bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cognitive Constraints on Learning to Read in Children with an Intellectual Disability Who Are Deaf and Hard of Hearing
Authors: van Wingerden Evelien , van Tilborg Arjan , van Balkom Hans 
Published: September 2018

Abstract
Learning to read is challenging for children who have hearing impairments and concurrent intellectual disabilities because they face barriers due to both conditions. In many developmental domains, including executive functioning and language development, auditory and intellectual disabilities mutually influence each other; a deficit in one domain hinders coping mechanisms to compensate for distortions in the other. The resulting impact is more than the sum of the parts. It affects the way students learn to read and the way they process written text in many ways. Little is known about the key factors in literacy development for children with both hearing impairments and intellectual disabilities. This chapter integrates recent findings on reading development in children with both of these conditions to define a research base for two exploratory studies on literacy attainment in these learners. Recommendations for literacy education are based on these studies.
Assessment of Pragmatic Abilities in Deaf and Hard-of-Hearing Learners in Relation to Social Skills
Authors: Zaidman-Zait Anat , Most Tova 
Published: September 2018

Abstract
Pragmatic behaviors are related to the social use of language in an appropriate and effective way. As a result of their hearing loss, many deaf and hard-of-hearing (DHH) learners who use spoken language have pragmatic difficulties in everyday interactions. Assessing pragmatic competence is the most challenging aspect of language ability to assess and there are few efficient, valid, and reliable sound tools for this purpose in DHH learners. The successful use of pragmatic skills is particularly important to DHH children’s social and emotional functioning in the educational system, including their self-confidence, motivation, social adjustment, peer acceptance, and popularity. This chapter discusses the assessment of pragmatic abilities in DHH learners and argues that pragmatic abilities are fundamental to DHH learners’ social-emotional functioning. A case example will be provided and implications for educational assessment and intervention will be discussed.
Revisiting Curricula for Deaf Students
Authors: Ohna Stein Erik 
Published: September 2018

Abstract
The Norwegian National Curriculum in 1997 introduced four subject curricula for deaf students as part of new legislation giving deaf students who have acquired sign language as their first language the right to instruction in the use of sign language and through the medium of sign language. A few years later, new hearing technologies contributed to substantial changes in the educational context. This situation has challenged the school system, schools, and teachers. The chapter is organized in three sections. First, the educational system and the process leading to the introduction of new legislation is presented. The second section deals with information about the use of curricula for deaf students. The last section discusses issues of students’ achievements, classroom processes, and national policies.
What a Sexy Tale!
Authors: Hogh-Olesen Henrik 
Published: September 2018

Abstract
Chapter 3 explores even further back in evolutionary history and examines whether there are traces of the aesthetic impulse in species other than our own. Do other species have a sense of aesthetics? Do they make aesthetic choices, and do they exhibit examples of aesthetic behavior? Among other things, this chapter looks at bird song and crane dance. It follows the fascinating bowerbirds as they create their remarkable and colorful constructions. And it follows the action as experiments are conducted with chimpanzees in the lab. The chapter also discusses honest signals, innate sensibilities, sexual selection, and the evolution of beauty.
Who Lives Here?
Authors: Hogh-Olesen Henrik 
Published: September 2018

Abstract
Chapter 6 follows the aesthetic impulse full circle and explores the human need to decorate objects and surroundings, as well as the marking of property and status in the public domain. Furthermore, it looks at phenomena such as folk art, street art, and graffiti. The purpose of the chapter is to show that such extravaganzas too make biological sense and thereby strengthen the argument that aesthetic behavior is natural for humans. Decorations signal personal fitness, ability, care, effort, resources, as well as power, because they ensure social status, for instance to attract more sexual partners. Like our body ornamentation, decoration is immediate communication transmitting key social and evolutionary information to the surroundings.
Art and the Brain’s Reward System
Authors: Hogh-Olesen Henrik 
Published: September 2018

Abstract
Chapter 7 takes the investigation of the aesthetic impulse into the human brain to understand, first, why only we—and not our closest relatives among the primates—express ourselves aesthetically; and second, how the brain reacts when presented with aesthetic material. Brain scans are less useful when you are interested in the Why of aesthetic behavior rather than the How. Nevertheless, some brain studies have been ground-breaking, and neuroaesthetics offers a pivotal argument for the key function of the aesthetic impulse in human lives; it shows us that the brain’s reward circuit is activated when we are presented with aesthetic objects and stimuli. For why reward a perception or an activity that is evolutionarily useless and worthless in relation to human existence?
Spectral Theory and Differential Operators
Authors: Edmunds David , Evans Des 
Published: September 2018

Abstract
This book gives an account of those parts of the analysis of closed linear operators acting in Banach or Hilbert spaces that are relevant to spectral problems involving differential operators, and makes applications to such questions. After the exposition of the abstract theory in the first four chapters, Sobolev spaces are introduced and their main properties established. The remaining seven chapters are largely concerned with second-order elliptic differential operators and related boundary-value problems. Particular attention is paid to the spectrum of the Schrödinger operator. Its original form contains material of lasting importance that is relatively unaffected by advances in the theory since 1987, when the book was first published. The present edition differs from the old by virtue of the correction of minor errors and improvements of various proofs. In addition, it contains Notes at the ends of most chapters, intended to give the reader some idea of recent developments together with additional references that enable more detailed accounts to be accessed.
Identification of Modulators That Activate the Constitutive Androstane Receptor From the Tox21 10K Compound Library
Authors: Lynch Caitlin , Mackowiak Bryan , Huang Ruili , Li Linhao , Heyward Scott , Sakamuru Srilatha , Wang Hongbing , Xia Menghang 
Published: September 2018

Abstract
The constitutive androstane receptor (CAR; NR1I3) is a nuclear receptor involved in all phases of drug metabolism and disposition. However, recently it’s been implicated in energy metabolism, tumor progression, and cancer therapy as well. It is, therefore, important to identify compounds that induce human CAR (hCAR) activation to predict drug-drug interactions and potential therapeutic usage. In this study, we screen the Tox21 10,000 compound collection to characterize hCAR activators. A potential novel structural cluster of compounds was identified, which included nitazoxanide and tenonitrozole, whereas known structural clusters, such as flavones and prazoles, were also detected. Four compounds, neticonazole, diphenamid, phenothrin, and rimcazole, have been identified as novel hCAR activators, one of which, rimcazole, shows potential selectivity toward hCAR over its sister receptor, the pregnane X receptor (PXR). All 4 compounds translocated hCAR from the cytoplasm into the nucleus demonstrating the first step to CAR activation. Profiling these compounds as hCAR activators would enable an estimation of drug-drug interactions, as well as identify prospective therapeutically beneficial drugs.
Perspectives from animal demography on incorporating evolutionary mechanism into plant population dynamics
Authors: Paniw Maria 
Published: September 2018

AbstractWith a growing number of long-term, individual-based data on natural populations available, it has become increasingly evident that environmental change affects populations through complex, simultaneously occurring demographic and evolutionary processes. Analyses of population-level responses to environmental change must therefore integrate demography and evolution into one coherent framework. Integral projection models (IPMs), which can relate genetic and phenotypic traits to demographic and population-level processes, offer a powerful approach for such integration. However, a rather artificial divide exists in how plant and animal population ecologists use IPMs. Here, I argue for the integration of the two sub-disciplines, particularly focusing on how plant ecologists can diversify their toolset to investigate selection pressures and eco-evolutionary dynamics in plant population models. I provide an overview of approaches that have applied IPMs for eco-evolutionary studies and discuss a potential future research agenda for plant population ecologists. Given an impending extinction crisis, a holistic look at the interacting processes mediating population persistence under environmental change is urgently needed.
Coverage-versus-Length plots, a simple quality control step for de novo yeast genome sequence assemblies
Authors: Douglass Alexander P. , O’Brien Caoimhe E. , Offei Benjamin , Coughlan Aisling Y. , Ortiz-Merino Raúl A. , Butler Geraldine , Byrne Kevin P. , Wolfe Kenneth H. 
Published: September 2018

AbstractIllumina sequencing has revolutionized yeast genomics, with prices for commercial draft genome sequencing now below $200. The popular SPAdes assembler makes it simple to generate a de novo genome assembly for any yeast species. However, whereas making genome assemblies has become routine, understanding what they contain is still challenging. Here, we show how graphing the information that SPAdes provides about the length and coverage of each scaffold can be used to investigate the nature of an assembly, and to diagnose possible problems. Scaffolds derived from mitochondrial DNA, ribosomal DNA, and yeast plasmids can be identified by their high coverage. Contaminating data, such as cross-contamination from other samples in a multiplex sequencing run, can be identified by its low coverage. Scaffolds derived from the bacteriophage PhiX174 and Lambda DNAs that are frequently used as molecular standards in Illumina protocols can also be detected. Assemblies of yeast genomes with high heterozygosity, such as interspecies hybrids, often contain two types of scaffold: regions of the genome where the two alleles assembled into two separate scaffolds and each has a coverage level C, and regions where the two alleles co-assembled (collapsed) into a single scaffold that has a coverage level 2C. Visualizing the data with Coverage-versus-Length (CVL) plots, which can be done using Microsoft Excel or Google Sheets, provides a simple method to understand the structure of a genome assembly and detect aberrant scaffolds or contigs. We provide a Python script that allows assemblies to be filtered to remove contaminants identified in CVL plots.100-word article summaryWe describe a simple new method, Coverage-versus-Length plots, for examining de novo genome sequence assemblies. These plots enable researchers to detect scaffolds that have unusually high or unusually low coverage, which allows contaminants, and scaffolds that come from atypical parts of the organism’s DNA complement, to be detected. We show that contaminants are common in yeast genomes sequenced in multiplex Illumina runs. We provide instructions for making plots using Microsoft Excel or Google Sheets, and software for filtering assemblies to remove contaminants. Contaminants can be detected and removed, even without knowing their source.
Brain-derived neurotrophic factor and TrkB levels in mice that lack vesicular zinc: Effects of age and sex
Authors: McAllister Brendan B. , Bihelek Nicoline , Mychasiuk Richelle M. , Dyck Richard H. 
Published: September 2018

ABSTRACTIn certain neurons, zinc ions are stored in synaptic vesicles by zinc transporter 3 (ZnT3). Vesicular zinc can then be released synaptically to modulate myriad targets. In vitro evidence indicates that these targets may include brain-derived neurotrophic factor (BDNF) and its receptor, tropomyosin receptor kinase B (TrkB). But the effects of vesicular zinc on BDNF and TrkB in the intact brain are unclear. Studies of mice that lack ZnT3 – and, as a result, vesicular zinc – have shown abnormalities in BDNF and TrkB levels, but results have been mixed and are therefore difficult to interpret. This might be caused by differences in the age or sex of mice tested. In the present study, we measured BDNF and TrkB levels in the hippocampus and neocortex, comparing wild type and ZnT3 knockout mice of both sexes at two ages (5 and 12 weeks). We also examined BDNF mRNA expression and protein levels at an intermediate age (8-10 weeks). We found that, regardless of age or sex, BDNF and TrkB protein levels did not differ between wild type and ZnT3 knockout mice. There were sex-specific differences in BDNF protein and mRNA expression, however. BDNF protein levels increased with age in female mice but not in males. And in females, but not males, ZnT3 KO mice exhibited great hippocampal BDNF mRNA expression than wild type mice. We conclude that, at least in naïve mice housed under standard laboratory conditions, elimination of vesicular zinc does not affect BDNF or TrkB protein levels.
Molecular mechanism of off-target effects in CRISPR-Cas9
Authors: Ricci Clarisse G. , Chen Janice S. , Miao Yinglong , Jinek Martin , Doudna Jennifer A. , McCammon J. Andrew , Palermo Giulia 
Published: September 2018

AbstractCRISPR-Cas9 is the state-of-the-art technology for editing and manipulating nucleic acids. However, the occurrence of off-target mutations can limit its applicability. Here, all-atom enhanced molecular dynamics (MD) simulations – using Gaussian accelerated MD (GaMD) – are used to decipher the mechanism of off-target binding at the molecular level. GaMD reveals that base pair mismatches in the target DNA at specific distal sites with respect to the Protospacer Adjacent Motif (PAM) induce an extended opening of the RNA:DNA heteroduplex, which leads to newly discovered interactions between the unwound nucleic acids and the protein counterpart. The conserved interactions between the target DNA strand and the L2 loop of the catalytic HNH domain constitute a “lock” effectively decreasing the conformational freedom of the HNH domain and its activation for cleavage. Remarkably, depending on their position at PAM distal sites, DNA mismatches leading to off-target cleavages are unable to “lock” the HNH domain, thereby identifying the ability to “lock” HNH as a key determinant. Consistently, off-target sequences hampering the catalysis have been shown to “trap” somehow the HNH domain in an inactive “conformational checkpoint” state (Dagdas et al. Sci Adv, 2017). As such, this mechanism identifies the molecular basis underlying off-target cleavages and contributes in clarifying a long-lasting open issue of the CRISPR-Cas9 function. It also poses the foundation for designing novel and more specific Cas9 variants, which could be obtained by magnifying the “locking” interactions between HNH and the target DNA in the presence of any incorrect off-target sequence, thus preventing undesired cleavages.
Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis
Authors: Graham Sarah E. , Nielsen Jonas B. , Zawistowski Matthew , Zhou Wei , Fritsche Lars G. , Gabrielsen Maiken E. , Skogholt Anne Heidi , Surakka Ida , Fermin Damian , Kheterpal Sachin , Brummett Chad M. , Lee Seunggeun , Kang Hyun Min , Abecasis Goncalo , Romundstad Solfrid , Hallan Stein , Sampson Matthew G. , Hveem Kristian , Willer Cristen J. 
Published: September 2018

AbstractChronic Kidney Disease (CKD) is a growing health burden currently affecting 10-15% of adults worldwide. Estimated glomerular filtration rate (eGFR) as a marker of kidney function is commonly used to diagnose CKD. Previous genome-wide association study (GWAS) meta-analyses of CKD and eGFR or related phenotypes have identified a number of variants associated with kidney function, but these only explain a fraction of the variability in kidney phenotypes attributed to genetic components. To extend these studies, we analyzed data from the Nord-Trøndelag Health Study (HUNT), which is more densely imputed than previous studies, and performed a GWAS meta-analysis of eGFR with publicly available summary statistics, more than doubling the sample size of previous meta-analyses. We identified 147 loci (53 novel loci) associated with eGFR, including genes involved in transcriptional regulation, kidney development, cellular signaling, metabolism, and solute transport. Moreover, genes at these loci show enriched expression in urogenital tissues and highlight gene sets known to play a role in kidney function. In addition, sex-stratified analysis identified three regions (prioritized genes:PPM1J, MCL1, andSLC47A1) with more significant effects in women than men. Using genetic risk scores constructed from these eGFR meta-analysis results, we show that associated variants are generally predictive of CKD but improve detection only modestly compared with other known clinical risk factors. Collectively, these results yield additional insight into the genetic factors underlying kidney function and progression to CKD.
Comprehensive evaluation of differential serodiagnosis between Zika and dengue viral infection
Authors: Chao Day-Yu , Whitney Matthew T. , Davis Brent S. , Medina Freddy A , Munoz Jorge L , Chang Gwong-Jen J. 
Published: September 2018

SummaryDiagnostic testing for Zika virus (ZIKV) or dengue virus (DENV) infection can be accomplished by a nucleic acid detection method; however, a negative result does not exclude infection due to the low virus titer during infection depending on the timing of sample collection. Therefore, a ZIKV- or DENV-specific serological assay is essential for the accurate diagnosis of patients and to prevent potential severe health outcomes. A retrospective study design with dual approaches of collecting human serum samples for testing was developed. All serum samples were extensively evaluated by using both non-infectious virus-like particles (VLPs) and soluble non-structural protein 1 (NS1) in the standard immunoglobulin M (IgM) antibody-capture enzyme-linked immunosorbent assay (MAC-ELISA). Both VLP- and NS1-MAC-ELISAs were found to have similar sensitivity for detecting anti-premembrane/envelope and NS1 antibodies from ZIKV-infected patient sera. Group cross reactive (GR)-antibody-ablated homologous fusion peptide-mutated (FP)-VLPs consistently showed higher P/N values than homologous wild-type VLPs. Therefore, FP-VLPs were used to develop the algorithm for differentiating ZIKV from DENV infection. Overall, the sensitivity and specificity of the FP-VLP-MAC-ELISA and the NS1-MAC-ELISA were each higher than 80% with no statistical significance. A novel approach to differentiate ZIKV from DENV infection serologically has been developed. The accuracy can reach up to 95% when combining both VLP and NS1 assays. In comparison to current guidelines using neutralization tests to measure ZIKV antibody, this approach can facilitate laboratory screening for ZIKV infection, especially in regions where DENV infection is endemic and capacity for neutralization testing does not exist.
Consensus outlier detection in survival analysis using the rank product test
Authors: Carrasquinha Eunice , Veríssimo André , Vinga Susana 
Published: September 2018

AbstractSurvival analysis is a well known technique in the medical field. The identification of individuals whose survival time is too short or to long given their profile, assumes great importance for the detection of new prognostic factors. The study of these outlying observations have gained increasing relevancy with the availability of high-throughput molecular and clinical data for large cohorts of patients. Several methods for outlier detection in survival data have been proposed, which include the analysis of the residuals, the measurement of the concordance c-index, and methods based on quantile regression for censored data. However, different results are obtained depending on the type of method used. In order to solve the disparity of results we proposed to apply the Rank Product test. A simulated dataset, and two clinical datasets were used to illustrate our proposed consensus outlier detection method, one from myeloma disease and the other from The Cancer Genome Atlas (TCGA) ovarian cancer. Finally, the Rank Product with multiple testing corrections was performed in order to identify which observations have the highest rank amongst the methods considered. Our results illustrate the potential of this consensus approach for the automated retrieval of outliers and also the identification of biomarkers associated with survival in large datasets.
Red and black: A β-carotene-binding protein carrying a red pigment regulates body-color transition in locusts
Authors: Yang Meiling , Wang Yanli , Liu Qing , Liu Zhikang , Jiang Feng , Wang Huimin , Guo Xiaojiao , Zhang Jianzhen , Kang Le 
Published: September 2018

AbstractChanges of body color have important effects for animals in adapting to variable environments. The migratory locust exhibits body color polyphenism between solitary and gregarious individuals, with the former displaying a uniform green coloration and the latter having a prominent pattern of black dorsal and brown ventral surface. However, the molecular mechanism underlying the density-dependent body color changes of conspecific locusts remain largely unknown. Here, we found that up regulation of β-carotene-binding protein promotes the accumulation of red pigment, which added to the green color palette present in solitary locusts changes it from green to black, and that down regulation of this protein led to the reverse, changing the color of gregarious locusts from black to green. Our results provide insight that color changes of locusts are dependent on variation in the red β-carotene pigment binding to βCBP. This finding of animal coloration corresponds with trichromatic theory of color vision.