bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benefits of improved air quality on aging lungs – Impacts of genetics and obesity
Authors: Hüls Anke , Sugiri Dorothea , Abramson Michael J , Hoffmann Barbara , Schwender Holger , Ickstadt Katja , Krämer Ursula , Schikowski Tamara 
Published: January 2019

AbstractIntroductionThe beneficial effect of improving air quality on lung function in the elderly remains unclear. We examined associations between decline in air pollutants and lung function and effect modifications by genetics and BMI in elderly German women.MethodsData were analysed from the prospective SALIA cohort study (N=601). Spirometry was conducted at baseline (1985-1994; 55 years), in 2007-2010 and in 2012-2013. Air pollution concentrations at home addresses were determined for each time point using land-use regression models. GLI z-scores were calculated. Weighted genetic risk scores (GRS) were determined from lung function-related risk alleles and used to investigate interactions with improved air quality. Adjusted linear mixed models were fitted.ResultsAir pollution levels decreased substantially during the study period. Reduction of air pollution was associated with an increase of z-scores for FEV1 and FEV1/FVC. For a decrease of 10 μg/m3 in NO2, the z-score for FEV1 increased by 0.14 (95%CI: 0.01; 0.26). However, with an increasing number of lung function-related risk alleles, the benefit from improved air quality decreased (GRSxNO2-interaction:p=0.029). Interactions with BMI were not significant.ConclusionsReduction of air pollution is associated with a relative improvement of lung function in elderly women, but also depends on their genetic make-up.
Effects of Standing on Spinal Alignment and Lumbar Intervertebral Discs in Young, Healthy Individuals Determined by Positional Magnetic Resonance Imaging
Authors: Weber Christian I. , Hwang Ching-Ting , Dillen Linda R. Van , Tang Simon Y. 
Published: January 2019

AbstractTraditional diagnostic imaging of the spine is performed in supine, a relatively unloaded position. However, the spine is subjected to complex loading environments in daily activities such as standing. Therefore, we seek to quantify the changes from supine to standing in the spines of young, healthy individuals in standing using a positional MRI system. This is an observational study that examined the changes in the spine and individual intervertebral discs (IVDs) during supine and standing of forty healthy participants (19 males / 21 females) without a history of low back pain. The regional lumbar spinal alignment was measured by the sagittal Cobb angle. Segmental IVD measurements included the segmental Cobb angle, anterior to posterior height (A/P) ratio, and IVD width measured at each L1/L2 - L5/S1 levels. The intra-observer intra-class correlation (ICC) consistency model showed values for measurements ranged from 0.76-0.98. The inter-observer ICC values ranged from 0.68-0.99. The Cobb angle decreased in standing. The L5/S1 segmental Cobb angle decreased in standing. The L2/L3 and L3/L4 A/P ratios increased and the L5/S1 A/P ratio decreased in standing. No differences in IVD width were observed from supine to standing. This study examined the regional lumbar spinal alignment and segmental IVD changes from supine to standing in young, healthy individuals without LBP using pMRI. In developing and validating these measurements, we have also established the normative data for healthy, asymptomatic population that could be useful for other investigations examining how individuals with spinal or IVD pathologies may adapt between supine and standing.
Enteropathogen seroepidemiology among children in low-resource settings
Authors: Arnold Benjamin F. , Martin Diana L. , Juma Jane , Mkocha Harran , Ochieng John B. , Cooley Gretchen M. , Omore Richard , Goodhew E. Brook , Morris Jamae F. , Costantini Veronica , Vinjé Jan , Lammie Patrick J. , Priest Jeffrey W. 
Published: January 2019

AbstractLittle is known about enteropathogen seroepidemiology among children in low-resource settings. We measured serological IgG response to eight enteropathogens (Giardia intestinalis, Cryptosporidium parvum, Entamoeba histolytica, Salmonella enterica, enterotoxigenicEscherichia coli, Vibrio cholerae, Campylobacter jejuni, norovirus) using multiplex bead assays in cohorts from Haiti, Kenya, and Tanzania. By age 2 years, most children had evidence of exposure by IgG response to the pathogens studied. We discovered a shift in IgG distributions for many pathogens as children age, caused by boosting and waning from repeated exposures, which complicates interpretation of seroprevalence among older children. Longitudinal profiles revealed important variation in enteropathogen IgG response above seropositivity cutoffs, underscoring the importance of longitudinal designs to estimate seroincidence rates as a measure of force of infection. In longitudinal cohorts there was a linear relationship between seroprevalence and prospective seroincidence rates, suggesting the two measures provide similar information about variation in pathogen transmission.
Individual differences in the effects of priors on perception: a multi-paradigm approach
Authors: Tulver Kadi , Aru Jaan , Rutiku Renate , Bachmann Talis 
Published: January 2019

AbstractThe present study investigated individual differences in how much subjects rely on prior information, such as expectations or knowledge, when faced with perceptual ambiguity. The behavioural performance of forty-four participants was measured on four different visual paradigms (Mooney face recognition, illusory contours, blur detection and representational momentum) in which priors have been shown to affect perception. In addition, questionnaires were used to measure autistic and schizotypal traits in the non-clinical population. We hypothesized that someone who in the face of ambiguous or noisy perceptual input relies heavily on priors, would exhibit this tendency across a variety of tasks. This general pattern would then be reflected in high pairwise correlations between the behavioural measures and an emerging common factor. On the contrary, our results imply that there is no single factor that explains the individual differences present in the aforementioned tasks, as further evidenced by the overall lack of robust correlations between the separate paradigms. Instead, a two-factor structure reflecting differences in the hierarchy of perceptual processing was the best fit for explaining the individual variance in these tasks. This lends support to the notion that mechanisms underlying the effects of priors likely originate from several independent sources and that it is important to consider the role of specific tasks and stimuli more carefully when reporting effects of priors on perception.
The KZFP/KAP1 system controls transposable elements-embedded regulatory sequences in adult T cells
Authors: Marzetta Flavia , Simó-Riudalbas Laia , Duc Julien , Planet Evarist , Verp Sonia , Turelli Priscilla , Trono Didier 
Published: January 2019

ABSTRACTTransposable elements-embedded regulatory sequences (TEeRS) are subjected to early embryonic repression through sequence-specific recruitment of KRAB zinc finger proteins (KZFPs), their cofactor KAP1/TRIM28 and associated chromatin modifiers. This modulates the TEeRS-mediated regulation of gene expression in embryonic stem cells (ESCs) and leads to DNA methylation-induced silencing. However, KZFPs are broadly expressed in adult tissues, suggesting that they control TEeRS throughout life. Confirming this hypothesis, we reveal here that the KZFP/KAP1 system exerts a highly dynamic control of TEeRS in adult human CD4+ T lymphocytes. First, we observed that in these cells many TEs are still bound by KAP1, the recruitment of which is dynamically regulated upon T cell receptor stimulation. Second, we found that KAP1 depletion induces broad transcriptional alterations in T cells, with de-repression of TE-based regulatory elements leading to the illegitimate activation of nearby genes. Finally, we show that the tissue-restricted expression of KZFPs correlates with KAP1-mediated lineage-specific chromatin signatures and transcriptional repression. These data support a model where TE-targeting KZFPs and KAP1 are important regulators of gene expression in adult human cells.
Acute Myeloid Leukemia Driven by the CALM-AF10 Fusion Gene is Dependent on BMI1
Authors: Barbosa Karina , Ghosh Anwesha , Deshpande Anagha , Chen Bo-Rui , Sun Younguk , Weetall Marla , Armstrong Scott A. , Bohlander Stefan K. , Deshpande Aniruddha J. 
Published: January 2019

ABSTRACTA subset of acute myeloid and lymphoid leukemia cases harbor a t(10;11)(p13;q14) translocation resulting in the CALM-AF10 fusion gene. Standard chemotherapeutic strategies are often ineffective in treating patients with CALM-AF10 fusions. Hence, there is an urgent need to identify molecular pathways dysregulated in CALM-AF10-positive leukemias which may lay the foundation for novel targeted therapies. Here we demonstrate that the Polycomb Repressive Complex 1 geneBMI1is consistently overexpressed in adult and pediatric CALM-AF10-positive leukemias. We demonstrate that geneticBmi1depletion abrogates CALM-AF10-mediated transformation of murine hematopoietic stem and progenitor cells (HSPCs). Furthermore, CALM-AF10-positive murine and human AML cells are profoundly sensitive to the small-molecule BMI1 inhibitor PTC209 as well as to PTC596, a compound in clinical development that has been shown to result in downstream degradation of BMI1 protein. PTC-596 significantly prolongs survival of mice injected with a human CALM-AF10 cell line in a xenograft assay. In summary, these results validate BMI1 as abonafidecandidate for therapeutic targeting in AML with CALM-AF10 rearrangements.
Distinct genetic signatures of cortical and subcortical regions associated with human memory
Authors: Tan Pin Kwang , Ananyev Egor , Hsieh Po-Jang (Brown) 
Published: January 2019

ABSTRACTDespite the discovery of gene variants linked to memory performance, understanding the genetic basis of human memory remains a challenge. Here, we devised a framework combining human transcriptome data and a functional neuroimaging map to uncover the genetic signatures of memory in functionally-defined cortical and subcortical memory regions. Results were validated with animal literature and our framework proved to be highly effective and specific to the targeted cognitive function versus a control function. Genes preferentially expressed in cortical memory regions are linked to associative learning and ribosome biogenesis. Genes expressed in subcortical memory regions are associated with synaptic signaling and epigenetic processes. Cortical and subcortical regions share a number of memory-related biological processes and genes, e.g. translational initiation and GRIN1. Thus, cortical and subcortical memory regions exhibit distinct genetic signatures that potentially reflect functional differences in health and disease, and propose gene candidates for the targeted treatment of memory disorders.
Landscape-scale simulations as a tool in multi-criteria decision making for agri-environment schemes
Authors: Topping Chris J. , Dalby Lars , Valdez Jose W. 
Published: January 2019

AbstractIncreasing concerns over the environmental impacts of agriculture in Europe has led to the introduction of agri-environment schemes (AES) to help mitigate biodiversity loss. However, effectiveness of AES has been mixed and only partially successful in achieving desired outcomes. To improve effectiveness and reduce high costs, multi-criteria decision analysis (MCDA) can help support decision-making and determine the most effective management action. Although MCDA has great potential for evaluating policy measures, it rarely considers the context-dependency of species responses to management practices across different landscapes. Landscape simulations can, therefore, be valuable for reducing the uncertainties when predicting the consequences of management actions. A potential suitable simulation system is the Animal, Landscape, and Man Simulation System (ALMaSS), a mechanistic simulation with can improve MCDA with the automatic integration of a species ecology and behaviour and landscape context. The aim of this study was to demonstrate the effectiveness of ALMaSS in evaluating AES management practices across different landscapes and estimate their ability to achieve the proposed conservation outcomes of three typical species of conservation interest. In this study, the effect of a particular management strategy on a species was dependent on the landscape context, in our case, a combination of landscape structure and the type and distribution of farms, and varied depending on the metrics being measured. Although we did not aim to make recommendations of particular management strategies, we demonstrate how simulations can be used for MCDA to select between management strategies with different costs. Despite the complexity of ALMaSS models, the simulation results provided are easy to interpret. Landscape simulations, such as ALMaSS, can be an important tool in multi-criteria decision making by simulating a wide range of managements and contexts and provide supporting information for filtering management options based on specific conservation goals.
A new Image Segmentation Algorithm with Applications in Confocal Microscopy Analysis
Authors: Sánchez-Aragón M. , Casares F. 
Published: January 2019

AbstractGene regulatory networks (GRNs) represent the molecular interactions that govern the behavior of cells in tissues during development. The building and analysis of GRNs require quantitative information on gene expression from tissues. Laser Scanning Confocal Microscopy (LSCM) is commonly used to obtain such information, where immunofluorescence signal can be used as a correlate of gene expression or protein levels. However, a critical step for the extraction of this information is the segmentation of LSCM digital images. Popular segmentation algorithms are frequently based on watershed methods. Here we present an algorithm for the 3D segmentation ofnucleifrom LSCM (x,y,z) image stacks based on regional merging and graph contractions. This algorithm outperforms watershed methods, especially when the density of images along the z-axis is low and there is a high nuclear signal crowding. In addition, it reduces the parameterization since no filter is needed in order to prevent signal noise side effects (e.g. oversegmentation). Based on this algorithm, we developed an application (iFLIC, immunoFLuorescence Imaging Cytometry tool) for the Java Virtual Machine (JVM). The application supports basic operations for reading, writing and filtering 8-bit depth multicolor TIFF image formats, including indexed file directories (IFD), which are provided by the Java Advanced Imaging (JAI) library. It also provides with basic 3D-rendering and ROI specification that make extensive use of the Java3D library. iFLIC is also a plugin based application powered by the Java Plugin Platform (JPF), so each specific operation is declared as a unique command associated to one plugin and linked to a common interface. Results from segmentation can be exported both as TIFF images and a descriptive file format (iFLIC format)
Rapidly processed stool swabs approximate stool microbiota profiles
Authors: Bokulich Nicholas A. , Maldonado Juan , Kang Dae-Wook , Krajmalnik-Brown Rosa , Caporaso J. Gregory 
Published: January 2019

AbstractStudies of the intestinal microbiome commonly utilize stool samples to measure microbial composition in the distal gut. However, collection of stool can be difficult from some subjects under certain experimental conditions. In this study we validate the use of swabs of fecal matter to approximate measurements of microbiota in stool using 16S rRNA gene Illumina amplicon sequencing, and evaluate the effects of shipping time at ambient temperatures on accuracy. Results indicate that swab samples reliably replicate stool microbiota bacterial composition, alpha diversity, and beta diversity when swabs are processed quickly (< 2 days), but sample quality quickly degrades after this period, accompanied by increased abundances of Enterobacteriaceae. Fresh swabs appear to be a viable alternative to stool sampling when standard collection methods are challenging, but extended exposure to ambient temperatures prior to processing threatens sample integrity.
Widespread selection for high and low secondary structure in coding sequences across all domains of life
Authors: Gebert Daniel , Jehn Julia , Rosenkranz David 
Published: January 2019

AbstractCodon composition, GC-content and local RNA secondary structures can have a profound effect on gene expression and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that in some cases selection favors more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and if this is a universal phenomenon in nature.We searched for signs of structural selection in a global manner, analyzing a set of one million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed software PACKEIS. We show that codon composition and amino acid identity are main determinants of RNA secondary structure. In addition, we show that the arrangement of synonymous codons within coding sequences is non-random, yielding extremely high, but also extremely low secondary structures significantly more often than expected by chance.Together, we demonstrate that selection for high and low secondary structure is a widespread phenomenon. Our results provide another line of evidence that synonymous mutations are less neutral than commonly thought, which is of importance for many evolutionary models.
Risks to pollinators from different land-use transitions: bee species’ responses to agricultural expansion show strong phylogenetic signal
Authors: Palma Adriana De , Kuhlmann Michael , Pearse William D. , Flynn Emma , Roberts Stuart P.M. , Potts Simon G. , Purvis Andy 
Published: January 2019

AbstractBee species worldwide are facing a future of further land-use change and intensification. Populations of closely-related species with similar ecological characteristics are likely to respond similarly to such pressures. Such phylogenetic signal in species’ responses could undermine the stability of pollination services in agricultural and natural systems. We use abundance data from a global compilation of bee assemblages in different land uses to assess the sensitivity of 573 bee species to agricultural expansion, intensification and urbanization; and combine the results with the Bee Tree of Life to assess phylogenetic signal. In addition, we assess whether variation in species’ sensitivity to land-use change is better explained by phylogenetic or available functional trait differences. Bee species show strong phylogenetic signal in sensitivity to agricultural land expansion but only a weak signal in sensitivity to agricultural intensification and urbanisation. Sensitivities were usually best explained by a combination of functional and phylogenetic distances. This finding suggests that the commonly-recorded traits, despite being meaningful as functional response traits, do not capture all important determinants of bee species’ vulnerability or resistance. However, it also suggests that model-based predictions of the sensitivity of poorly known species may be sufficient to help guide conservation efforts.
Transcriptome analysis of the Molecular Mechanism underlying Immunity- and Reproduction trade-off in Locusta migratoria Infected by Micrococcus luteus
Authors: Wang Shaohua , Liu Xiaojun , Xia Zhiyong , Xie Guoqiang , Tang Bin , Wang Shigui 
Published: January 2019

AbstractImmune response and reproductive success are two of the main energy-consuming processes in living organisms. However, it is unclear which process is prioritized when both are required. Therefore, the present study was designed to examine this question using one of the world’s most destructive agricultural pests, the migratory locust Locusta migratoria. Transcripts from the ovaries and fat bodies of newly emerged locusts were analyzed, using RNA-seq based transcriptome and qualitative real-time PCR, at 4 h and 6 d after being infected with the gram-positive bacteria Microcroccus luteus, and changes in the main biological pathways involved in reproduction and immunization were analyzed using bioinformatics. At 4 h after infection, 348 and 133 transcripts were up- and down-regulated, respectively, whereas 5699 and 44 transcripts were up- and down-regulated, respectively, at 6 d after infection. Meanwhile, KEGG analysis indicated that vital pathways related with immunity and reproduction, such as Insulin resistance, FoxO signaling, Lysosome, mTOR signaling, and Toll-like receptor signaling pathways were up-regulated. Among the differentially expressed genes, 22 and 17 were related to immunity and reproduction, respectively, and the expression levels of PPO1 and antimicrobial peptide defensin 3 were increased (log2FC = 5.93 and 6.75, respectively), whereas those of VgA and VgB were reduced (log2FC = −17.82 and −18.13, respectively). These results indicated that that locusts allocate energy and resources to maintain their own survival by increasing immune response when dealing with both immune and reproductive processes. The present study provides the first report of expression levels for genes related with reproduction and immunity in locusts, thereby providing a reference for future studies, as well as theoretical guidance for investigations of locust control.
Global and regional white matter development in early childhood
Authors: Reynolds Jess E. , Grohs Melody N. , Dewey Deborah , Lebel Catherine 
Published: January 2019

AbstractWhite matter development continues throughout childhood and into early adulthood, but few studies have examined early childhood, and the specific trajectories and regional variation in this age range remain unclear. The aim of this study was to characterize developmental trajectories and sex differences of white matter in typically developing young children. Three hundred and ninety-six diffusion tensor imaging datasets from 120 children (57 male) aged 2-8 years were analyzed using tractography. Fractional anisotropy (FA) increased and mean diffusivity (MD) decreased in all white matter tracts by 5-15% over the 6-year period, likely reflecting increases in myelination and axonal packing. Males showed steeper slopes in a number of brain areas. Overall, early childhood is associated with substantial development of all white matter and appears to be an important period for the development of occipital and limbic connections, which showed the largest changes. This study provides a detailed characterization of age-related white matter changes in early childhood, offering baseline data that can be used to understand cognitive and behavioural development, as well as to identify deviations from normal development in children with various diseases, disorders, or brain injuries.