bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elephant dung, chewed antlers, weathered bones: documenting a unique taphonomic collection
Authors: Pappa Spyridoula , Adams Neil , Brewer Philippa , Parfitt Simon , Carnegie Gillian , Lewis Mark 
Published: January 2018

The Antony John Sutcliffe Collection is a unique taphonomic reference collection held within the Department of Earth Sciences at the Natural History Museum (NHM). Sutcliffe was the Curator of Fossil Mammal at the NHM from 1957 to 1987, during which time he collected a large assemblage of modern comparative vertebrate material, including complete skulls, bones, teeth and soft tissues (skin and faeces) of numerous species from across the world including sites in East Africa, Canada, Alaska, Siberia and northwest Europe. Sutcliffe studied Pleistocene mammals and was particularly interested in the alterations to their remains after death and how they come to be fossilised, i.e., their taphonomy.
The specimens were either collected during Sutcliffe’s own fieldwork or gifted to him by international colleagues, and are often accompanied by detailed notes on their provenance and original letters of donation.
After a preliminary study in 2013, and given the value of the collection for future taphonomic studies, a curatorial project ran from 2015 to 2017 aiming to document the entire collection on EMu (the museum’s collection management system), recording the anatomy, taxonomy, previous and new locations within the museum, and any associated documentation of over 1500 specimens. Photographs of each object were included and all specimens have been registered, safely repacked and rehoused at Wandsworth museum store, where they are now accessible to researchers. The specimens have the potential to form curated taphonomic reference standards for use by researchers around the world.
Stability analysis of MTopGO for module identification in PPI networks
Authors: Vella Danila , Tucker Allan , Bellazzi Riccardo 
Published: January 2018

MTopGo is a novel algorithm of module identification for PPI Network analysis, it is designed to consider two key aspects of these models, the topological properties of the network and the apriori knowledge about the proteins involved, represented by GO annotations.
MTopGO rely on random components, thus stability of the results across different runs is a critical aspect of the algorithm. Moreover, when evaluating an algorithm specific for PPI Networks an important aspect is the stability in presence of false positive and false negative edges. In this work, two different stability analyses have been executed to evaluate MTopGO performance. Firstly, one to evaluate the stability of the result over many runs starting from a same input, to consider the range of variability introduced by the random components of the algorithm; secondly, one to evaluate the robustness of the output clusters when the input is affected by noise and uncertainty.
The results showed that MTopGO was more stable in case of false negative edges than false positive edges (adding false edges to a PPI Network was more damaging than removing existing links).
R Python, and Ruby clients for GBIF species occurrence data
Authors: Chamberlain Scott A , Boettiger Carl 
Published: January 2018

Background. The number of individuals of each species in a given location forms the basis for many sub-fields of ecology and evolution. Data on individuals, including which species, and where they're found can be used for a large number of research questions. Global Biodiversity Information Facility (hereafter, GBIF) is the largest of these. Programmatic clients for GBIF would make research dealing with GBIF data much easier and more reproducible.
Methods. We have developed clients to access GBIF data for each of the R, Python, and Ruby programming languages: rgbif, pygbif, gbifrb.
Results. For all clients we describe their design and utility, and demonstrate some use cases.
Discussion. Programmatic access to GBIF will facilitate more open and reproducible science - the three GBIF clients described herein are a significant contribution towards this goal.
Network diffusion on multiple-layers: current approaches and integrative analysis of Rheumatoid Arthritis data.
Authors: Di Nanni Noemi , Gnocchi Matteo , Moscatelli Marco , Milanesi Luciano , Mosca Ettore 
Published: January 2018

Network Diffusion has been proposed in several applications, thanks to its ability of amplifying biological signals and prioritizing genes that may be associated with a disease. Not surprising, the success of Network Diffusion on a “single layer” led to the first approaches for the joint analysis of multi-omics data.
Here, we review integrative methods based on Network Diffusion that have been proposed with several aims (e.g. patient stratification, module detection, function prediction). We used Network Diffusion to analyse, in the context of physical and functional protein-protein interactions, genetic variation, DNA methylation and gene expression data from a study on Rheumatoid Arthritis. We identified functionally related genes with multiple alterations.
Drop-out from the tuberculosis contact investigation cascade in a routine public health setting in urban Uganda: A prospective, multi-center study
Authors: Armstrong-Hough Mari , Turimumahoro Patricia , Meyer Amanda , Ochom Emmanuel , Babirye Diana , Ayakaka Irene , Mark David , Ggita Joseph , Cattamanchi Adithya , Dowdy David , Mugabe Frank , Fair Elizabeth , Haberer Jessica , Katamba Achilles , Davis J. Lucian 
Published: January 2018

Setting Seven public tuberculosis (TB) units in Kampala, Uganda, where Uganda’s national TB program recently introduced household contact investigation, as recommended by 2012 guidelines from WHO.
Objective To apply a cascade analysis to implementation of household contact investigation in a programmatic setting. Design Prospective, multi-center observational study.
Methods We constructed a cascade for household contact investigation to describe the proportions of: 1) index patient households recruited; 2) index patient households visited; 3) contacts screened for TB; and 4) contacts completing evaluation for, and diagnosed with, active TB.
Results 338 (33%) of 1022 consecutive index TB patients were eligible for contact investigation. Lay health workers scheduled home visits for 207 (61%) index patients and completed 104 (50%). Among 287 eligible contacts, they screened 256 (89%) for symptoms or risk factors for TB. 131 (51%) had an indication for further TB evaluation. These included 59 (45%) with symptoms alone, 58 (44%) children <5, and 14 (11%) with HIV. Among 131 contacts found to be symptomatic or at risk, 26 (20%) contacts completed evaluation, including five (19%) diagnosed with and treated for active TB, for an overall yield of 1.7%. The cumulative conditional probability of completing the entire cascade was 5%.
Conclusion Major opportunities exist for improving the effectiveness and yield of TB contact investigation by increasing the proportion of index households completing screening visits by lay health workers and the proportion of at-risk contacts completing TB evaluation.
Publiphilia Impactfactorius: a new psychiatric syndrome among biomedical scientists?
Authors: Tijdink Joeri K , Smulders Yvo M , Bouter Lex M 
Published: January 2018

Abstract

Introduction
Personality traits differ significantly between professionals, and the biomedical field is no exception. However, whether specific clusters of personality traits are indeed typical for biomedical scientists is unknown. This can be of particular interest since personality traits impact on behavior, and sloppy science or even scientific misconduct may be linked to specific clusters of personality traits. To explore clusters of personality traits among biomedical scientists, and to associate the clusters with academic position and research misbehaviour we designed a cross-sectional study with cluster analysis of personality traits among a stratified sample of Dutch biomedical scientists working in academic medical centers.
Methods
We used the NEO-BIG5, Rosenberg Self-esteem, Achievement Motivation Inventory and the Dark Triad (narcissistic, Machiavellianistic and psychopathic personality traits) as validated questionnaires. Self-reported research misconduct was assessed via a separate questionnaire.
Results
We included 537 active biomedical scientists completed a web-based survey (response rate 65%). Cluster analysis revealed the existence of three personality clusters among biomedical scientists: the ‘perfectionist’, the ‘ideal son-in-law’ and the ‘sneaky grandiose’. The latter cluster showed a consistent set of (subclinical) personality traits such as narcissism, psychopathy and Machiavellianism, that are indicative of the presence of a mental disorder, but could not be classified as such in terms of the DSM-IV TR or ICD-10. Male gender, higher academic hierarchical position, perceived publication pressure and, importantly, self-reported scientific misbehaviour were associated with the ‘sneaky grandiose’ personality cluster.
Discussion
These findings suggest that biomedical scientists in the ‘sneaky grandiose’ personality cluster have a relatively high propensity to engage in research misbehaviour. A small proportion of the ‘sneaky grandiose’ might suffer from a psychiatric condition characterized by pathological preoccupation with publishing and being cited. We therefore propose to name this syndrome ‘Publiphilia Impactfactorius’ (PI), and we suggest this affliction should be considered in revised versions of DSM5 and ICD-10. We provide tentative diagnostic criteria for PI. Early identification and intensive treatment or, alternatively, expulsion and annihilation of colleagues who suffer from PI may prevent further accumulation of research waste.
Effect of an oral dietary supplementation by a formulation based on silibinin-phosphatidylcholine complex in cats with liver diseases
Authors: Biasibetti Elena , Cocca Tiziana , Capucchio Maria Teresa , Togni Stefano , Giacomelli Luca , Giraudo Leonardo , Bigliati Mauro , Barbara Marco 
Published: January 2018

Background: Liver pathology in cats represents a frequent clinical condition occurring in animals of any age. Dietary supplementation with hepatoprotective and antioxidant products could represent a beneficial strategy to prevent and treat these disorders. We evaluated the tolerability and efficacy of long-term treatment with a multi-component, dietary supplement containing functional natural ingredients with recognized hepatoprotective properties in cats suffering from liver diseases
Methods: 20 European domestic cats of either gender, 10 with hepatic lipidosis and 10 with cholangitis received for 180 consecutive days a multi-component formulation based on the silibinin-phosphatidylcholine complex as paste or tablet. Clinical assessment and blood and urine parameters were evaluated at T0 (inclusion time) and after 7, 28, 60, 90 and 180 days from the initiation of the study.
Results: The oral supplementation with the silibinin-phosphatidylcholine complex significantly reduced the activity of liver enzymes in serum (alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, γ -glutamyl transferase) and the content of total bilirubin, albumin, pre- and post- bile acids, in cats with hepatic lipidosis or cholangitis, normalizing their liver function parameters. Moreover, following the supplementation, the appetite was restored in all cats and the frequent episodes of diarrhea and vomit reported at inclusion almost disappeared.
Discussion: Dietary supplementation with the silibinin-phosphatidylcholine complex containing functional natural ingredients with recognized hepatoprotective and antioxidant actions might represent an effective strategy to improve the conditions of liver dysfunction, such as hepatitis lipidosis and cholangitis, in cats.
Resounding failure to replicate links between developmental language disorder and cerebral lateralisation
Authors: Wilson Alexander C , Bishop Dorothy V M 
Published: January 2018

Background. It has been suggested that failure to establish cerebral lateralisation may be related to developmental language disorder (DLD). There has been weak support for any link with handedness, but more consistent reports of associations with functional brain lateralisation for language. The consistency of lateralisation across different functions may also be important. We aimed to replicate previous findings of an association between DLD and reduced laterality on a quantitative measure of hand preference (reaching across the midline) and on language laterality assessed using functional transcranial Doppler ultrasound.
Methods. From a sample of twin children aged from 6 to 15 years, we identified 107 cases of DLD and 156 typically-developing (TD) comparison cases, all of whom had useable data from fTCD yielding a laterality index (LI), as well as measures of handedness.
Results. Indices of handedness and language laterality for this twin sample were similar to those previously reported with these measures for single-born children. There was no difference between the DLD and TD groups on quantitative measures of handedness or language lateralisation, or on a categorical measure of consistency of left hemisphere dominance. Contrary to prediction, there was a greater incidence of right lateralisation for language in the TD group (19.90%) than the DLD group (9.30%), confirming that atypical laterality is not inconsistent with typical language development. We also failed to replicate associations between language laterality and language test scores.
Discussion. Given the large sample studied here and the range of measures, we suggest that previous reports of atypical manual or language lateralisation in DLD may have been false positives.
Geographical differences in the effects of age and height at peak height velocity on final body height: An analysis of a population-based cross-sectional growth curve in Japan
Authors: Yokoya Masana 
Published: January 2018

Background. The aim of this study was to elucidate the effect of geographical differences in the age at peak height velocity (APHV) and height at peak height velocity (HPHV) on final height, at a prefectural level, and to evaluate the current average height status of 47 prefectures in Japan.
Methods. We elucidated the association between the geographical differences in a prefectural-level cross-sectional population-based infancy-childhood-puberty (ICP) growth curve, derived from prefectural mean height data (age: 5-17 years, 2006-2013), APHV and HPHV, for final height.
Results. The correlation between the APHV and final height was very weak; however, the results of a multiple regression analysis showed that the final height of each prefecture can be accurately predicted based on the APHV and HPHV. This result showed that the earlier the APHV and higher the HPHV, the higher the final height. An earlier APHV reduced the height gain in the puberty component; however, this did not reduce the final height.
Discussion. From the perspective of the average value of each prefecture, in the present situation, the effect of an earlier APHV in increasing the amount of growth of the childhood component exceeded its effect in reducing the growth of the puberty component. In short, the final height of the prefectures depends on how large the height growth is in the early stages of childhood. However, the HPHV tended to be region-specific, and it is unlikely that it can increase the average height in this population in the future.
Prolonged exposure to ethylene may provide Rhodococcus sp. the ability to delay the effects of ripening in several species of climacteric fruit.
Authors: Perry Guenevere 
Published: January 2018

Post-harvest biotechnology is a growing industry. Many farmers are looking for economic and organic methods to preserve crops while effectively decreasing post-harvest losses. Previous studies suggested Rhodococcus rhodochrous DAP 96253 specifically cultured on cofactor enriched media (cofactors, cobalt and urea) enabled the bacteria to delay climacteric ripening in several species of fruit, (Pierce et al., 2008; Pierce et al., 2011).
However, Rhodococcus rhodochrous not cultured on enriched media, but induced with hydrocarbons were also enabled to delay fruit ripening. Hydrocarbon induction doubled NHase activity and significantly improved bacteria ability to delay the effects of fruit ripening on a molecular level. Bacteria reduced cyanide concentration released by plant tissue in the atmosphere by half, and decreased glucose concentration within plant tissue by 18g/L. Experimental results suggest that R. rhodochrous may use a novel pathway to that includes an inducible monooxygenase like enzyme that allows Rhodococcus rhodochrous cells the ability to delay ripening in various species of climacteric fruits.
Cricket umpire assistance and ball tracking system using a single smartphone camera
Authors: Arora Udit , Verma Sohit , Sahni Sarthak , Sharma Tushar 
Published: January 2018

Several ball tracking algorithms have been reported in literature. However, most of them use high-quality video and multiple cameras, and the emphasis has been on coordinating the cameras or visualizing the tracking results. This paper aims to develop a system for assisting the umpire in the sport of Cricket in making decisions like detection of no-balls, wide-balls, leg before wicket and bouncers, with the help of a single smartphone camera. It involves the implementation of Computer Vision algorithms for object detection and motion tracking, as well as the integration of machine learning algorithms to optimize the results.
Techniques like Histogram of Gradients (HOG) and Support Vector Machine (SVM) are used for object classification and recognition. Frame subtraction, minimum enclosing circle, and contour detection algorithms are optimized and used for the detection of a cricket ball. These algorithms are applied using the Open Source Python Library - OpenCV. Machine Learning techniques - Linear and Quadratic Regression are used to track and predict the motion of the ball. It also involves the use of open source Python library VPython for the visual representation of the results. The paper describes the design and structure for the approach undertaken in the system for analyzing and visualizing off-air low-quality cricket videos.
Knockout of c-mos gene does not affect tumor progression in murine models of lung and colorectal cancer
Authors: Chen Zhengxi , Qiao Ju , Chen Zhenqi , Xiao Qian 
Published: January 2018

Background. The c-mos proto-oncogene was one of the first proto-oncogenes to be cloned. Apart from its role in meiosis, many efforts have been made to illuminate the mechanisms by which c-mos acts as an oncogene. c-mos or its coding messenger RNA have been confirmed in most somatic tissues at low levels. However, a detailed role of c-mos as an oncogene in somatic cells remains unknown.
Methods. In this study, we analyzed online databases to find out the correlation between Mos expression and poor survival rates in human cancer patients. Then, we investigated whether the involvement of c-mos in tumor progression via applying Apcmin intestinal cancer model and KrasG12D lung cancer model.
Results. First, we found the expression of Mos differed between human and mice, and a significant correlation between high Mos expression and poor survival rates in lung cancer patients. Interestingly, we tested that the effects of deficient c-mos in both Apcmin intestinal cancer model and KrasG12D lung cancer model. Despite the abovementioned significant correlation, the results did not show a strong inhibitory effect on murine models of lung and intestine tumors. We find no evidence of a direct role for c-mos in tumor progression in abovementioned mice models.
Discussion. It indicated that functions of c-mos gene might be species-specific and that c-mos involvement in tumor progression was circumstantial and it probably depended on other oncogene activation.
Keywords: c-mos, Kras, Apc, survival rate, murine model, lung cancer, colorectal cancer
Enhancing knowledge of head and neck anatomy in preclinical medical students using low fidelity simulation
Authors: St. Hilaire Rose Clarie , Buckley Lisa , Gilbert Gregory E. , Leighton Kim , Barremkala Mallikarjuna , Callender Diana , Pederson David 
Published: January 2018

Background: Simulation-based medical education is more prevalent in undergraduate preclinical medical education and acts as a foundation for clinical learning in years three and four. Currently, there is a call to teach clinical application of basic science material in preclinical years one and two.
Methods: Two groups of students participated in this investigation; a historical control of 270 students from the 2010 matriculating class and students receiving the intervention (anatomy lecture plus airway management simulation) from the 2012 matriculating class (n=337). Descriptive statistics were calculated for demographic and academic performance variables. Unadjusted and adjusted odds of passage of mid-term and final assessment were calculated. The final assessment was defined as one correct, two correct, and all three questions correct.
Results: Adjusted odds of passage of mid-term exam for the control group were 3.9 (95% CI: 2.7-5.9), virtually unchanged from the unadjusted odds of passage. Control group results for final exam passage as defined as one correct increased from .7 to .9 when adjusted for variables (95% CI:.3-2.5). Odds of passage of final assessment, for the control group, for adjusted models for two or greater correct increased from 4.1 to 5.6 (95% CI:2.6-13.7) and from 34.1 to 44.0 (95% CI: 21.7-102.5) when three answers (or 100%) are needed for passage.
Conclusions: When passage criteria for the final exam were defined as one correct, addition of a simulation exercise to the anatomy lecture increased the rate of passage by 11% after adjusting for covariates. However, when passage criteria for the final exam was defined as two or three correct, addition of a simulation exercise to the anatomy lecture decreased the rate of passage.
Comprehensive comparison of four species of Onchidiidae provides insights on morphological and molecular adaptations of invertebrates from shallow seas to wetlands
Authors: Xu Guolv , Yang Tiezhu , Wang Dongfeng , Li Jie , Liu Xin , Wu Xin , Shen Heding 
Published: January 2018

Background.The Onchidiidae family provides ideal species of marine invertebrates for the study of the evolution from seas to wetlands. However, different species of Onchidiidae have rarely been considered in comparative studies.
Methods.A total of 40 samples were collected from four species (10 specimens per onchidiid). In addition, we systematically investigated the histological and molecular differences to elucidate the morphological foundations underlying these adaptations.
Results.Histological analysis enabled the structural comparison of respiratory organs (gill, lung-sac, dorsal skin) among onchidiids. Transcriptome sequencing of four representative onchidiids was performed to further expound the molecular mechanisms with their respective habitats. Twenty-six Single nucleotide polymorphism (SNP) markers of Onchidium struma presented the DNA polymorphism determining some visible genetic traits. Non-muscle myosin heavy chain II (NMHC II) and myosin heavy chain (MyHC) played an essential role in amphibian developmental processes and are expressed differentially invarious onchidiids and tissues. The species with higher terrestrial ability and higher integrated expression of Os-MHC (NMHC II gene) and MyHC gene illustrated the expression level associated with the evolutionary degree.
Conclusions.The present study indicates that different adaptions occurred in four species in various environments.We hope to provide a valuable reference point and a source of inspiration for amphibian investigatorsstudying the morphological characteristics and molecular mechanisms underlying the transition of invertebrates from shallow seas to wetlands.