bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal prenatal depression is associated with decreased placental expression of the imprinted gene PEG3
Authors: Janssen A. B. , Capron L. E. , O'Donnell K. , Tunster S. J. , Ramchandani P. G. , Heazell A. E. P. , Glover V. , John R. M. 
Published: August 2016

BackgroundMaternal prenatal stress during pregnancy is associated with fetal growth restriction and adverse neurodevelopmental outcomes, which may be mediated by impaired placental function. Imprinted genes control fetal growth, placental development, adult behaviour (including maternal behaviour) and placental lactogen production. This study examined whether maternal prenatal depression was associated with aberrant placental expression of the imprinted genes paternally expressed gene 3 (PEG3), paternally expressed gene 10 (PEG10), pleckstrin homology-like domain family a member 2 (PHLDA2) and cyclin-dependent kinase inhibitor 1C (CDKN1C), and resulting impaired placental human placental lactogen (hPL) expression.MethodA diagnosis of depression during pregnancy was recorded from Manchester cohort participants’ medical notes (n = 75). Queen Charlotte's (n = 40) and My Baby and Me study (MBAM) (n = 81) cohort participants completed the Edinburgh Postnatal Depression Scale self-rating psychometric questionnaire. Villous trophoblast tissue samples were analysed for gene expression.ResultsIn a pilot study, diagnosed depression during pregnancy was associated with a significant reduction in placental PEG3 expression (41%, p = 0.02). In two further independent cohorts, the Queen Charlotte's and MBAM cohorts, placental PEG3 expression was also inversely associated with maternal depression scores, an association that was significant in male but not female placentas. Finally, hPL expression was significantly decreased in women with clinically diagnosed depression (44%, p < 0.05) and in those with high depression scores (31% and 21%, respectively).ConclusionsThis study provides the first evidence that maternal prenatal depression is associated with changes in the placental expression of PEG3, co-incident with decreased expression of hPL. This aberrant placental gene expression could provide a possible mechanistic explanation for the co-occurrence of maternal depression, fetal growth restriction, impaired maternal behaviour and poorer offspring outcomes.
Changes in functional connectivity of the amygdala during cognitive reappraisal predict symptom reduction during trauma-focused cognitive–behavioral therapy among adolescent girls with post-traumatic stress disorder
Authors: Cisler J. M. , Sigel B. A. , Steele J. S. , Smitherman S. , Vanderzee K. , Pemberton J. , Kramer T. L. , Kilts C. D. 
Published: August 2016

BackgroundWhile trauma-focused cognitive–behavioral therapy (TF-CBT) is the ‘gold standard’ treatment for pediatric post-traumatic stress disorder (PTSD), little is known about the neural mechanisms by which TF-CBT produces clinical benefit. Here, we test the hypothesis that PTSD symptom reduction during TF-CBT among adolescent girls with PTSD is associated with changes in patterns of brain functional connectivity (FC) with the amygdala during cognitive reappraisal.MethodAdolescent girls with PTSD related to physical or sexual assault (n = 34) were enrolled in TF-CBT, delivered in an approximately 12-session format, in an open trial. Before and after treatment, they were engaged in a cognitive reappraisal task, probing neural mechanisms of explicit emotion regulation, during 3 T functional magnetic resonance imaging.ResultsAmong adolescent girls completing TF-CBT with usable pre- and post-treatment scans (n = 20), improvements in self-reported emotion from pre- to post-treatment were positively related to improvements in PTSD symptoms. Adolescent girls with greater post-treatment symptom reduction were also able to suppress amygdala–insula FC while re-appraising, which was not evident in girls with less symptom reduction. Pre- to post-treatment changes in right amygdala to left insula FC that scaled with PTSD symptom reduction also scaled with improvements in emotion regulation.ConclusionsThese preliminary results suggest the neurocircuitry mechanisms through which TF-CBT produces clinical outcomes, providing putative brain targets for augmenting TF-CBT response.
A role for flies (Diptera) in the transmission ofCampylobacterto broilers?
Authors: ROYDEN A. , WEDLEY A. , MERGA J. Y. , RUSHTON S. , HALD B. , HUMPHREY T. , WILLIAMS N. J. 
Published: August 2016

SUMMARYCampylobacteris the leading cause of bacterial diarrhoeal disease worldwide, with raw and undercooked poultry meat and products the primary source of infection. Colonization of broiler chicken flocks withCampylobacterhas proved difficult to prevent, even with high levels of biosecurity. Dipteran flies are proven carriers ofCampylobacterand their ingress into broiler houses may contribute to its transmission to broiler chickens. However, this has not been investigated in the UK.Campylobacterwas cultured from 2195 flies collected from four UK broiler farms. Of flies cultured individually, 0·22% [2/902, 95% confidence interval (CI) 0–0·53] were positive by culture forCampylobacterspp. Additionally, 1293 flies were grouped by family and cultured in 127 batches: 4/127 (3·15%, 95% CI 0·11-6·19) from three broiler farms were positive forCampylobacter. Multilocus sequence typing of isolates demonstrated that the flies were carrying broiler-associated sequence types, responsible for human enteric illness. Malaise traps were used to survey the dipteran species diversity on study farms and also revealed up to 612 flies present around broiler-house ventilation inlets over a 2-h period. Therefore, despite the low prevalence ofCampylobactercultured from flies, the risk of transmission by this route may be high, particularly during summer when fly populations are greatest.
Systemic chromosome instability in Shugoshin-1 mice resulted in compromised glutathione pathway, activation of Wnt signaling and defects in immune system in the lung
Authors: Yamada H Y , Kumar G , Zhang Y , Rubin E , Lightfoot S , Dai W , Rao C V 
Published: August 2016

AbstractMitotic error-mediated chromosome instability (CIN) can lead to aneuploidy, chromothripsis, DNA damage and/or whole chromosome gain/loss. CIN may prompt rapid accumulation of mutations and genomic alterations. Thus, CIN can promote carcinogenesis. This CIN process results from a mutation in certain genes or environmental challenge such as smoking, and is highly prevalent in various cancers, including lung cancer. A better understanding of the effects of CIN on carcinogenesis will lead to novel methods for cancer prevention and treatment. Previously Shugoshin-1 (Sgo1−/+) mice, a transgenic mouse model of CIN, showed mild proneness to spontaneous lung and liver cancers. In this study, adoptive (T/B-cell based) immunity-deficient RAG1−/− Sgo1−/+ double mutant mice developed lung adenocarcinomas more aggressively than did Sgo1−/+ or RAG1−/− mice, suggesting immune system involvement in CIN-mediated lung carcinogenesis. To identify molecular causes of the lung adenocarcinoma, we used systems biology approach, comparative RNAseq, to RAG1−/− and RAG1−/− Sgo1−/+. The comparative RNAseq data and follow-up analyses in the lungs of naive Sgo1−/+ mice demonstrate that, (i) glutathione is depleted, making the tissue vulnerable to oxidative stress, (ii) spontaneous DNA damage is increased, (iii) oncogenic Wnt signaling is activated, (iv) both major branches of the immune system are weakened through misregulations in signal mediators such as CD80 and calreticulin and (v) the actin cytoskeleton is misregulated. Overall, the results show multi-faceted roles of CIN in lung carcinoma development in Sgo1−/+ mice. Our model presents various effects of CIN and will help to identify potential targets to prevent CIN-driven carcinogenesis in the lung.
Genome sequencing of a single tardigrade Hypsibius dujardini individual
Authors: Arakawa Kazuharu , Yoshida Yuki , Tomita Masaru 
Published: August 2016

AbstractTardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molecular studies of tardigrades are prone to contamination. To minimize the possibility of microbial contaminations and to obtain high-quality genomic information, we have developed an ultra-low input library sequencing protocol to enable the genome sequencing of a single tardigrade Hypsibius dujardini individual. Here, we describe the details of our sequencing data and the ultra-low input library preparation methodologies.
Mapping internal connectivity through human migration in malaria endemic countries
Authors: Sorichetta Alessandro , Bird Tom J. , Ruktanonchai Nick W. , zu Erbach-Schoenberg Elisabeth , Pezzulo Carla , Tejedor Natalia , Waldock Ian C. , Sadler Jason D. , Garcia Andres J. , Sedda Luigi , Tatem Andrew J. 
Published: August 2016

AbstractHuman mobility continues to increase in terms of volumes and reach, producing growing global connectivity. This connectivity hampers efforts to eliminate infectious diseases such as malaria through reintroductions of pathogens, and thus accounting for it becomes important in designing global, continental, regional, and national strategies. Recent works have shown that census-derived migration data provides a good proxy for internal connectivity, in terms of relative strengths of movement between administrative units, across temporal scales. To support global malaria eradication strategy efforts, here we describe the construction of an open access archive of estimated internal migration flows in endemic countries built through pooling of census microdata. These connectivity datasets, described here along with the approaches and methods used to create and validate them, are available both through the WorldPop website and the WorldPop Dataverse Repository.
Spatially-explicit models of global tree density
Authors: Glick Henry B. , Bettigole Charlie , Maynard Daniel S. , Covey Kristofer R. , Smith Jeffrey R. , Crowther Thomas W. 
Published: August 2016

AbstractRemote sensing and geographic analysis of woody vegetation provide means of evaluating the distribution of natural resources, patterns of biodiversity and ecosystem structure, and socio-economic drivers of resource utilization. While these methods bring geographic datasets with global coverage into our day-to-day analytic spheres, many of the studies that rely on these strategies do not capitalize on the extensive collection of existing field data. We present the methods and maps associated with the first spatially-explicit models of global tree density, which relied on over 420,000 forest inventory field plots from around the world. This research is the result of a collaborative effort engaging over 20 scientists and institutions, and capitalizes on an array of analytical strategies. Our spatial data products offer precise estimates of the number of trees at global and biome scales, but should not be used for local-level estimation. At larger scales, these datasets can contribute valuable insight into resource management, ecological modelling efforts, and the quantification of ecosystem services.
Functional impact of splice isoform diversity in individual cells
Authors: Yap Karen , Makeyev Eugene V. 
Published: August 2016

Alternative pre-mRNA splicing provides an effective means for expanding coding capacity of eukaryotic genomes. Recent studies suggest that co-expression of different splice isoforms may increase diversity of RNAs and proteins at a single-cell level. A pertinent question in the field is whether such co-expression is biologically meaningful or, rather, represents insufficiently stringent splicing regulation. Here we argue that isoform co-expression may produce functional outcomes that are difficult and sometimes impossible to achieve using other regulation strategies. Far from being a ‘splicing noise’, co-expression is often established through co-ordinated activity of specific cis-elements and trans-acting factors. Further work in this area may uncover new biological functions of alternative splicing (AS) and generate important insights into mechanisms allowing different cell types to attain their unique molecular identities.
Sparse polynomial approximation of parametric elliptic PDEs.
Part II: lognormal coefficients
Authors: Bachmayr Markus , Cohen Albert , DeVore Ronald , Migliorati Giovanni 
Published: August 2016

We consider the linear elliptic equation −
div(a∇u) = f on
some bounded domain D, where a has the form a = exp(b)
with b a
random function defined as b(y) = ∑ j ≥
1yjψj
where y =
(yj) ∈ ℝNare i.i.d. standard scalar Gaussian variables and
(ψj)j ≥
1 is a given sequence of functions in L∞(D). We study the
summability properties of Hermite-type expansions of the solution map
y → u(y) ∈ V := H01(D)

, that is, expansions of the form u(y) = ∑
ν ∈
ℱuνHν(y),
where
Hν(y) = ∏j≥1Hνj(yj)

are the tensorized Hermite polynomials indexed by the
set ℱ of finitely supported
sequences of nonnegative integers. Previous results [V.H. Hoang and C. Schwab,
M3AS 24 (2014) 797−826] have demonstrated that, for any
0 <p ≤
1, the ℓp summability of the
sequence (j ∥ψj ∥L∞)j ≥
1 implies ℓp summability of the
sequence (∥ uν∥V)ν ∈ ℱ.
Such results ensure convergence rates n− s with
s = (1/p)−(1/2)
of polynomial approximations obtained by best
n-term
truncation of Hermite series, where the error is measured in the mean-square sense, that
is, in L2(ℝN,V,γ) ,
where γ is
the infinite-dimensional Gaussian measure. In this paper we considerably improve these
results by providing sufficient conditions for the ℓp summability of
(∥uν∥V)ν ∈ ℱ
expressed in terms of the pointwise summability properties of the sequence (|ψj|)j ≥ 1. This leads to a refined
analysis which takes into account the amount of overlap between the supports of the
ψj. For instance, in
the case of disjoint supports, our results imply that, for all 0 <p< 2 the
ℓp summability of
(∥uν∥V)ν ∈
ℱfollows from the weaker assumption that (∥ψj∥L∞)j ≥
1is ℓq summable for q := 2p/(2−p)

. In the case of arbitrary supports, our results imply
that the ℓp summability of
(∥uν∥V)ν ∈ ℱ
follows from the ℓp summability of
(jβ∥ψj∥L∞)j ≥
1 for some β>1/2

, which still represents an improvement over the
condition in [V.H. Hoang and C. Schwab, M3AS 24 (2014)
797−826]. We also explore
intermediate cases of functions with local yet overlapping supports, such as wavelet
bases. One interesting observation following from our analysis is that for certain
relevant examples, the use of the Karhunen−Loève basis for the representation of b might be suboptimal
compared to other representations, in terms of the resulting summability properties of
(∥uν∥V)ν ∈ ℱ.
While we focus on the diffusion equation, our analysis applies to other type of linear
PDEs with similar lognormal dependence in the coefficients.
Plant Cysteine Oxidases are Dioxygenases that Directly Enable Arginyl Transferase-Catalyzed Arginylation of N-End Rule Targets
Authors: White Mark D. , Klecker Maria , Hopkinson Richard J. , Weits Daan , Mueller Carolin , Naumann Christin , O’Neill Rebecca , Wickens James , Yang Jiayu , Brooks-Bartlett Jonathan C. , Garman Elspeth F. , Grossman Tom N. , Dissmeyer Nico , Flashman Emily 
Published: August 2016

AbstractCrop yield loss due to flooding is a threat to food security. Submergence-induced hypoxia in plants results in stabilisation of group VII ETHYLENE RESPONSE FACTORS (ERF-VIIs), which aid survival under these adverse conditions. ERF-VII stability is controlled by the N-end rule pathway, which proposes that ERF-VII N-terminal cysteine oxidation in normoxia enables arginylation followed by proteasomal degradation. The PLANT CYSTEINE OXIDASEs (PCOs) have been identified as catalysts of this oxidation. ERF-VII stabilisation in hypoxia presumably arises from reduced PCO activity. We directly demonstrate that PCO dioxygenase activity produces Cys-sulfinic acid at the N-terminus of an ERF-VII peptide, which then undergoes efficient arginylation by an arginyl transferase (ATE1). This is the first molecular evidence showing N-terminal Cys-sulfinic acid formation and arginylation by N-end rule pathway components, and the first ATE1 substrate in plants. The PCOs and ATE1 may be viable intervention targets to stabilise N-end rule substrates, including ERF-VIIs to enhance submergence tolerance in agronomy.
Emergent rules for codon choice elucidated by editing rare arginine codons inEscherichia coli
Authors: Napolitano Michael G. , Landon Matthieu , Gregg Christopher J. , Lajoie Marc J. , Govindarajan Lakshmi N. , Mosberg Joshua A. , Kuznetsov Gleb , Goodman Daniel B. , Vargas-Rodriguez Oscar , Isaacs Farren J. , Söll Dieter , Church George M. 
Published: August 2016

AbstractThe degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as non-coding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain ofEscherichia coliwith all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU, but the remaining thirteen “recalcitrant” AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multi-dimensional “safe replacement zone” (SRZ) within which alternative codons are more likely to be viable. To further evaluate synonymous and non-synonymous alternatives to essential AGRs, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild type allele, allowing us to exhaustively evaluate the fitness impact of all 64 codon alternatives. Using this method, we confirmed relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes.Significance StatementThis work presents the genome-wide replacement of all rare AGR arginine codons in the essential genes ofEscherichia coliwith synonymous CGN alternatives. Synonymous codon substitutions can lethally impact non-coding function by disrupting mRNA secondary structure and ribosomal binding site-like motifs. Here we quantitatively define the range of tolerable deviation in these metrics and use this relationship to provide critical insight into codon choice in recoded genomes. This work demonstrates that genome-wide removal of AGR is likely to be possible, and provides a framework for designing genomes with radically altered genetic codes.
Mapping eQTL by leveraging multiple tissues and DNA methylation
Authors: Acharya Chaitanya R. , Owzar Kouros , Allen Andrew S. 
Published: August 2016

AbstractBackgroundDNA methylation is an important tissue-specific epigenetic event that influences transcriptional regulation of gene expression. Differentially methylated CpG sites may act as mediators between genetic variation and gene expression, and this relationship can be exploited while mapping multi-tissue expression quantitative trait loci (eQTL). Current multi-tissue eQTL mapping techniques are limited to only exploiting gene expression patterns across multiple tissues either in a joint tissue or tissue-by-tissue frameworks. We present a new statistical approach that enables us to model the effect of germ-line variation on tissue-specific gene expression in the presence of effects due to DNA methylation.ResultsOur method efficiently models genetic and epigenetic variation to identify genomic regions of interest containing combinations of mRNA transcripts, CpG sites, and SNPs by jointly testing for genotypic effect and higher order interaction effects between genotype, methylation and tissues. We demonstrate using Monte Carlo simulations that our approach, in the presence of both genetic and DNA methylation effects, gives an improved performance (in terms of statistical power) to detect eQTLs over the current eQTL mapping approaches. When applied to an array-based dataset from 150 neuropathologically normal adult human brains, our method identifies eQTLs that were undetected using standard tissue-by-tissue or joint tissue eQTL mapping techniques. As an example, our method identifies eQTLs in a BAX inhibiting gene (TMBIM1), which may have a role in the pathogenesis of Alzheimer disease.ConclusionsOur score test-based approach does not need parameter estimation under the alternative hypothesis. As a result, our model parameters are estimated only once for each mRNA - CpG pair. Our model specifically studies the effects of non-coding regions of DNA (in this case, CpG sites) on mapping eQTLs. However, we can easily model micro-RNAs instead of CpG sites to study the effects of post-transcriptional events in mapping eQTL. Our model’s flexible framework also allows us to investigate other genomic events such as alternative gene splicing by extending our model to include gene isoform-specific data.
Influences on New Jersey public library budget requests
Authors: Beckett Edith K. 
Published: August 2016

Purpose
This research study aims to examine influences on the public library funding decision from the perspectives of New Jersey mayors and public library directors.

Design/methodology/approach
Content analysis was used to explore statements of 84 public library directors and 45 mayors about what was most/least effective in a recent library budget request.

Findings
Although they may differ on the relative importance of a specific concept, the public library directors and mayors in this study have high levels of agreement about what information is important in the budget decision process.

Research limitations/implications
The primary limitations of the findings of this study stem from the reliability of self-reported data and the low response rates. While the researcher believes that the findings and conclusions are valid for the survey respondents, it is less certain that they are valid for all public libraries in New Jersey, and it is not recommended that the conclusions be extended to public libraries outside of the state which differ in state mandates and other circumstances.

Practical implications
Understanding more about the factors that can influence library funding decisions provides insight into the very complex public library funding process and may help public library directors and mayors engage in mutually satisfactory budget negotiations.

Originality/value
This study contributes to the Library and Information Science research literature on library budgets by examining influences on the public library funding decision, specifically adding the perspectives of mayors and public library directors on a recent budget cycle.