many insect body parts. Pteridine levels correlate well with age, and wild caught insects may be accurately aged by measuring pteridine levels. The relationship between pteridines and age varies with a number of internal and external factors among many species. Thus far, no studies have investigated the relationship of pteridines with age in honey bees. Methods. We established single-cohort colonies to obtain age-matched nurse and forager bees. Nurses and foragers were collected every 3-5 days for up to 42 days. Heads were removed and weighed before pteridines were purified and analyzed using previously established fluorometric methods. Results. Our analysis showed that pteridine levels were higher in foragers than nurses of the same age, and pteridine levels significantly increased with age in a linear manner. Head weight significantly varied with age increasing until approximately 28 days of age, then declining thereafter for both nurse and forager bees. Discussion. Although the relationship between pteridine levels and age was significant, a large amount of variation in the data yielded an 8-day window in age estimation. This allows an unambiguous method to determine whether a bee may be a young nurse or old forager. Pteridine levels in bees do not correlate with age as well as in other insects. However, most studies used insects reared under tightly controlled laboratory conditions, while we used free-living bees. The dynamics of head weight change with age is likely to be due to growth and atrophy of the hypopharyngeal glands. Taken together, these methods represent a useful tool for assessing colony demography after a colony experiences a stress event. Future studies utilizing these methods will provide a more holistic view of colony health.
Uropygial gland and bib colouration in the house sparrow
Authors: Moreno-Rueda Gregorio
Published: January 2018

Birds frequently signal different qualities by plumage colouration, mainly during mating. However, plumage colouration is determined during the moult, and therefore it would indicate the quality of individual birds during the moult, not its current quality. Recent studies, however, suggest that birds could modify plumage colouration by using cosmetic preen oil. In this study, I show that bib colouration is related to uropygial gland size and body condition in male house sparrows (Passer domesticus). Moreover, I conducted an experiment in which a group of sparrows were inoculated with an antigen, mimicking an illness. In control birds, short-term changes in bib colouration were related to both body condition and change in uropygial gland size. Therefore, birds that spent more preen oil (thus, reducing uropygial gland size), showed a greater colouration change. However, bib colouration did not change with use of preen oil in experimental birds inoculated with the antigen. That is, the simulated illness cancelled the effect of preen oil on bib colouration. Given that the experiment did not affect preen oil production, this finding suggests that the immune challenge provoked a change in the composition of preen oil, affecting its cosmetic properties. In short, the results of this study suggest that (1) male house sparrows produce cosmetic preen oil that alters the colouration of their bibs; (2) the more effort in preening, the more change in bib colouration; and (3) in this way, bib colouration has the potential to signal current health status, since less healthy birds showed less capacity to change bib colouration.