bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Machine Learning to Measure Relatedness Between Genes: A Multi-Features Model
Authors: Wang Yan , Yang Sen , Zhao Jing , Du Wei , Liang Yanchun , Wang Cankun , Zhou Fengfeng , Tian Yuan , Ma Qin 
Published: March 2019

AbstractMeasuring conditional relatedness between a pair of genes is a fundamental technique and still a significant challenge in computational biology. Such relatedness can be assessed by gene expression similarities while suffering high false discovery rates. Meanwhile, other types of features, e.g., prior-knowledge based similarities, is only viable for measuring global relatedness. In this paper, we propose a novel machine learning model, named Multi-Features Relatedness (MFR), for accurately measuring conditional relatedness between a pair of genes by incorporating expression similarities with prior-knowledge based similarities in an assessment criterion. MFR is used to predict gene-gene interactions extracted from the COXPRESdb, KEGG, HPRD, and TRRUST databases by the 10-fold cross validation and test verification, and to identify gene-gene interactions collected from the GeneFriends and DIP databases for further verification. The results show that MFR achieves the highest area under curve (AUC) values for identifying gene-gene interactions in the development, test, and DIP datasets. Specifically, it obtains an improvement of 1.1% on average of precision for detecting gene pairs with both high expression similarities and high prior-knowledge based similarities in all datasets, comparing to other linear models and coexpression analysis methods. Regarding cancer gene networks construction and gene function prediction, MFR also obtains the results with more biological significances and higher average prediction accuracy, than other compared models and methods. A website of the MFR model and relevant datasets can be accessed from http://bmbl.sdstate.edu/MFR.
A join point regression analysis of trends in mortality due to osteoporosis in Spain
Authors: Dragomirescu Ioana , Llorca Javier , Gómez-Acebo Inés , Dierssen-Sotos Trinidad 
Published: March 2019

AbstractOsteoporosis is a major health problem in terms of fracture probability and disability. The aim of this ecological study is to identify the temporal trends in osteoporosis mortality in Spain from 1999 to 2015. Data on the Spanish population and number of deaths due to osteoporosis were obtained from the Spanish National Institute for Statistics. Age-adjusted mortality rates were estimated. Join point regression was used to identify the years when changes in mortality s and annual percentage change in mortality rates took place. Women presented a greater mortality rate decrease (p < 0.001), though this mortality difference by sex was reduced by half at the end of the period. The higher the age, the faster the mortality rate declined in women, while no clear pattern could be identified in men. In women, significant changes in trends were identified in three age groups (50–54, 60–64 and 80–84 years old). A sustained decrease in osteoporosis-associated mortality was found in women aged 75–79 and ≥85 years and men aged 60–64. In conclusion, mortality caused by osteoporosis in Spain is decreasing faster in the older age ranges especially in women.
Phylogeny and herbivory are related to avian cecal size
Authors: Hunt Andrew , Al-Nakkash Layla , Lee Andrew H. , Smith Heather F. 
Published: March 2019

AbstractAvian ceca, a pair of blind sacs arising from the junction of the ileum and colon, are homologous to the cecum in mammals. Cecal size is hypothesized to depend on dietary proclivities and pressures, with faunivorous species having short ceca, whereas herbivorous species have long ceca. Previous tests of this hypothesis, however, did not account for phylogenetic pseudoreplication among closely related taxa. We collated published data on cecal length, dietary category, flying ability, and body mass from 155 avian taxa. Character states were mapped onto a phylogenetic framework, and the permutation tail probability test was used to detect phylogenetic signal in each character. Phylogenetic signal is significant among the characters. As with the cecoappendicular complex in mammals, closely-related birds tend to have similar cecal length. To account for phylogenetic pseudoreplication, we performed phylogenetic generalized least squares regression on cecal length and body mass with dietary category, superordinal-level clade, and flying ability as cofactors. The best-fitting regression model supports the dietary hypothesis for the avian cecum. Among sampled birds of comparable body mass, mean cecal length is significantly longer in herbivorous species than in carnivorous ones (p = 0.008), presumably allowing the extraction of nutrients without the burden of fermenting bulky masses of dietary fiber. Exceptions to this trend, however, suggest that avian ceca are functionally complex and may have additional roles in water balance and nitrogen recycling.
Prenatal Tobacco Exposure Modulated the Association of Genetic variants with Diagnosed ADHD and its symptom domain in children: A Community Based Case–Control Study
Authors: Wang Yanni , Hu Dan , Chen Wenjing , Xue Hongli , Du Yukai 
Published: March 2019

AbstractThe purpose of our study was to test the hypothesis that prenatal tobacco smoking exposure (PSE) could modulate the association of genetic variants with ADHD. A community based case-control study was conducted among Chinese children and 168 ADHD patients and 233 controls were recruited by using combination diagnosis of DSM-IV, SNAP-IV and semi-structured clinical interview. Logistic regression analysis was performed to estimate the effect of prenatal tobacco smoking exposure and genotype frequencies on ADHD susceptibility individually by adjustment for potential confounders. Multiplicative and additive interaction analysis were performed to evaluate the interactions between risk genes and PSE with regard to ADHD. Prenatal tobacco smoke exposure was a significant risk factor of ADHD even after adjusted for other potential confounders. ADRA2A rs553668, DRD2 rs1124491 and SLC6A4 rs6354 were identified to be associated with ADHD. A significant multiplicative and additive gene-environment interactions were observed between the PSE and the ADRA2A rs553668 in relation to ADHD and ADHD-ODD. The risk of the genetic variants in ADHD was increased significantly if the child had prenatal tobacco exposure. The genetic risk for ADHD could be influenced by the presence of environmental risks. The environmental and the genetic risks are not distinct to each other. More gene-environment interaction studies were needed to reveal the etiology of ADHD.
Modeling organic carbon loss from a rapidly eroding freshwater coastal wetland
Authors: Braun Katherine N. , Theuerkauf Ethan J. , Masterson Andrew L. , Curry B. Brandon , Horton Daniel E. 
Published: March 2019

AbstractShoreline erosion can transition freshwater coastal wetlands from carbon sinks to carbon sources. No studies have explored the impacts of coastal geomorphic processes on freshwater wetland carbon budgets. To do so, we modified a saltmarsh carbon budget model for application in freshwater coastal wetlands. We validated the model with data from a shoreline wetland in the Laurentian Great Lakes. The model generates the carbon budget by differencing carbon export and carbon storage. The inputs for carbon storage are the carbon inventory and maximum wetland age. Inputs for carbon export include erosion rates and overwash extent. The model demonstrates that the wetland examined in this study transitioned to a source of carbon during periods of erosion. In fact, the net carbon export between 2015 and 2018 was 8.1% of the wetland’s original carbon stock. This study indicates that geomorphic change can dictate whether and how freshwater coastal wetlands serve as sources or sinks for terrestrial carbon, and that carbon stocks can fluctuate on a geologically rapid timescale. We recommend that such geomorphic processes be considered when developing carbon budgets for these marginal environments. Furthermore, the carbon budget model refined in this study can be used to prioritize wetlands in land management and conservation efforts.
Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana
Authors: Antunes Deborah , Jorge Natasha Andressa Nogueira , Garcia de Souza Costa Mauricio , Passetti Fabio , Caffarena Ernesto Raul 
Published: March 2019

AbstractRiboswitches are RNA sensors that affect post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch class is the most widespread riboswitch occurring in all three domains of life. Even though it controls different genes involved in the synthesis or transport of thiamine and its phosphorylated derivatives in bacteria, archaea, fungi, and plants, the TPP aptamer has a conserved structure. In this study, we aimed at understanding differences in the structural dynamics of TPP riboswitches from Escherichia coli and Arabidopsis thaliana, based on their crystallographic structures (TPPswec and TPPswat, respectively) and dynamics in aqueous solution, both in apo and holo states. A combination of Molecular Dynamics Simulations and Network Analysis empowered to find out slight differences in the dynamical behavior of TPP riboswitches, although relevant for their dynamics in bacteria and plants species. Our results suggest that distinct interactions in the microenvironment surrounding nucleotide U36 of TPPswec (and U35 in TPPswat) are related to different responses to TPP. The network analysis showed that minor structural differences in the aptamer enable enhanced intramolecular communication in the presence of TPP in TPPswec, but not in TPPswat. TPP riboswitches of plants present subtler and slower regulation mechanisms than bacteria do.
CRIS.py: A Versatile and High-throughput Analysis Program for CRISPR-based Genome Editing
Authors: Connelly Jon P. , Pruett-Miller Shondra M. 
Published: March 2019

AbstractCRISPR-Cas9 technology allows the creation of user-defined genomic modifications in cells and whole organisms. However, quantifying editing rates in pools of cells or identifying correctly edited clones is tedious. Targeted next-generation sequencing provides a high-throughput platform for optimizing editing reagents and identifying correctly modified clones, but the large amount of data produced can be difficult to analyze. Here, we present CRIS.py, a simple and highly versatile python-based program which concurrently analyzes next-generation sequencing data for both knock-out and multiple user-specified knock-in modifications from one or many edited samples. Compared to available NGS analysis programs for CRISPR based-editing, CRIS.py has many advantages: (1) the ability to analyze from one to thousands of samples at once, (2) the capacity to check each sample for multiple sequence modifications, including those induced by base-editors, (3) an output in an easily searchable file format enabling users to quickly sort through and identify correctly targeted clones.
Sex Affects the Relationship Between Third Party Punishment and Cooperation
Authors: Rodriguez-Ruiz Claudia , Muñoz-Reyes José Antonio , Iglesias-Julios Marta , Sanchez-Pages Santiago , Turiegano Enrique 
Published: March 2019

AbstractProsocial third-party punishment (3PP) is a punitive behavior against antisocial individuals, which might explain extended cooperativeness in humans. 3PP shows sexual dimorphism, being more frequent in men than in women. We studied whether sexually dimorphic features related to sexual hormones during development (facial dimorphism and 2D:4D) influence the tendency to engage in 3PP in a sample of 511 women and 328 men. After playing a Prisoner’s Dilemma, participants had to decide whether to penalize the defection of a third player who had exploited his/her counterpart’s cooperation. In line with previous studies, we observe that men are more prone to engage in 3PP than women. We find that this sex difference is due to cooperative men being more likely to punish than cooperative women. In addition, men with higher facial masculinity are less likely to engage in 3PP, whereas no features influence 3PP in women. We discuss the possibility that sex differences in the motivations and fitness implications underlying 3PP might be driving the observed results.
Neural Dynamics of Shooting Decisions and the Switch from Freeze to Fight
Authors: Hashemi Mahur M. , Gladwin Thomas E. , de Valk Naomi M. , Zhang Wei , Kaldewaij Reinoud , van Ast Vanessa , Koch Saskia B. J. , Klumpers Floris , Roelofs Karin 
Published: March 2019

AbstractReal-life shooting decisions typically occur under acute threat and require fast switching between vigilant situational assessment and immediate fight-or-flight actions. Recent studies suggested that freezing facilitates action preparation and decision-making but the neurocognitive mechanisms remain unclear. We applied functional magnetic resonance imaging, posturographic and autonomic measurements while participants performed a shooting task under threat of shock. Two independent studies, in unselected civilians (N = 22) and police recruits (N = 54), revealed that preparation for shooting decisions under threat is associated with postural freezing, bradycardia, midbrain activity (including the periaqueductal gray-PAG) and PAG-amygdala connectivity. Crucially, stronger activity in the midbrain/PAG during this preparatory stage of freezing predicted faster subsequent accurate shooting. Finally, the switch from preparation to active shooting was associated with tachycardia, perigenual anterior cingulate cortex (pgACC) activity and pgACC-amygdala connectivity. These findings suggest that threat-anticipatory midbrain activity centred around the PAG supports decision-making by facilitating action preparation and highlight the role of the pgACC when switching from preparation to action. These results translate animal models of the neural switch from freeze-to-action. In addition, they reveal a core neural circuit for shooting performance under threat and provide empirical evidence for the role of defensive reactions such as freezing in subsequent action decision-making.
Regulation of folate and methionine metabolism by multisite phosphorylation of human methylenetetrahydrofolate reductase
Authors: Zheng Yuxiang , Ramsamooj Shivan , Li Qian , Johnson Jared L. , Yaron Tomer M. , Sharra Klaus , Cantley Lewis C. 
Published: March 2019

AbstractMethylenetetrahydrofolate reductase (MTHFR) catalyzes the irreversible conversion of 5,10-methylene-tetrahydrofolate (THF) to 5-methyl-THF, thereby committing one-carbon units to the methionine cycle. While MTHFR has long been known to be allosterically inhibited by S-adenosylmethionine (SAM), only relatively recently has N-terminal multisite phosphorylation been shown to provide an additional layer of regulation. In vitro, the multiply phosphorylated form of MTHFR is more sensitive to allosteric inhibition by SAM. Here we sought to investigate the kinases responsible for MTHFR multisite phosphorylation and the physiological function of MTHFR phosphorylation in cells. We identified DYRK1A/2 and GSK3A/B among the kinases that phosphorylate MTHFR. In addition, we found that MTHFR phosphorylation is maintained by adequate cellular SAM levels, which are sensed through the C-terminal SAM binding domain of MTHFR. To understand the function of MTHFR phosphorylation in cells, we generated MTHFR CRISPR knockin mutant lines that effectively abolished MTHFR phosphorylation and compared them with the parental cell lines. Whereas the parental cell lines showed increased 5-methyl-THF production in response to homocysteine treatment, the knockin cell lines had high basal levels of 5-methyl-THF and did not respond to homocysteine treatment. Overall, our results suggest that MTHFR multisite phosphorylation coordinates with SAM binding to inhibit MTHFR activity in cells.
Dental integration and modularity in pinnipeds
Authors: Wolsan Mieczyslaw , Suzuki Satoshi , Asahara Masakazu , Motokawa Masaharu 
Published: March 2019

AbstractMorphological integration and modularity are important for understanding phenotypic evolution because they constrain variation subjected to selection and enable independent evolution of functional and developmental units. We report dental integration and modularity in representative otariid (Eumetopias jubatus, Callorhinus ursinus) and phocid (Phoca largha, Histriophoca fasciata) species of Pinnipedia. This is the first study of integration and modularity in a secondarily simplified dentition with simple occlusion. Integration was stronger in both otariid species than in either phocid species and related positively to dental occlusion and negatively to both modularity and tooth-size variability across all the species. The canines and third upper incisor were most strongly integrated, comprising a module that likely serves as occlusal guides for the postcanines. There was no or weak modularity among tooth classes. The reported integration is stronger than or similar to that in mammals with complex dentition and refined occlusion. We hypothesise that this strong integration is driven by dental occlusion, and that it is enabled by reduction of modularity that constrains overall integration in complex dentitions. We propose that modularity was reduced in pinnipeds during the transition to aquatic life in association with the origin of pierce-feeding and loss of mastication caused by underwater feeding.
Epidemiological evaluation of Latvian control measures for African swine fever in wild boar on the basis of surveillance data
Authors: Schulz Katja , Oļševskis Edvīns , Staubach Christoph , Lamberga Kristīne , Seržants Mārtiņš , Cvetkova Svetlana , Conraths Franz Josef , Sauter-Louis Carola 
Published: March 2019

AbstractA wild boar population infected with African Swine Fever (ASF) constitutes a constant threat to commercial pig farms and therefore to the economy of the affected country. Currently, ASF is still spreading in several countries and the implementation of intensive measures such as reducing wild boar population densities seems not to be able to stop the further spread of the disease. In addition, there are still substantial knowledge gaps regarding the epidemiology of the disease. To identify risk factors for a higher probability of a wild boar sample being virological or serological positive, comprehensive statistical analyses were performed based on Latvian surveillance data. Using a multivariable Bayesian regression model, the effects of implemented control measures on the proportion of hunted or found dead wild boar or on the estimated virus prevalence were evaluated. None of the control measures applied in Latvia showed a significant effect on the relevant target figure. Also, the estimated periodic prevalence of wild boar that had tested ASF positive by PCR appeared to remain unaffected over time. Therefore, there is an urgent need to reconsider the implemented control measures. The results of this study and the course of ASF in other affected countries, raise the question, whether an endemic situation of ASF in wild boar is reversible.
Effects of the high-inequality of income on the breast cancer mortality in Brazil
Authors: dos Santos Figueiredo Francisco Winter , Adami Fernando 
Published: March 2019

AbstractAs well as breast cancer mortality, the income inequality in Brazil is different between Federative units, including between units of the same region. To assess the effects of the high-inequality of income on breast cancer mortality in Brazilian Federative Units, in the 2010 year. This is an ecologic study. Deaths from breast cancer in Brazilian women according to Federative units were obtained from the Department of Informatics of the Unified Health System. Mortality by breast cancer was estimated per 100,000 women and age-standardized by the direct method according to World Health Organization population. Income inequality was measured by the Gini index obtained from the United Nations Development Programme. The High-inequality of income was classified by the third tercile of the distribution from the Gini index of the Federative units. Univariate analysis was performed according to data normality. Linear regressions were performed by the stepwise backward method. The confidence level was 5%. Stata® (Stata Corp, LC) 11.0. was used. The High-inequality of income was associated with worse social and demographic indicators. The age-standardized breast cancer mortality was larger in the high-inequality of income Federative units. In the adjusted analysis, these Federative units presented a mean of 2 more deaths (ranging from the 0.4 to 3.7 deaths, r² = 0.79; p = 0.018) by breast cancer per 100,000 women when compared to the Federative units without high-inequality of income. In the Brazilian Federative units, the high-inequality of income was associated with age-standardized breast cancer mortality more.
Seabird nutrients are assimilated by corals and enhance coral growth rates
Authors: Savage Candida 
Published: March 2019

AbstractNutrient subsidies across ecotone boundaries can enhance productivity in the recipient ecosystem, especially if the nutrients are transferred from a nutrient rich to an oligotrophic ecosystem. This study demonstrates that seabird nutrients from islands are assimilated by endosymbionts in corals on fringing reefs and enhance growth of a dominant reef-building species, Acropora formosa. Nitrogen stable isotope ratios (δ15N) of zooxanthellae were enriched in corals near seabird colonies and decreased linearly with distance from land, suggesting that ornithogenic nutrients were assimilated in corals. In a one-year reciprocal transplant experiment, A. formosa fragments grew up to four times faster near the seabird site than conspecifics grown without the influence of seabird nutrients. The corals influenced by elevated ornithogenic nutrients were located within a marine protected area with abundant herbivorous fish populations, which kept nuisance macroalgae to negligible levels despite high nutrient concentrations. In this pristine setting, seabird nutrients provide a beneficial nutrient subsidy that increases growth of the ecologically important branching corals. The findings highlight the importance of catchment–to–reef management, not only for ameliorating negative impacts from land but also to maintain beneficial nutrient subsidies, in this case seabird guano.