bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gibbs Process Determines Survival and Reveals Contact-Inhibition Genes in Glioblastoma Multiforme
Authors: Kannan Lavanya , Agarwal Tarjani , Snuderl Matija , Zagzag David , Sulman Erik , Huse Jason , Kannan Kasthuri 
Published: April 2019

AbstractTumor growth is a spatiotemporal birth-and-death process with loss of heterotypic contact-inhibition of locomotion (CIL) of tumor cells promoting invasion and metastasis. Therefore, representing tumor cells as two-dimensional points, we can expect the tumor tissues in histology slides to reflect realizations of spatial birth-and-death process which can be mathematically modeled to reveal molecular mechanisms of CIL, provided the mathematics models the inhibitory interactions. Gibbs process as an inhibitory point process is a natural choice since it is an equilibrium process of the spatial birth-and-death process. That is if the tumor cells maintain homotypic contact inhibition, the spatial distributions of tumor cells will result in Gibbs hard core process over long time scales. In order to verify if this is the case, we applied the Gibbs process to 411 TCGA Glioblastoma multiforme patient images. Our imaging dataset included all cases for which diagnostic slide images were available.The model revealed two clusters, one of which - the “Gibbs cluster,” showed the convergence of the Gibbs process with significant survival difference. Further smoothing the discretized (and noisy) inhibition metric, for both increasing and randomized survival time, we found a significant association of the patients in the Gibbs cluster with increasing survival time. The mean inhibition metric also revealed the point at which the homotypic CIL establishes in tumor cells. Besides, RNAseq analysis between patients with loss of heterotypic CIL and intact homotypic CIL in the Gibbs cluster unveiled cell movement gene signatures and differences in Actin cytoskeleton and RhoA signaling pathways as key molecular alterations. These genes and pathways have established roles in CIL. Taken together, our integrated analysis of patient images and RNAseq data provides for the first time a mathematical basis for CIL in tumors, explains survival as well as uncovers the underlying molecular landscape for this key tumor invasion and metastatic phenomenon.
FYN tyrosine kinase, a downstream target of receptor tyrosine kinases, modulates anti-glioma immune responses
Authors: Comba Andrea , Dunn Patrick J , Argento Anna E , Kadiyala Padma , Ventosa Maria , Patel Priti , Zamler Daniel B , Nunez Felipe J , Zhao Lili , Castro Maria G , Lowenstein Pedro R. 
Published: April 2019

ABSTRACTBackgroundHigh grade gliomas are aggressive and immunosuppressive brain tumors. Molecular mechanisms that regulate the inhibitory immune tumor microenvironment (TME) and glioma progression remain poorly understood. FYN tyrosine kinase is a downstream target of the oncogenic receptor tyrosine kinases pathway and is overexpressed in human gliomas. FYN’s rolein vivoin glioma growth remains unknown. We investigated whether FYN regulates glioma initiation, growth and invasion.MethodsWe evaluated the role of FYN using genetically engineered mouse glioma models (GEMM). We also generated FYN knockdown stem cells to induce gliomas in immune-competent and immune-deficient mice (NSG, CD8−/−, CD4−/−). We analyzed molecular mechanism by RNA-Seq and bioinformatics analysis. Flow cytometry was used to characterize immune cellular infiltrates in the FYN knockdown glioma TME.ResultsWe demonstrate that FYN knockdown in diverse immune-competent GEMMs of glioma reduced tumor progression and significantly increased survival. Gene ontologies (GOs) analysis of differentially expressed genes in wild type vs. FYN knockdown gliomas showed enrichment of GOs related to immune reactivity. However, in NSG, CD8−/− and CD4−/− immune-deficient mice, FYN knockdown gliomas failed to show differences in survival. These data suggest that the expression of FYN in glioma cells reduces anti-glioma immune activation. Examination of glioma immune infiltrates by flow-cytometry displayed reduction in the amount and activity of immune suppressive myeloid derived cells (MDSCs) in the FYN glioma TME.ConclusionsGliomas employ FYN mediated mechanisms to enhance immune-suppression and promote tumor progression. We propose that FYN inhibition within glioma cells could improve the efficacy of anti-glioma immunotherapies.Key pointsInhibition of FYN tyrosine kinase in genetically engineered mouse glioma models delays tumor initiation and progression. The oncogenic effects of FYN in vivo are mediated by downregulation of anti-glioma immunity.Importance of the StudyFYN is an effector of receptor tyrosine kinases (RTK) signaling in glioma. However, its rolein vivoremains unknown. Our study demonstrates that FYN tyrosine kinase is a novel regulator of the anti-glioma immune response. We show that FYN inactivation suppresses glioma growth, increases survival, and enhances anti-tumor immune reactivity. Our findings suggest that suppressing the expression of FYN in glioma cells could provide a novel therapeutic target.
The drivers of economic growth in South Asia: evidence from a dynamic system GMM approach
Authors: Rahman Mohammad Mafizur , Rana Rezwanul Hasan , Barua Suborna 
Published: April 2019

PurposeThe purpose of this paper is to explore the drivers of economic growth in South Asia region for the period of 1975–2016 using the World Bank data.Design/methodology/approachPanel corrected standard error (static estimation) approach and one-step system generalised method of moments (dynamic estimation) approach are used.FindingsBoth the static and dynamic estimations indicate that energy use, gross capital formation and remittances are the main drivers of economic growth in South Asian countries. The effects of all these variables are positive and significant. The extent of the effect of energy use is much higher than that of other two variables on the economic growth. A 1 per cent increase in the growth of energy consumption can expedite the gross domestic product growth by approximately 3 per cent in South Asia. However, the key variables, such as trade, government expenditure and foreign direct investment demonstrate no significant effect.Originality/valueThe current research is original in the sense that it investigated the issue with a new data set using improved econometric techniques. Moreover, in South Asia as a whole, this kind of study is totally absent, particularly with panel data of a large number of years. Furthermore, this study has taken into account the problem of heterogeneity and the biases created by cross-section dependence, which were mostly absent in previous studies. Therefore, the findings of this research are new contributions to the existing literature.
Female employment in India: determinants of choice of sector of activity
Authors: Mahapatro Sandhya 
Published: April 2019

Purpose
The purpose of this paper is to examine whether the choice of employment sector for women is driven by the structure of the labour market or determined by the household socioeconomic condition.

Design/methodology/approach
Data for the study were drawn from the National Sample Survey 68th round (2011–2012). The sector of employment was assessed through females’ participation as an unpaid labour, employer/own account worker, informal wage worker, formal wage worker and unemployed. A multinomial logit model was used to examine the factors that determine the sector of employment.

Findings
Although education increases formal employment among women, most of them are unemployed or entering into informal employment. It indicates that the labour market has not been able to integrate educated women into formal employment.

Research limitations/implications
Increase in female education accompanied by a slow growth of employment creates the challenge to accommodate the educated and skilled women in formal employment.

Originality/value
This study examines the factors determining the sectoral participation of employment to assess the responses of the current labour market for the females, especially educated females who have not been adequately addressed. The findings of the study have significant implications for formulating appropriate labour market policies for the educated female labour force.
Rock physics modelling and inversion for saturation‐pressure changes in time‐lapse seismic studies
Authors: Lang Xiaozheng , Grana Dario 
Published: April 2019

ABSTRACTTime‐lapse seismic data are generally used to monitor the changes in dynamic reservoir properties such as fluid saturation and pore or effective pressure. Changes in saturation and pressure due to hydrocarbon production usually cause changes in the seismic velocities and as a consequence changes in seismic amplitudes and travel times. This work proposes a new rock physics model to describe the relation between saturation‐pressure changes and seismic changes and a probabilistic workflow to quantify the changes in saturation and pressure from time‐lapse seismic changes. In the first part of this work, we propose a new quadratic approximation of the rock physics model. The novelty of the proposed formulation is that the coefficients of the model parameters (i.e. the saturation‐pressure changes) are functions of the porosity, initial saturation and initial pressure. The improvements in the results of the forward model are shown through some illustrative examples. In the second part of the work, we present a Bayesian inversion approach for saturation‐pressure 4D inversion in which we adopt the new formulation of the rock physics approximation. The inversion results are validated using synthetic pseudo‐logs and a 3D reservoir model for CO2sequestration.
Gentamicin as Empirical Treatment in Hemodialysis Patients: Safety, Pharmacokinetics, and Pharmacodynamics
Authors: Guisado‐Gil Ana B , Herrera‐Hidalgo Laura , Santos‐Rubio María D , Gil‐Sacaluga Luis , Molina José , Lepe‐Jiménez José A , Camacho‐Martínez Pedro , Gil‐Navarro María V 
Published: April 2019

AbstractThe aim of this study was to describe the safety profile and pharmacokinetic/pharmacodynamic parameters in end‐stage renal disease patients who received gentamicin as empirical treatment in catheter‐related bacteremia when they showed infection signs, regardless of the timing of the next HD. Patients received gentamicin 3 mg/kg before blood culture extraction when they showed infection signs and regardless of the timing of next hemodialysis session. Serum concentrations were collected after the gentamicin administration (peak level) and before the next HD (trough level). Toxicities and adverse drug events were registered. The main pharmacokinetic/pharmacodynamic goal for Gram‐negative infections was peak:minimum inhibitory concentration (MIC) ≥10. Sixteen patients were included. Nephrotoxicity was not assessed in this population, and no ototoxicity was found. According to microbial isolation and gentamicin susceptibility, the value of peak:MIC was 5.4 ± 2.0. The administration of gentamicin in these conditions was safe. Estimated pharmacokinetic values were consistent with previous studies and appropriate according to peak:MIC goal for Gram‐negative organisms with MIC ≤1 mg/L.
Identification of novel species of marine magnetotactic bacteria affiliated with Nitrospirae phylum
Authors: Qian Xin‐Xin , Liu Jia , Menguy Nicolas , Li Jinhua , Alberto François , Teng Zhaojie , Xiao Tian , Zhang Wenyan , Wu Long‐Fei 
Published: April 2019

SummaryMagnetotactic bacteria (MTB) are a group of Gram‐negative bacteria characterized by synthesizing magnetosomes and swimming along geomagnetic field lines. Phylogenetically, they belong to different taxonomic lineages including Proteobacteria, Nitrospirae, Omnitrophica, Latescibacteria and Planctomycetes phyla on the phylogenetic tree. To date, six Nitrospirae MTB phylotypes have been identified from freshwater or low‐salinity environments and described in the literature. Here, we report the identification of two Nitrospirae MTB phylotypes collected, for the first time, from the marine environment. Both have a spherical morphology with a cell size of ~ 5 μM and similar motility but are different colours (black‐brown and ivory‐white) under the optic microscope. They synthesized bullet‐shaped iron‐oxide magnetosomes that were arranged in multiple bundles of chains. Moreover, the cytoplasm of the black‐brown Nitrospirae MTB contained sulphur inclusions that conferred on cells a rough, granular appearance. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that they are two novel species and cluster with the previously reported MTB affiliated with the phylum Nitrospirae, thus extending the distribution of Nitrospirae MTB from freshwater to the marine environment.
Liana cover in the canopies of rainforest trees is not predicted by local ground‐based measures
Authors: Cox Casey J. , Edwards Will , Campbell Mason J. , Laurance William F. , Laurance Susan G. W. 
Published: April 2019

AbstractLianas (woody climbers) are structural parasites of trees that compete with them for light and below‐ground resources. Most studies of liana–tree interactions are based on ground‐level observations of liana stem density and size, with these assessments generally assumed to reflect the amount of liana canopy cover and overall burden to the tree. We tested this assumption in a 1‐ha plot of lowland rainforest in tropical Australia. We recorded 1072 liana stems (≥1 cm diameter at breast height {dbh}) ha−1 across all trees (≥10 cm dbh) on the plot and selected 58 trees for detailed study. We estimated liana canopy cover on selected trees that hosted 0–15 liana individuals, using a 47‐m‐tall canopy crane. Notably, we found no significant correlations between liana canopy cover and three commonly used ground‐based measurements of liana abundance as follows: liana stem counts per tree, liana above‐ground biomass per tree and liana basal area per tree. We also explored the role of tree size and liana infestation and found that larger trees (≥20 cm dbh) were more likely to support lianas and to host more liana stems than smaller trees (≤20 cm dbh). This pattern of liana stem density, however, did not correlate with greater liana coverage in the canopy. Tree family was also found to have a significant effect on likelihood of hosting lianas, with trees in some families 3–4 times more likely to host a liana than other families. We suggest that local ground‐based measures of liana–tree infestation may not accurately reflect liana canopy cover for individual trees because they were frequently observed spreading through neighbouring trees at our site. We believe that future liana research will benefit from new technologies such as high‐quality aerial photography taken from drones when the aim is to detect the relative burden of lianas on individual trees.
Local extinctions may be evidenced by the holes of the morphometric hypervolume in dung beetle communities
Authors: Alves Victor Michelon , Hernández Malva Isabel Medina 
Published: April 2019

AbstractThe body shape of a species is associated with its evolutionary history and can reflect behavioural peculiarities related to the ecological niche of each species. Morphology can characterise the morphometric niche of species and can be represented as body shape points within a morphometric universe. This information can be to calculate the morphometric diversity of communities through hypervolume metrics, and the hole sizes that remain in the morphometric hypervolume, which are empty areas with no species. Such holes may be ‘natural’ or caused by a local extinction. In this study, we evaluate the ecological community of dung beetles through the lens of morphometric diversity. We evaluated 38 dung beetle species from 30 subtropical communities in southern Brazil sampled in the summer of 2015, including 15 forest remnant communities from the Atlantic Forest and 15 communities from adjacent maize cultivations. The shape of 495 dung beetle specimens was measured using geometric morphometric and hypervolume techniques to calculate the morphometric diversity and the hole size of each of the 30 communities. We found that the taxonomic diversity positively correlated with the morphometric diversity and negatively correlated with the size of the holes. We also found that forest communities had higher values of morphometric diversity and smaller holes in the hypervolume than the maize cultivation communities, suggesting that local extinction may reduce community body shape spaces.
A review of the prognostic value of irrigation on root canal treatment success
Authors: Chubb David Wayne Ronald 
Published: April 2019

AbstractThe aim of this review is to discuss the requirements for effective irrigation of the root canal system and its role in treatment outcome. A review of the literature regarding irrigants, methods of irrigation and regimens was undertaken. It indicates that irrigation is comprised of a multitude of factors, and that effective irrigant delivery and agitation achieves mechanical, chemical and microbiological functions, which are prerequisites for obtaining a clean canal system. However, most studies are ex vivo and assess intermediate outcome values rather than treatment success. Additionally, there is an absence of high‐level evidence evaluating the effect of irrigation on the outcome of root canal treatment. Therefore, citing irrigation as a significant factor that affects root canal treatment success cannot be done. This highlights the need to further investigate the prognostic value of irrigation on root canal treatment success.
Validation of SNP associations with bovine ovulation and twinning rate
Authors: Kirkpatrick B. W. , Thallman R. M. , Kuehn L. A. 
Published: April 2019

SummaryPrevious work identified SNP associations with twinning rate in the US Holstein population and developed a model for genomic prediction. The current study was conducted to assess the association of these SNPs with twinning rate and ovulation rate in a genetically diverse, outbred population selected for twinning and ovulation rate. A total of 18 SNPs that were components of a prediction equation for twinning rate in Holstein cattle were genotyped on 731 animals from the USDA Meat Animal Research Center production efficiency or twinning population. These 731 individuals were sires and dams well represented in the pedigrees of animals from the twinner population, and their genotypes were used in predicting genotypes for animals in the larger population (n = 16 035). Twinning rate and ovulation rate were analyzed in a two‐trait repeated records analysis with marker associations analyzed individually as fixed effects. Criteria for marker validation were effect estimate with a sign consistent with previous estimates and significance at a nominal P < 0.01. Of the 14 SNPs passing quality control assessments, only one was validated. A SNP in the 5′ flanking region of the IGF1 gene, discovered previously in a positional candidate gene analysis, was significantly associated with twinning rate in the USDA twinning population (P < 0.0002). This SNP may have utility in genomic prediction of twinning rate beyond the Holstein population.
Playing with Infrastructure like a Carishina: Feminist Cycling in an Era of Democratic Politics
Authors: Gamble Julie 
Published: April 2019

AbstractThis article discusses transit infrastructure as a site of radical possibility and limitation in an age of participatory democracy across Latin America. I focus on multiple spaces of participation in Quito, Ecuador to elucidate how citizenship and infrastructure are co‐produced through gendered processes. I first analyse city space of Quito from a gendered and infrastructural lens to consider how urban environments are dictated by violence and insecurity. Then, against this backdrop, I explore the spatial strategies of the feminist bicycle collective, Carishina en Bici, which translates from Quechua to “bad housewives that cycle”. Here, I draw on the concept of “deep play” to reveal how public practices in Quito question the equitable impacts of local democratic experimentation. To examine Carishinas’ spatial practices, I focus on an urban alleycat race, the Carishina Race, to show how strategic practices of solidarity reinsert feminist possibilities in urban space.
Fluid restriction negatively affects energy intake and growth in very low birthweight infants with haemodynamically significant patent ductus arteriosus
Authors: Hansson Lena , Lind Torbjörn , Wiklund Urban , Öhlund Inger , Rydberg Annika 
Published: April 2019

AbstractAimWe explored if fluid restriction in very low birthweight (VLBW) infants with a haemodynamically significant patent ductus arteriosus (PDA) affected energy and protein intakes and growth.MethodsRetrospectively, we identified 90 VLBW infants that were admitted to Umea University Hospital, Sweden, between 2009 and 2012: 42 with and 48 without haemodynamically significant PDA (hsPDA). Anthropometric, fluid, energy and protein intake data during the first 28 days of life were expressed as z‐scores.ResultsIn the 42 infants diagnosed with hsPDA, fluid intake was restricted after diagnosis, resulting in a decrease in energy and protein intake. No decrease was observed in the other 48 infants in the cohort. Multivariate analysis showed that the z‐score of weight change depended on both ductus arteriosus status and energy intake; thus, infants with hsPDA did not grow as expected with the energy provided to them.ConclusionEnergy and protein intake was diminished in prematurely born infants with hsPDA when fluid was restricted after diagnosis. The initial reduction in intakes may have contributed to the lower postnatal growth observed in these infants.
The Incredible Years® Teacher Classroom Management programme and its impact on teachers’ professional self‐efficacy, work‐related stress, and general well‐being: Results from theSTARSrandomized controlled trial
Authors: Hayes Rachel , Titheradge Daniel , Allen Kate , Allwood Matt , Byford Sarah , Edwards Vanessa , Hansford Lorraine , Longdon Bryony , Norman Shelley , Norwich Brahm , Russell Abigail Emma , Price Anna , Ukoumunne Obioha C. , Ford Tamsin 
Published: April 2019

BackgroundTeaching is a stressful occupation with poor retention. The Incredible Years® Teacher Classroom Management (TCM) programme is a training programme that research has demonstrated may be an effective intervention for improving children's mental health, but little research has explored any impacts there may be on the teachers’ own professional confidence and mental health.AimsIn this paper, we evaluate whetherTCMmay lead to changes in teachers’ well‐being, namely a reduction in burnout and an improvement in self‐efficacy and mental health.SampleEighty schools across the South West of England were recruited between September 2012 and September 2014. Headteachers were asked to nominate one class teacher to take part.MethodsEighty teachers were randomized to either attend aTCMcourse (intervention) or not (control).TCMwas delivered to groups of up to 12 teachers in six whole‐day workshops that were evenly spread between October and April. At baseline and 9‐month follow‐up, we measured teachers’ mental health using the Everyday Feelings Questionnaire (EFQ), burnout using the Maslach Burnout Inventory‐General Survey (MBI‐GS), and self‐efficacy using the Teachers’ Sense of Efficacy Scale‐Short (TSES‐Short).ResultsUsing linear regression models, there was little evidence of differences at follow‐up between the intervention and control teachers on the outcomes (the smallestp‐value was .09).ConclusionsOur findings did not replicate previous research thatTCMimproved teachers’ sense of efficacy. However, there were limitations with this study including low sample size.