bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Eye-Tracking Method for Directly Assessing Children's Visual-Motor Integration
Authors: Fears Nicholas E , Bailey Brooke C , Youmans Blair , Lockman Jeffrey J 
Published: February 2019

Abstract

Background
Visual-motor integration is an integral component of many adaptive behaviors and has been linked to school readiness. In young school-age children, visual-motor integration is typically assessed with the Beery-Buktenica Developmental Test of Visual Motor Integration (Beery VMI), a standardized instrument that measures children's ability to copy 2-dimensional forms. The Beery VMI is scored according to children's final written product, but does not directly measure the process of visual-motor integration that underlies children's form copying.

Objective
We describe a new way of directly assessing visual-motor integration in real time. We demonstrate how head-mounted eye-tracking technology for young children can be used to describe the dynamics of visual-motor integration when children copy forms.

Design
This study used a cross-sectional design.

Methods
Typically developing kindergarten children (N = 20) were tested as they wore an eye-tracker while performing the Beery VMI.

Results
Participants’ success (b = −0.66; SE = 0.08; Cohen f2 = 1.11) and their efficiency in visual (b = 0.29; SE = 0.02; Cohen f2 = 0.55) and motor (b = 0.12; SE = 0.01; Cohen f2 = 0.90) processes during form copying decreased as the stimulus complexity increased.

Limitations
A small convenience sample was used to determine proof of concept. A larger, more representative sample is necessary to provide generalizable results.

Conclusions
The new methods used here offer the possibility of more fine-grained assessments of eye-hand coordination in typically developing children and children with such clinical conditions as dysgraphia and developmental coordination disorder.
Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters
Authors: Álvarez-Carretero Sandra , Goswami Anjali , Yang Ziheng , Dos Reis Mario 
Published: February 2019

AbstractDiscrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modeled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population “noise”) and the correlation among characters leads to biased estimates of divergence times and rate, especially if the correlation and population noise are high. We apply our new method to the analysis of quantitative characters (cranium landmarks) and molecular data from carnivoran mammals. Our results show that time estimates are affected by whether the correlations and population noise are accounted for or ignored in the analysis. The estimates are also affected by the type of data analyzed, with analyses of morphological characters only, molecular data only, or a combination of both; showing noticeable differences among the time estimates. Rate variation of morphological characters among the carnivoran species appears to be very high, with Bayesian model selection indicating that the independent-rates model fits the morphological data better than the autocorrelated-rates model. We suggest that using morphological continuous characters, together with molecular data, can bring a new perspective to the study of species evolution. Our new model is implemented in the MCMCtree computer program for Bayesian inference of divergence times.
Development of a tablet app designed to improve African Americans’ screening colonoscopy rates
Authors: Miller Sarah J , Sly Jamilia R , Gaffney Kemi B , Jiang Zhiye , Henry Brittney , Jandorf Lina 
Published: February 2019

Abstract
Compared with other racial/ethnic groups, African Americans have the highest colorectal cancer (CRC) morbidity and mortality rates. It is critical to help improve African Americans’ CRC prevention efforts in order to reduce the burden of CRC in this community. The aim of this study was to develop and field test a tablet app, called e-Motivate, designed to improve African Americans’ screening colonoscopy rates. The e-Motivate app was field tested, using an iterative approach. The first version of the app, e-Motivate 1.0, was field tested on 20 African Americans over the age of 50. Participants engaged in a think aloud exercise and provided feedback regarding the app’s usability and acceptability. The results of the first field test were used to modify the app and develop e-Motivate 2.0. The field test procedures were repeated on a new group of participants (N = 18). The results from the second field test were used to make final modifications to the app. Overall, participants responded positively to the app. Qualitative analyses showed that participants found the app to be easy to use and helpful. Furthermore, descriptive statistics revealed that participants found the app to be highly usable and acceptable, exceeding recommended benchmarks for usability and acceptability. Critiques of the app were used to modify and finalize the intervention. The results from the proposed study suggest that the e-Motivate app is highly feasible and acceptable. The next step in this line of research is to conduct a randomized clinical trial to formally test the efficacy of the e-Motivate app for improving screening colonoscopy rates among African Americans.
Baltic amber Staphylinini (Coleoptera: Staphylinidae: Staphylininae): a rove beetle fauna on the eve of our modern climate
Authors: Brunke Adam James , Żyła Dagmara , Yamamoto Shûhei , Solodovnikov Alexey 
Published: February 2019

AbstractCenozoic climate cooling, particularly during the Eocene, has drastically shaped modern biological assemblages through a shift from an equable greenhouse to a polarized icehouse. Present-day Europe lies in a highly seasonal and temperate area that strongly embodies this modern icehouse climate. Baltic amber provides a Middle Eocene snapshot of the European fauna before this large-scale change. Here, we focused on the rove beetle tribe Staphylinini and conducted a comprehensive phylogenetic study of all known Baltic amber fossils in a total-evidence phylogenetic framework that integrates morphology with molecular data from six gene fragments. Based on our well-resolved topology, we propose the following: †Baltognathina subtrib. nov., Afroquediina subtrib. nov., Antimerina subtrib. nov., †Baltognathus aenigmaticus gen. et sp. nov., †Eolophorus gen. nov., †Laevisaurus robustus and †Laevisaurus gracilis gen. et spp. nov., †Hemiquedius europaeus sp. nov. and †Bolitogyrus fragmentus sp. nov. †Quedius cretaceus is placed as junior synonym of †Cretoquedius infractus. The earliest definitive fossils of Quediina are reported herein from the Eocene. The Staphylinini fauna of Middle Eocene Europe combined thermophilic, freeze-intolerant lineages with freeze-tolerant, temperate lineages and, unlike most other staphylinid or beetle lineages, all have since become extinct in the Palaearctic region.
A case for environmental statistics of early-life effects
Authors: Frankenhuis Willem E. , Nettle Daniel , Dall Sasha R. X. 
Published: February 2019

There is enduring debate over the question of which early-life effects are adaptive and which ones are not. Mathematical modelling shows that early-life effects can be adaptive in environments that have particular statistical properties, such as reliable cues to current conditions and high autocorrelation of environmental states. However, few empirical studies have measured these properties, leading to an impasse. Progress, therefore, depends on research that quantifies cue reliability and autocorrelation of environmental parameters in real environments. These statistics may be different for social and non-social aspects of the environment. In this paper, we summarize evolutionary models of early-life effects. Then, we discuss empirical data on environmental statistics from a range of disciplines. We highlight cases where data on environmental statistics have been used to test competing explanations of early-life effects. We conclude by providing guidelines for new data collection and reflections on future directions.This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine'.
The evolution of early-life effects on social behaviour—why should social adversity carry over to the future?
Authors: Kuijper Bram , Johnstone Rufus A. 
Published: February 2019

Numerous studies have shown that social adversity in early life can have long-lasting consequences for social behaviour in adulthood, consequences that may in turn be propagated to future generations. Given these intergenerational effects, it is puzzling why natural selection might favour such sensitivity to an individual’s early social environment. To address this question, we model the evolution of social sensitivity in the development of helping behaviours, showing that natural selection indeed favours individuals whose tendency to help others is dependent on early-life social experience. In organisms with non-overlapping generations, we find that natural selection can favour positive social feedbacks, in which individuals who received more help in early life are also more likely to help others in adulthood, while individuals who received no early-life help develop low tendencies to help others later in life. This positive social sensitivity is favoured because of an intergenerational relatedness feedback: patches with many helpers tend to be more productive, leading to higher relatedness within the local group, which in turn favours higher levels of help in the next generation. In organisms with overlapping generations, this positive feedback is less likely to occur, and those who received more help may instead be less likely to help others (negative social feedback). We conclude that early-life social influences can lead to strong between-individual differences in helping behaviour, which can take different forms dependent on the life history in question.
This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine’.
Revisiting mechanisms and functions of prenatal hormone-mediated maternal effects using avian species as a model
Authors: Groothuis Ton G. G. , Hsu Bin-Yan , Kumar Neeraj , Tschirren Barbara 
Published: February 2019

Maternal effects can adaptively modulate offspring developmental trajectories in variable but predictable environments. Hormone synthesis is sensitive to environmental factors, and maternal hormones are thus a powerful mechanism to transfer environmental cues to the next generation. Birds have become a key model for the study of hormone-mediated maternal effects because the embryo develops outside the mother's body, facilitating the measurement and manipulation of prenatal hormone exposure. At the same time, birds are excellent models for the integration of both proximate and ultimate approaches, which is key to a better understanding of the evolution of hormone-mediated maternal effects. Over the past two decades, a surge of studies on hormone-mediated maternal effects has revealed an increasing number of discrepancies. In this review, we discuss the role of the environment, genetic factors and social interactions in causing these discrepancies and provide a framework to resolve them. We also explore the largely neglected role of the embryo in modulating the maternal signal, as well as costs and benefits of hormone transfer and expression for the different family members. We conclude by highlighting fruitful avenues for future research that have opened up thanks to new theoretical insights and technical advances in the field.This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine’.
Preterm birth in evolutionary context: a predictive adaptive response?
Authors: Williams Thomas C. , Drake Amanda J. 
Published: February 2019

Preterm birth is a significant public health problem worldwide, leading to substantial mortality in the newborn period, and a considerable burden of complications longer term, for affected infants and their carers. The fact that it is so common, and rates vary between different populations, raising the question of whether in some circumstances it might be an adaptive trait. In this review, we outline some of the evolutionary explanations put forward for preterm birth. We specifically address the hypothesis of the predictive adaptive response, setting it in the context of the Developmental Origins of Health and Disease, and explore the predictions that this hypothesis makes for the potential causes and consequences of preterm birth. We describe how preterm birth can be triggered by a range of adverse environmental factors, including nutrition, stress and relative socioeconomic status. Examining the literature for any associated longer-term phenotypic changes, we find no strong evidence for a marked temporal shift in the reproductive life-history trajectory, but more persuasive evidence for a re-programming of the cardiovascular and endocrine system, and a range of effects on neurodevelopment. Distinguishing between preterm birth as a predictive, rather than immediate adaptive response will depend on the demonstration of a positive effect of these alterations in developmental trajectories on reproductive fitness.This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine'.
Molecular subtyping and prognostic assessment based on tumor mutation burden in patients with lung adenocarcinomas
Authors: Wang Changzheng , Li Fuqiang , Xie Guoyun , Qiao Sitan , Shi Xulian , Deng Jianlian , Liang Han , Lin Cong , Zhao Xin , Wu Kui , Zhang Xiuqing 
Published: February 2019

AbstractTumor mutation burden (TMB) is a potential biomarker for response to immunotherapy. The subset of patients with TMB has not been well characterized in lung adenocarcinomas. Here we performed molecular subtyping based on TMB and compared the features of different subtypes including clinical features, somatic driver genes and mutational signatures. We found that patients with lower tumor mutation burden had a longer disease-free survival, while higher tumor mutation burden is associated with smoking and aging. Analysis of somatic driver genes and mutational signatures demonstrates a significant association between somaticRYR2mutations and the subtype with higher mutation burden. Overall, our study identified two molecular subtypes based on TMB and described the corresponding difference in their clinical and genomic levels.
Bacterial transformation buffers environmental fluctuations through the reversible integration of mobile genetic elements
Authors: Carvalho Gabriel , Fouchet David , Danesh Gonché , Godeux Anne-Sophie , Laaberki Maria-Halima , Pontier Dominique , Charpentier Xavier , Venner Samuel 
Published: February 2019

AbstractHorizontal gene transfer (HGT) is known to promote the spread of genes in bacterial communities, which is of primary importance to human health when these genes provide resistance to antibiotics. Among the main HGT mechanisms, natural transformation stands out as being widespread and encoded by the bacterial core genome. From an evolutionary perspective, transformation is often viewed as a mean to generate genetic diversity and mixing within bacterial populations. However, another recent paradigm proposes that its main evolutionary function would be to cure bacterial genomes from their parasitic mobile genetic elements (MGEs). Here, we propose to combine these two seemingly opposing points of view because MGEs, although costly for bacterial cells, can carry functions that are point-in-time beneficial to bacteria under stressful conditions (e.g. antibiotic resistance genes under antibiotic exposure). Using computational modeling, we show that, in stochastic environments (unpredictable stress exposure), an intermediate transformation rate maximizes bacterial fitness by allowing the reversible integration of MGEs carrying resistance genes but costly for the replication of host cells. By ensuring such reversible genetic diversification (acquisition then removal of MGEs), transformation would be a key mechanism for stabilizing the bacterial genome in the long term, which would explain its striking conservation.
Gtf2i and Gtf2ird1 mutation are not sufficient to reproduce mouse phenotypes caused by the Williams Syndrome critical region
Authors: Kopp Nathan , McCullough Katherine , Maloney Susan E. , Dougherty Joseph D. 
Published: February 2019

AbstractWilliams syndrome is a neurodevelopmental disorder caused by a 1.5-1.8Mbp deletion on chromosome 7q11.23, affecting the copy number of 26-28 genes. Phenotypes of Williams syndrome include cardiovascular problems, craniofacial dysmorphology, deficits in visual spatial cognition, and a characteristic hypersocial personality. There are still no genes in the region that have been consistently linked to the cognitive and behavioral phenotypes, although human studies and mouse models have led to the current hypothesis that the general transcription factor 2 I family of genes, GTF2I and GTF2IRD1, are responsible. Here we test the hypothesis that these two transcription factors are sufficient to reproduce the phenotypes that are caused by deletion of the Williams syndrome critical region (WSCR). We compare a new mouse model with loss of function mutations in both Gtf2i and Gtf2ird1 to an established mouse model lacking the complete WSCR. We show that the complete deletion model has deficits across several behavioral domains including social communication, motor functioning, and conditioned fear that are not explained by loss of function mutations in Gtf2i and Gtf2ird1. Furthermore, transcriptome profiling of the hippocampus shows changes in synaptic genes in the complete deletion model that are not seen in the double mutants. Thus, we have thoroughly defined a set of molecular and behavioral consequences of complete WSCR deletion, and shown that other genes or combinations of genes are necessary to produce these phenotypic effects.
Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean
Authors: Bayer Barbara , Hansman Roberta L. , Bittner Meriel J. , Noriega-Ortega Beatriz E. , Niggemann Jutta , Dittmar Thorsten , Herndl Gerhard J. 
Published: February 2019

AbstractAmmonia-oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20-40% of the ocean’s prokaryotic plankton and thus play an important role in global nitrogen cycle. However, it remains enigmatic to what extent these chemolithoautotrophic archaea are releasing dissolved organic matter (DOM). A combination of targeted and untargeted metabolomics was used to characterise the exometabolomes of three model AOA strains of theNitrosopumilusgenus. Furthermore, we compared the composition of intra- and extracellular dissolved free amino acids (DFAA). Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivity, dominated by nitrogen-containing compounds. A significant fraction of the released DOM consisted of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. In growingNitrosopumiluscultures, hydrophobic amino acids were likely released as a result of passive diffusion corresponding to ammonia oxidation activity, while glycine was continuously released at high rates. Our results suggest that AOA release several ecologically and biochemically relevant metabolites, potentially fueling heterotrophic prokaryotes in the ocean.
Peptide Secondary Structure Prediction using Evolutionary Information
Authors: Singh Harinder , Singh Sandeep , Singh Raghava Gajendra Pal 
Published: February 2019

ABSTRACTBACKGROUNDIn the past, large numbers of methods have been developed for predicting secondary structure of proteins. Best of author’s knowledge no method has been specifically developed for predicting secondary structure of peptides. We analyzed secondary structure of peptides and proteins; it was observed that same peptide in protein adopt different secondary structures. Considering the wide application of peptides in therapeutic market, we made attempt to develop a method called PEP2D for predicting secondary structure of peptides.RESULTSIn this study, 3107 unique peptides have been used to train, test and evaluate peptide secondary structure prediction models. It was observed that regular secondary structure content (e.g., helix, beta-sheet) increased with length of peptides. Firstly, models based on various machine-learning techniques have been developed using binary profile of peptides and achieved maximum overall accuracy (Q3) 79.5%. The performance of models further improved from 79.5% to 83.5% using evolutionary information in the form of PSSM profile. We also evaluate performance of protein secondary structure prediction method PSIPRED on our dataset and achieved maximum accuracy 76.9%; particularly poor (Q3 71.4%) for small peptides having length less than 10 residues. Overall, PEP2D has better prediction of beta-sheets (Q3 74%) and coil region (Q3 87%) of peptides as compare to PSIPRED (Q3 54.4% for beta-sheet and Q3 77.9% for coil). We also measure performance of PSIPRED and PEP2D in terms of segment overlap (SOV); achieved 69.3 and 76.7 respectively.CONCLUSIONOur observations indicate that there is a need of developing separate method for predicting secondary structure of peptides. It was also observed that models based on PSSM profile perform poor on small peptides in comparison to long peptides. Based on our study, we developed method for predicting secondary structure of peptides. In order to provide service to user, a webserver/standalone has been developed (https://webs.iiitd.edu.in/raghava/pep2d/).