bluuebunny/crossref_metadata_2025 huggingface dataset:
Problems in using p-curve analysis and text-mining to detect rate of p-hacking and evidential value
Authors: Bishop Dorothy V , Thompson Paul A
Published: January 2018

Background: The p-curve is a plot of the distribution of p-values reported in a set of scientific studies. Comparisons between ranges of p-values have been used to evaluate fields of research in terms of the extent to which studies have genuine evidential value, and the extent to which they suffer from bias in the selection of variables and analyses for publication, p-hacking. Methods: P-hacking can take various forms. Here we used R code to simulate the use of ghost variables, where an experimenter gathers data on several dependent variables but reports only those with statistically significant effects. We also examined a text-mined dataset used by Head et al. (2015) and assessed its suitability for investigating p-hacking. Results: We first show that when there is ghost p-hacking, the shape of the p-curve depends on whether dependent variables are intercorrelated. For uncorrelated variables, simulated p-hacked data do not give the "p-hacking bump" just below .05 that is regarded as evidence of p-hacking, though there is a negative skew when simulated variables are inter-correlated. The way p-curves vary according to features of underlying data poses problems when automated text mining is used to detect p-values in heterogeneous sets of published papers. Conclusions: The absence of a bump in the p-curve is not indicative of lack of p-hacking. Furthermore, while studies with evidential value will usually generate a right-skewed p-curve, we cannot treat a right-skewed p-curve as an indicator of the extent of evidential value, unless we have a model specific to the type of p-values entered into the analysis. We conclude that it is not feasible to use the p-curve to estimate the extent of p-hacking and evidential value unless there is considerable control over the type of data entered into the analysis. In particular, p-hacking with ghost variables is likely to be missed.
A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelays proteins of organisms with fully sequenced genomes
Authors: Salvado Baldiri , Vilaprinyo Ester , Sorribas Albert , Alves Rui
Published: January 2018

Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK), Response Regulator (RR) and Histidine Phosphotranfer (HPt) domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.
The apparent permeabilities of Caco-2 cells to marketed drugs: magnitude, and independence from both biophysical properties and endogenite similarities
Authors: O'Hagan Steve , Kell Douglas B
Published: January 2018

We bring together fifteen, nonredundant, tabulated collections (amounting to 696 separate measurements) of the apparent permeability (Papp) of Caco-2 cells to marketed drugs. While in some cases there are some significant interlaboratory disparities, most are quite minor. Most drugs are not especially permeable through Caco-2 cells, with the median Papp value being some 16.10-6 cm.s-1. This value is considerably lower than those (1310 and 230.10-6 cm.s-1) recently used in some recent simulations that purported to show that Papp values were too great to be transporter-mediated only. While these values are outliers, all values, and especially the comparatively low values normally observed, are entirely consistent with transporter-only mediated uptake, with no need to invoke phospholipid bilayer diffusion. The apparent permeability of Caco-2 cells to marketed drugs is poorly correlated with either simple biophysical properties, the extent of molecular similarity to endogenous metabolites (endogenites), or any specific substructural properties. In particular, the octanol:water partition coefficient, log P, shows negligible correlation with Caco-2 permeability. The data are best explained on the basis that most drugs enter (and exit) Caco-2 cells via a multiplicity of transporters of comparatively weak specificity.
Estimation of methane emission factor for enteric fermentation of growing-finishing Hanwoo steers using the IPCC Tier 2 approach
Authors: Jo Namchul , Kim Jongnam , Seo Seongwon
Published: January 2018

Enteric methane (CH4) production by cattle is one of the major sources of greenhouse gas (GHG) emissions in the livestock sector. In order to develop a national GHG inventory and establish a mitigation strategy for GHG emissions from livestock production, accurate estimation of enteric CH4 production by cattle is required. In this regard, the Tier 2 method in the Intergovernmental Panel on Climate Change (IPCC) guidelines is the most widely used. The objective of this study was to estimate and evaluate the CH4 emission factor (MEF; kg CH4/head/year) for enteric fermentation using the IPCC Tier 2 method in Hanwoo steers, a dominant beef production species in Korea raised in a unique feeding system (e.g., a duration of > 16 months in a feedlot). Methane emission factor for enteric fermentation was estimated using the IPCC Tier 2 method (T2) on Korea- and Hanwoo-specific data obtained from the literature. The MEF values were also estimated and compared using the IPCC Tier 1 (T1), the IPCC Tier 2 methodology with estimated gross energy GE intake based on actual dry matter intake (T2DMI), and the Japanese Tier 3 method (JT3). JT3 was chosen due to the similarity in the beef cattle production system between the two countries. Estimated MEF using T2 were 43.4, 33.9, and 36.2 kg CH4/head/year for the growing, finishing, and overall period, respectively. The overall MEF estimated using T2 was 23% lower than the estimate by T1 (47.0 kg CH4/head/year). There were significant differences in the estimated MEF for enteric fermentation of Hanwoo steers among the T2, T2DMI, and JT3 methods. JT3 estimated the highest values in all periods possibly due to overestimation of the conversion ratio of feed energy to CH4. No significant difference was found in the overall MEF of Hanwoo steers between T2 and T2DMI. However, T2DMI estimated 8% higher and 14% lower MEF than T2 for the growing and finishing period, respectively, mainly because the IPCC Tier 2 model significantly over-predicts the GE intake of Hanwoo steers at the high level of intake. The IPCC Tier 2 methodology is preferred to IPCC Tier 1 in estimating the MEF for enteric fermentation of Hanwoo steers, and the DMI model for Japanese cattle can be used to predict DMI of Hanwoo steers. In order to reduce the uncertainty of the estimates and search for a better mitigation strategy, however, development of a country-specific methodology and parameter estimates for enteric CH4 production of Hanwoo is required.
First experience with combined use of adaptive statistical iterative reconstruction and gemstone spectral imaging in spinal fusion CT images
Authors: Wang Fengdan , Zhang Yan , Jin Zhengyu , Zwar Richard
Published: January 2018

Objective. To explore whether the image noises and the metal artifacts could be further managed by the combined use of two technologies, the adaptive statistical iterative reconstruction (ASIR) and the monochromatic imaging generated by gemstone spectral imaging (GSI) dual-energy CT. Materials and Methods. Fifty-one patients with 318 spinal pedicle screws were prospectively scanned with dual energy CT by using fast kV-switching GSI between 80 and 140 kVp. The monochromatic GSI images at 110 keV were reconstructed either without ASIR or with ASIR of various levels (30%, 50%, 70% and 100%). For these five sets of images, both objective and subjective image quality assessments were performed to evaluate the image quality. Results. With objective image quality assessment, the metal artifacts (measured by an artifacts index) significantly decreased when increasing levels of ASIR was utilized (p < 0.001). Moreover, adding ASIR to GSI also decreased the image noise (p < 0.001) and improved the signal-to-noise ratio (SNR, p < 0.001). With subjective image quality analysis, the inter-reader agreements were good, with intra-class correlation coefficients (ICC) of 0.89 to 0.99. Meanwhile, the visualization of the peri-implant soft tissue was improved at higher ASIR levels (p < 0.001). Conclusion. Combined use of ASIR and GSI is shown to decrease the image noise and improve the image quality in post-spinal fusion CT scans. Optimal results were achieved with ASIR levels of over 70%.
Enterobacter cancerogenus produces short chain N-3-oxo-acylhomoserine lactones quorum sensing molecules
Authors: Chan Kok-Gan , Tan Wen-Si
Published: January 2018

Enterobacter cancerogenus strain M004 genome size is 5.67 Mb. Here, its luxI homologue, designated as ecnI which is ecnI gene (633 bp) was cloned and overexpressed. Its AHL synthesis activity was verified using the high-resolution liquid chromatography-mass spectrometry analysis revealed the production of N-(3-oxo-hexanoyl)-L-homoserine lactone (3-oxo-C6-HSL) and N-(3-oxo-hexanoyl)-L-homoserine lactone (3-oxo-C8-HSL). The cloning and characterization of luxI homologue of E. cancerogenus strain M004 was firstly reported here.
Using crocodilian tails as models for dinosaur tails
Authors: Mallison Heinrich , Pittman Michael , Schwarz Daniela
Published: January 2018

The tails of extant crocodilians are anatomically the closest approximation of the tails of non-avian dinosaurs, and therefore a good starting point for any reconstruction of non-avian dinosaur tail muscles. However, we here demonstrate some methodological problems using crocodile tails, firstly regarding the general reconstruction of tail mobility from osteology, secondly for the reconstruction of tail musculature for the quantification of muscle forces, especially the m. caudofemoralis longus, and thirdly with respect to the anatomical differences between crocodilians and non-avian dinosaurs, especially in relation to the reconstruction of m. caudofemoralis brevis. Our results show that, given the current limited knowledge of crocodilian tails, volumetric reconstructions should be created on the basis of more gross morphological data than is usually used, and that biomechanical studies should include sensitivity analysis with greater parameter ranges than often applied.
Thermal summation model and instar determination of all developmental stages of necrophagous beetle, Sciodrepoides watsoni (Spence) (Coleoptera: Leiodidae: Cholevinae)
Authors: Jakubec Pavel
Published: January 2018

Necrophagous beetles are underrepresented in forensic entomology studies despite their undeniable utility for the field. In our article we would like to address this problem and provide information regarding developmental biology and instar determination of Sciodrepoides watsoni (Spence, 1813), which is very common species occurring across the Holarctic region. We collected adult specimens from several localities across the Czech Republic to establish a laboratory culture with constant temperature regime and long day photoperiod. These adults were divided between five treatments that differed only in temperature (15, 18, 21, 25 and 28°C). Emerging larvae were separated and their individual development was photographically documented every day until adulthood. Parameters of thermal summation models and their standard errors were calculated for each developmental stage. We also propose head width as a new character for larval instar determination together with a new methodology for future studies of size based characters.
Women’s Health Initiative Findings on Glioma Incidence after Hormone Therapy in Post-Menopausal Women
Authors: Karsy Michael , Arslan Erol , Kummer Nicolas , Moy Fred
Published: January 2018

Glioblastoma multiforme is a grade IV astrocytoma arising de novo or progressing from lower grade II and III gliomas. Currently the etiology of glioma and prediction of disease progression are unknown. Recent epidemiological studies have suggested that hormonal factors, including estrogen treatment, may impact glioma risk however these studies have been limited to case-control trials and retrospective cohort studies. Here, we evaluate results from the Women’s Health Initiative, which involved 161,808 women with robust data regarding hormone exposures. During a median of 12.7 years of follow-up, 167 cases of glioma (130 cases of GBM) were ascertained. The relationship between gliomas and hormone therapy (HT; estrogen-alone [E-alone] or estrogen plus progestin [E+P]) was evaluated using Cox proportional hazards models as well as Kaplan-Meier time-to-event analysis. There was no association with gliomas for the E-alone group (HR=0.76, 95% CI=0.43,1.36) but there was an inverse association for E+P (HR=0.48, 95% CI= 0.26, 0.88, p=0.02) after accounting for patient, hormone exposure and reproductive factors. Kaplan-Meier survival analysis demonstrated a significant reduction in time-to-incidence for the E+P group (p=0.0035). Findings from the matched case-control arm of the WHI trial did not demonstrate significant impact of HT on glioma incidence. The results of this study suggest a reduction in glioma risk after treatment with estrogen plus progesterone however a further large scale case-controlled study is warranted to evaluate the impact of HT on this disease.
Inconsistencies among secondary sources of chukar partridge (Alectoris chukar) introductions to the United States
Authors: Moulton Michael P , Cropper, Jr Wendell P , Broz Andrew J
Published: January 2018

An important source of information concerning the fates of intentionally introduced exotic bird species has been collections of historical data that sometimes include species released, numbers released, locations of release, and establishment success. These data have been used to assess potential predictors of establishment success such as propagule pressure, site-level factors, and species characteristics. In order to better understand the limitations of such historical compilations, we compared data for the Chukar (Alectoris chukar) introductions to the USA from two often used compilations and from other sources associated with Chukar introduction programs. We found the major compilations of Long (1981) and Lever (1987) are inconsistent and likely to be incomplete, and inaccurate, in terms of the taxa introduced, the numbers introduced, and the fates of these introductions. Propagule pressure analyses have often assumed that every bird in every release must be summed to represent the propagule pressure necessary for establishment. We found, however, that large numbers of birds were released into states and counties with already established populations. Additionally, in numerous states very large numbers of Chukars were unsuccessfully released. We conclude that site-level factors were more important influences of establishment success than propagule pressure was.
Rates and modes of body size evolution in early carnivores and herbivores: a case study from Captorhinidae
Authors: Brocklehurst Neil
Published: January 2018

Body size is an extremely important characteristic, impacting on a variety of ecological and life-history traits. It is therefore important to understand the factors which may affect its evolution, and diet has attracted much interest in this context. A recent study, examining the evolution of the earliest terrestrial herbivores in the Late Carboniferous and Early Permian, concluded that in the four herbivorous clades examined there was a trend towards increased body size, and that this increase was more substantial than that observed in closely related carnivorous clades. However, this hypothesis was not based on quantitative examination, and phylogenetic comparative methods provide a more robust means of testing such hypotheses. Here, the evolution of body size within different dietary regimes is examined in Captorhinidae, the most diverse and longest lived of these earliest high fibre herbivores. Evolutionary models were fit to their phylogeny to test for variation in rate and mode of evolution between the carnivorous and herbivorous members of this clade, and an analysis of rate variation throughout the tree was carried out. Estimates of ancestral body sizes were calculated in order to compare the rates and direction of evolution of lineages with different dietary regimes. Support for the idea that the high fibre herbivores within captorhinids are being drawn to a higher adaptive peak in body size than the carnivorous members of this clade is weak. A shift in rates of body size evolution is identified, but this does not coincide with the evolution of high-fibre herbivory, instead occurring earlier in time and at a more basal node. Herbivorous lineages which show an increase in size are not found to evolve at a faster rate than those which show a decrease; in fact it is those which experience a size decrease which evolve at significantly higher rates. The opposite is true of the carnivorous lineages, suggesting that in captorhinids it is the carnivores which show the greater trend towards increased body size. It is possible the shift in rates of evolution is related to the improved food processing ability of the more derived captorhinids rather than a shift in diet, but the evidence for this is circumstantial.
Using LIDAR Remote Sensing for identifying suitable habitat for a critically endangered carnivore in Nahuelbuta Range in South-Central Chile
Authors: Carrasco Gonzalo , Briones Raul
Published: January 2018

The range of Nahuelbuta has an outstanding biogeographic importance and high endemism of flora and fauna. In this range, the Valdivian temperate forest extends north along the maritime watershed, while the sclerophyllous forest extends south along the continental slope and northern coastal plain. The L. fulvipes that inhabits this habitat is considered at high extinction risk due to both demographic and ecological factors, such as disease, predation by cougars or other fox species. Our study was conducted in Caramávida using camera traps (N = 84) during October 2011-March 2012 to observe L. fulvipes, this information was correlated with LIDAR data to generate: elevation model, forest height; and the raw data were used to estimate the vertical vegetation coverage for seven different layers of height, cover, leaf area index and vertical complexity index. Our results indicate the presence of 17 positive results with L. fulvipes watch. The values of occupancy, occupancy corrected for detectability, and detectability, indicate that the proportion of stations where the species was recorded was 20%, but the actual ratio would reach 25% after correcting for detectability. The presence data and vegetation analyzes indicate correlations with tree cover larger than 20 meters high and with a high diversity of vegetation in the vertical profile, which may propose the presence of sites with potential presence and corridors for this species. We conclude that this methodology can generate highly accurate and relevant vegetation variables that may provide some guidance regarding which are the areas where a species is potentially distributed and the design of corridors that may enrich their habitat.
Solid phase extraction and metabolic profiling of exudates from living copepods
Authors: Selander Erik , Heuschele Jan , Nylund Göran M , Pohnert Georg , Pavia Henrik , Bjærke Oda , Pender-Healy Larisa A , Tiselius Peter , Kiørboe Thomas
Published: January 2018

Copepods are ubiquitous in aquatic habitats. They exude bioactive compounds that mediate mate finding and induce defensive traits in prey organisms. Little is, however, known about the chemical nature of the copepod exometabolome that contributes to the chemical landscape in pelagic habitats. Here we describe the development of a closed loop solid phase extraction setup that allows for extraction of exuded metabolites from live copepods. We captured exudates from male and female Temora longicornis and analyzed the content with high resolution LC-MS. Chemometric methods revealed 87 compounds that constitute a specific chemical pattern either qualitatively or quantitatively indicating copepod presence. The majority of the compounds were present in both female and male exudates, but nine compounds were mainly or exclusively present in female exudates and hence potential pheromone candidates. Copepodamide G, known to induce defensive responses in phytoplankton, was among the ten compounds of highest relative abundance in both male and female extracts. The presence of copepodamide G shows that the method can be used to capture and analyze chemical signals from living source organisms. We conclude that solid phase extraction in combination with metabolic profiling of exudates is a useful tool to develop our understanding of the chemical interplay between pelagic organisms.
Microbial interactions and implications for oil biodegradation process in mangrove sediments
Authors: Daudt Grativol Adriana , Marchetti Albany , Wetler-Tonini Rita M , Venancio Thiago M , Gatts Carlos EN , Thompson Fabiano L , Rezende Carlos E
Published: January 2018

Mangrove sediment harbors a unique microbiome and is a hospitable environment for the growth of a diverse group of bacteria capable of oil biodegradation. Our goal was to understand bacterial community dynamics from mangrove sediments under heavy-oil contamination stress, and to look for common patterns that may be associated with oil biodegradation is such environments. We tested the hypothesis of a two-phase pattern of petroleum biodegradation, already reported in the literature, where key events in the degradation process take place in the first three weeks after the contamination. Two sample sites with different oil pollution history were compared through T-RFLP analyses and using a pragmatic approach based on the Microbial Resource Management Framework. Our data corroborated the already reported two-phase pattern of oil biodegradation, although the original proposed explanation is questioned, opening up the possibility to consider other plausible hypothesis of microbial interactions as the main drivers of this pattern.
A critical new ankylosaur specimen from the Wessex Formation of the Isle of Wight
Authors: Pond Stuart , Strachan Sarah , Naish Darren , Simpson Martin
Published: January 2018

Ankylosaurs (Dinosauria, Ankylosauria) have been known from the Lower Cretaceous English Wealden for over 170 years. Three Wealden ankylosaurian species are currently recognised: Hylaeosaurus armatus and Polacanthus rudgwickensis from the Wealden Sub-basin of Sussex, and Polacanthus foxii from both the Wessex Sub-basin of the Isle of Wight and the Wealden Sub-basin. Within recent years all have been interpreted as close relatives within the clade Polacanthidae or Polacanthinae, the monophyly of which is controversial. Most views of polacanthines as a whole are based on substantially better remains from North America. Despite the familiarity of Hylaeosaurus and Polacanthus, many questions remain about their anatomy, taxonomy and relationships and a thorough re-appraisal of the British taxa are needed. We discuss a new ankylosaur discovered in 1994 in the Wessex Formation at Chilton Chine, Isle of Wight. This partial skeleton (including limb and limb girdle elements, vertebrae and osteoderms) is one of the most complete ankylosaurs ever found in the UK and has the potential to resolve many questions about these dinosaurs. It has been provisionally referred to P. foxii but differs in several respects from the holotype and referred specimens of this taxon. Each bone has been recorded using photogrammetry and we have reconstructed the skeleton in 3D. The histology of the sacral shield shows a plywood-like structure with extensive, well ordered structural fibres, in contrast to previously reported Polacanthus specimens. Initial findings suggest that the specimen represents a new taxon. Its implications for Early Cretaceous ankylosaur diversity and taxonomy will be discussed.
Tiling the genome into consistently named subsequences enables precision medicine and machine learning with millions of complex individual data-sets
Authors: Guthrie Sarah , Connelly Abram , Amstutz Peter , Berrey Adam F. , Cesar Nicolas , Chen Jiahua , Chippada Radhika , Clegg Tom , Cosca Bryan , Li Jiayong , Ouyang Nancy , Sheffi Jonathan , Smith Brett , Vandewege Ward , Zaranek Alexander Wait
Published: January 2018

The scientific and medical community is reaching an era of inexpensive whole genome sequencing, opening the possibility of precision medicine for millions of individuals. Here we present tiling: a flexible representation of whole genome sequences that supports simple and consistent names, annotation, queries, machine learning, and clinical screening. We partitioned the genome into 10,655,006 tiles: overlapping, variable-length sequences that begin and end with unique 24-base tags. We tiled and annotated 680 public whole genome sequences from the 1000 Genomes Project Consortium (1KG) and Harvard Personal Genome Project (PGP) using ClinVar database information. These genomes cover 14.13 billion tile sequences (4.087 trillion high quality bases and 0.4321 trillion low quality bases) and 251 phenotypes spanning ICD-9 code ranges 140-289, 320-629, and 680-759. We used these data to build a Global Alliance for Genomics and Health Beacon and graph database. We performed principal component analysis (PCA) on the 680 public whole genomes, and by projecting the tiled genomes onto their first two principal components, we replicated the 1KG principle component separation by population ethnicity codes. Interestingly, we found the PGP self reported ethnicities cluster consistently with 1KG ethnicity codes. We built a set of support-vector ABO blood-type classifiers using 75 PGP participants who had both a whole genome sequence and a self-reported blood type. Our classifier predicts A antigen presence to within 1% of the current state-of-the art for in silico A antigen prediction. Finally, we found six PGP participants with previously undiscovered pathogenic BRCA variants, and using our tiling, gave them simple, consistent names, which can be easily and independently re-derived. Given the near-future requirements of genomics research and precision medicine, we propose the adoption of tiling and invite all interested individuals and groups to view, rerun, copy, and modify these analyses at https://curover.se/su92l- j7d0g-swtofxa2rct8495
Validation of the "Quality of Life in School" instrument in Canadian elementary school students
Authors: Ghotra Satvinder , McIsaac Jessie-Lee D , Kirk Sara FL , Kuhle Stefan
Published: January 2018

Background: School is an integral component of the life of a child and thus, quality of school life is an important part of the overall quality of life experienced by a child. Quality of school life may be an important outcome for the assessment of Health Promoting Schools, which is an approach used internationally to improve students’ educational and health outcomes in school in an integrated and holistic way. There are a few instruments available to measure the quality of school life but they are often not available in English, or they are not appropriate for use alongside with other instruments in a survey of young children. The Quality of Life in School (QoLS) instrument is a short self-report measure to assess elementary school students’ perception of their quality of school life in four domains. The instrument was developed in Israel and has been validated among Hebrew-speaking children. The aim of the current study was to evaluate the psychometric properties of the QoLS measure in Canadian elementary school children. Methods: 629 children attending grades 4 to 6 were recruited in a population-based cross-sectional study. The QoLS measure was administered to participating children by trained research assistants. In addition, their socio-demographic details and academic data were also obtained. The psychometric testing included exploratory factor analysis and reliability estimation using internal consistency (Cronbach’s Alpha). Construct validity was investigated using the known groups comparisons for discriminative validity and via convergent validity. Results: A four-factor structure was generated explaining 39% of the total variance in the model. The results showed good internal consistency and acceptable floor and ceiling effects. Cronbach's Alpha ranged from 0.75 to 0.93. Known groups comparisons showed that the QoLS measure discriminated well between subgroups on the basis of gender, grade, and academic achievement, thus providing evidence of construct validity. The convergent validity was also appropriate with all the four domains demonstrating moderate to strong correlations to each other and to the total QoLS score. Conclusions: QoLS appears to be a valid and reliable measure for quality of school life assessment in young Canadian children.
Surgical technique´s influence on overall survival, disease free interval and new lesion development interval in dogs with mammary tumors
Authors: dos Santos Horta Rodrigo , Eunice Lavalle Gleidice , Monteiro de Castro Cunha Rúbia , Layara de Moura Larissa , Baracat de Araújo Roberto , Dantas Cassali Geovanni
Published: January 2018

Mammary gland tumors represent 42% of all tumors in the bitch. Although there are numerous studies about disease development and progression, some questions remain concerning the surgical treatment. Many surgical techniques may be used for the treatment of canine mammary tumors similar to Medicine, the advantages and disadvantages of each procedure have been extensively discussed. The purpose of this study is to evaluate the influence of surgical procedure on survival, disease free interval and new lesion development interval in dogs with mammary tumors treated according to the biological behavior of these lesions. For this, 143 intact bitches were submitted to surgery for the treatment of mammary tumors between 2007 and 2011. Removal of mammary tumors was performed through the simplest and less invasive surgical procedure necessary for the complete removal of all tumors and main known lymphatic connections between affected glands: lumpectomy, mammectomy, regional mastectomy (including abdominal cranial mammary gland or not) or radical mastectomy. Mean clinical follow-up was 738.5 days. Considering only the first surgical event, 84.6% of animals had more than one mammary tumor, and 52.5% had tumors in both mammary chains. Comparing surgical techniques, there was no difference in ipsilateral and contralateral tumor development. Only 33 dogs developed new lesions in remaining mammary tissue, without correlation with primary lesion. Surgical technique had no effect on overall survival, disease-free interval and new lesion development interval in patients on this study, treated according to oncological surgery principles and established prognostic factors for mammary gland tumors in dogs. It is important to consider these results when deciding on the surgical management of dogs with mammary tumors, to avoid aggressive surgical procedures that will not translate into clinical advantages to the patient.
A new Lower Triassic ichthyopterygian assemblage from Fossil Hill, Nevada
Authors: Kelley Neil P , Motani Ryosuke , Embree Patrick , Orchard Michael J
Published: January 2018

We report a new ichthyopterygian assemblage from Lower Triassic horizons of the Prida Formation at Fossil Hill in central Nevada. Although fragmentary, the specimens collected so far document a diverse fauna. One partial jaw exhibits isodont dentition with blunt tipped, mesiodistally compressed crowns and striated enamel. These features are shared with the Early Triassic genus Utatsusaurus known from coeval deposits in Japan and British Columbia. An additional specimen exhibits a different dentition characterized by relatively small, rounded posterior teeth resembling other Early Triassic ichthyopterygians particularly Grippia. This Nevada assemblage marks a southward latitudinal extension for Early Triassic ichthyopterygians along the eastern margin of Panthalassa and indicates repeated circum-oceanic dispersal events in Early Triassic ichthyopterygians.
Effects of simulated darkness on the affective appraisal of a virtual environment
Authors: Toet Alexander , Houtkamp Joske M. , Vreugdenhil Paul E.
Published: January 2018

This study investigated whether simulated darkness influences the affective appraisal of a desktop virtual environment (VE). In the real world darkness often evokes thoughts of vulnerability, threat, and danger, and may automatically precipitate emotional responses consonant with those thoughts (fear of darkness). This influences the affective appraisal of a given environment after dark and the way humans behave in that environment in conditions of low lighting. Desktop VEs are increasingly deployed to study the effects of environmental qualities and (architectural or lighting) interventions on human behaviour and feelings of safety. Their (ecological) validity for these purposes depends critically on their ability to correctly address the user’s cognitive and affective experience. However, it is currently not known how and to what extent simulated darkness in desktop (i.e., non-immersive) VEs affects the user’s affective appraisal of the represented environment. In this study young female volunteers explored either a daytime or a night-time version of a desktop VE representing a deserted prototypical Dutch polder landscape. The affective appraisal of the VE and the emotional response of the participants were measured through self-report. To enhance the personal relevance of the simulation, a fraction of the participants was led to believe that the virtual exploration tour would prepare them for a follow-up tour through the real world counterpart of the VE. The results show that the VE was appraised as slightly less pleasant and more arousing in simulated darkness (compared to a daylight) condition. The fictitious follow-up assignment had no emotional effects and did not influence the affective appraisal of the VE. Further research is required to assess on the validity of desktop VEs for both etiological (e.g., the effects of signs of darkness on navigation behaviour and fear of crime) and intervention (e.g., effects of street lighting on feelings of safety) research.
Visualizing habitat use and behavior of whale sharks using the open tag, applications for ecotourism regulation.
Authors: Levenson Jacob J , Cooper Robert , Ware Colin , Sly Jacqueline , Wise David , de la Parra-Venegas Rafael , Dove Alistair D.M.
Published: January 2018

Background. The rapidly decreasing cost of components and growing open source electronics industry has enabled access to improved tools for monitoring the behavior of aquatic species on a fine scale never before achieved. We use the new Open Tag as a novel approach to visualizing feeding behavior of whale sharks. Methods. The Open Tag is a Arduino compatible open-source inertial measurement unit for recording high speed motion sensor data to a microSD memory card. A three dimensional gyroscope, accelerometer, and magnetometer allow for calculating pitch, yaw, and heading, while depth and temperature sample continuously. The rechargeable lithium battery allows for deployments up to 7 days sampling at 100Hz. The Open Tag is placed in a hydrodynamic syntactic foam float, with a band that stretches around the dorsal fin. A galvanic release incorporated into the tag allows for a release time to be programmed and a VHF tag (ATS) aids in recovery. Results. An Open Tag was successfully deployed on a whale shark for 101 hours in August of 2013 in Yucatan Mexico. Behaviors noted included frequent surface intervals, even during the night when previously believed whale sharks were normally in deeper waters. A maximum depth of 49 meters was observed, with dives to 25 meters recorded regularly. We were able to identify possible harassment at the surface and defecation events. Conclusion. The Open Tag fills a unique niche in whale shark studies as a useful tool to better understanding of fine scale habitat use and behavior. By incorporating these data into Trackplot with data on the position of ecotour vessels, we can visualize behavior and investigate potential erratic changes in depth, heading and lateral movement amplitude indicative of harassment
Design and validation of a next generation sequencing assay for hereditary breast and ovarian cancer
Authors: Kang Hyunseok P. , Maguire Jared R , Chu Clement S , Haque Imran S. , Lai Henry , Mar-Heyming Rebecca , Ready Kaylene , Vysotskaia Valentina S. , Evans Eric A.
Published: January 2018

Hereditary breast and ovarian cancer syndrome, caused by a germline deleterious variant in the BRCA1 or BRCA2 genes, is characterized by an increased risk for breast, ovarian, pancreatic and other cancers. Identification of those who have a BRCA1/2 mutation is important so that they can take advantage of genetic counseling, screening, and potentially life-saving prevention strategies. We describe the design and analytic validation of the Counsyl Inherited Cancer Screen, a next-generation-sequencing-based test to detect pathogenic variation in the BRCA1 and BRCA2 genes. We demonstrate that the test is capable of detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy-number variants (CNVs, also known as large rearrangements) with zero errors over a 96-sample validation set consisting of samples from cell lines and deidentified patient samples, including the well-characterized NA12878 sample from HapMap/1000 Genomes.
Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast
Authors: Messiha Hanan L. , Kent Edward , Malys Naglis , Carroll Kathleen M. , Swainston Neil , Mendes Pedro , Smallbone Kieran
Published: January 2018

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows us to predict changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis model to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardised enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network-scale models by merging smaller pathway-scale models.
Genome-wide approaches and technologies to assess human variation
Authors: Gonzaga-Jauregui Claudia
Published: January 2018

Current genome-wide technologies allow interrogation and exploration of the human genome as never before. Next-generation sequencing (NGS) technologies, along with high resolution Single Nucleotide Polymorphisms (SNP) arrays and array Comparative Genomic Hybrization (aCGH) enable assessment of human genome variation at the finest resolution from base pair changes such as simple nucleotide variants (SNVs) to large copy-number variants (CNVs). The application of these genomic technologies in the clinical setting has also enabled the molecular characterization of genetic disorders and the understanding of the biological functions of more genes in human development, disease, and health. In this review, the current approaches and platforms available for high-throughput human genome analyses, the steps involved in these different methodologies from sample preparation to data analysis, their applications, and limitations are summarized and discussed.
Palatability of flunixin and pharmacokinetics when administered to sheep through feed
Authors: Marini Danila , Pippia Joe , Colditz Ian G , Hinch Geoff G N , Petherick Carol J , Lee Caroline
Published: January 2018

Applying analgesics to feed is a potentially easy method of providing pain-relief to sheep and lambs that undergo painful husbandry procedures. In order for sheep to consume medicated feed it needs to be know if the medication has an adverse odour or flavour that may affect consumption. It is also important to determine if therapeutic concentrations of a non-steroidal anti-inflammatories (NSAIDs) can be achieved when administered to sheep as a feed supplement. Pelleted feed was supplemented with flunixin (4.0mg/kg liveweight) and administered to eight sheep, which they were able to consume over a 12 h period. Blood samples were taken over 48 h and plasma drug concentrations were determined using Ultra High Pressure Liquid Chromatography. The mean time required to reach maximum concentration was 6 ± 1.46 h and ranged from 1 to 12 h. Average maximum plasma concentration was 1.78 ± 0.17µg/mL and ranged from 1.61 to 2.80 µg/mL. The average half-life of flunixin was 7.95 ± 0.77 h and there was a mean retention time of 13.62 ± 1.17 h. Sheep did not show aversiveness to pellets supplemented with flunixin. When consuming medicated feed ad libitum all sheep were able to obtain inferred therapeutic concentrations of flunixin in plasma within 6 h. Provision of flunixin in the feed may provide a practical way to provide pain relief to sheep and lambs following painful husbandry procedures removing the need for multiple injections, reducing handling stress and minimising labour requirements.
A short history of MKNOL
Authors: Filip Katarzyna , Grynkiewicz Grzegorz
Published: January 2018

The Multidisciplinary Conference on Drug Research is being organized every two years since 1999 under auspices of Pharmaceutical Research Institute and constitutes a forum for presenting research results, exchange views and multi-faceted discussion between professionals associated with the broader science of medicine. The lectures cover topics in the field of medicinal chemistry, organic synthesis and technology, pharmaceutical analysis and clinical and pharmaceutical technology. Scientific program of MKNOL (Polish acronym of the conference) reflects the intention of Scientific Committee to comprise various aspects of drug discovery development process, stressing from the beginning the need for multidisciplinary communication of all researchers interested in scientific progress for betterment of human life. Past editions of the MKNOL: a) I. Muszyna, 3-5 March 1999, b) II. Jelenia Góra-Cieplice, 5-7 April 2000, c) III. Piła, 13-16 May 2002, d) IV. Gdańsk-Sobieszewo 17-19 May 2004, e) V. Darłówko Wschodnie, 15-17 May 2006, f) VI. Przemyśl-Krasiczyn, 26-28 May 2008, g) VII. Zakopane, 10-12 May 2010, h) VIII. Ossa koło Rawy Mazowieckiej, 30 May -1 June 2012, i) IX. Korytnica koło Szydłowa, 12-14 May 2014. We hope that the X MKNOL will be also a great opportunity to share new scientific achievements.
PhilDB: The time series database with built-in change logging
Authors: MacDonald Andrew
Published: January 2018

PhilDB is an open-source time series database that supports storage of time series datasets that are dynamic, that is it records updates to existing values in a log as they occur. PhilDB eases loading of data for the user by utilising an intelligent data write method. It preserves existing values during updates and abstracts the update complexity required to achieve logging of data value changes. It implements fast reads to make it practical to select data for analysis. Recent open-source systems have been developed to indefinitely store long-period high-resolution time series data without change logging. Unfortunately such systems generally require a large initial installation investment before use because they are designed to operate over a cluster of servers to achieve high-performance writing of static data in real time. In essence, they have a 'big data' approach to storage and access. Other open-source projects for handling time series data that avoid the 'big data' approach are also relatively new and are complex or incomplete. None of these systems gracefully handle revision of existing data while tracking values that changed. Unlike 'big data' solutions, PhilDB has been designed for single machine deployment on commodity hardware, reducing the barrier to deployment. PhilDB takes a unique approach to meta-data tracking; optional attribute attachment. This facilitates scaling the complexities of storing a wide variety of data. That is, it allows time series data to be loaded as time series instances with minimal initial meta-data, yet additional attributes can be created and attached to differentiate the time series instances when a wider variety of data is needed. PhilDB was written in Python, leveraging existing libraries. While some existing systems come close to meeting the needs PhilDB addresses, none cover all the needs at once. PhilDB was written to fill this gap in existing solutions. This paper explores existing time series database solutions, discusses the motivation for PhilDB, describes the architecture and philosophy of the PhilDB software, and performs a simple evaluation between InfluxDB, PhilDB, and SciDB.
Fully-automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA)
Authors: Salimi Nima , Loh Kar Hoe , Kaur Dhillon Sarinder , Chong Ving Ching
Published: January 2018

Background. Fish species may be identified based on their unique otolith shape or contour. Several pattern recognition methods have been proposed to classify fish species through morphological features of the otolith contours. However, there has been no fully-automated species identification model with the accuracy higher than 80%. The purpose of the current study is to develop a fully-automated model, based on the otolith contours, to identify the fish species with the high classification accuracy. Methods. Images of the right sagittal otoliths of 14 fish species from three families namely Sciaenidae, Ariidae, and Engraulidae were used to develop the proposed identification model. Short-time Fourier transform (STFT) was used, for the first time in the area of otolith shape analysis, to extract important features of the otolith contours. Discriminant Analysis (DA), as a classification technique, was used to train and test the model based on the extracted features. Results. Performance of the model was demonstrated using species from three families separately, as well as all species combined. Overall classification accuracy of the model was greater than 90% for all cases. In addition, effects of STFT variables on the performance of the identification model were explored in this study. Conclusions. Short-time Fourier transform could determine important features of the otolith outlines. The fully-automated model proposed in this study (STFT-DA) could predict species of an unknown specimen with acceptable identification accuracy. The current model has flexibility to be used for more species and families in future studies.