Morphological awareness and reading comprehension: Examining mediating factors.

PubMed

Levesque, Kyle C; Kieffer, Michael J; Deacon, S Hélène

2017-08-01

The relation between morphological awareness-defined as the awareness of and ability to manipulate the smallest units of meaning in language-and reading comprehension remains in need of specification. In this study, we evaluated four potential intervening variables through which morphological awareness may contribute indirectly to reading comprehension. We assessed word reading and vocabulary as well as children's ability to read and analyze the meaning of morphologically complex words (morphological decoding and morphological analysis, respectively). Controls of phonological awareness and nonverbal ability were included in the model. Participants were 221 English-speaking children in Grade 3. Multivariate path analyses revealed evidence of two indirect relations and one direct relation between morphological awareness and reading comprehension. In the first indirect path, morphological awareness contributed to morphological decoding, which then influenced word reading and finally reading comprehension. In a second indirect path, morphological awareness contributed to morphological analysis, which contributed to reading comprehension. Finally, in a direct path, morphological awareness contributed to reading comprehension beyond all other variables. These findings inform as to the potential mechanisms underlying the relation between morphological awareness and reading comprehension in children. Copyright © 2017 Elsevier Inc. All rights reserved.

Assertive Behavior and Cognitive Performance in Preschool Children

ERIC Educational Resources Information Center

Dorman, Lynn

1973-01-01

Assertive behaviors were related to each other and to intelligence test scores. An item analysis revealed that more assertive children did better on certain intelligence test items: comprehension, verbal, and discrimination. (ST)

Quantitative Proteomics Identifies Activation of Hallmark Pathways of Cancer in Patient Melanoma.

PubMed

Byrum, Stephanie D; Larson, Signe K; Avaritt, Nathan L; Moreland, Linley E; Mackintosh, Samuel G; Cheung, Wang L; Tackett, Alan J

2013-03-01

Molecular pathways regulating melanoma initiation and progression are potential targets of therapeutic development for this aggressive cancer. Identification and molecular analysis of these pathways in patients has been primarily restricted to targeted studies on individual proteins. Here, we report the most comprehensive analysis of formalin-fixed paraffin-embedded human melanoma tissues using quantitative proteomics. From 61 patient samples, we identified 171 proteins varying in abundance among benign nevi, primary melanoma, and metastatic melanoma. Seventy-three percent of these proteins were validated by immunohistochemistry staining of malignant melanoma tissues from the Human Protein Atlas database. Our results reveal that molecular pathways involved with tumor cell proliferation, motility, and apoptosis are mis-regulated in melanoma. These data provide the most comprehensive proteome resource on patient melanoma and reveal insight into the molecular mechanisms driving melanoma progression.

Rice Phospholipase A Superfamily: Organization, Phylogenetic and Expression Analysis during Abiotic Stresses and Development

PubMed Central

Singh, Amarjeet; Baranwal, Vinay; Shankar, Alka; Kanwar, Poonam; Ranjan, Rajeev; Yadav, Sandeep; Pandey, Amita; Kapoor, Sanjay; Pandey, Girdhar K.

2012-01-01

Background Phospholipase A (PLA) is an important group of enzymes responsible for phospholipid hydrolysis in lipid signaling. PLAs have been implicated in abiotic stress signaling and developmental events in various plants species. Genome-wide analysis of PLA superfamily has been carried out in dicot plant Arabidopsis. A comprehensive genome-wide analysis of PLAs has not been presented yet in crop plant rice. Methodology/Principal Findings A comprehensive bioinformatics analysis identified a total of 31 PLA encoding genes in the rice genome, which are divided into three classes; phospholipase A1 (PLA1), patatin like phospholipases (pPLA) and low molecular weight secretory phospholipase A2 (sPLA2) based on their sequences and phylogeny. A subset of 10 rice PLAs exhibited chromosomal duplication, emphasizing the role of duplication in the expansion of this gene family in rice. Microarray expression profiling revealed a number of PLA members expressing differentially and significantly under abiotic stresses and reproductive development. Comparative expression analysis with Arabidopsis PLAs revealed a high degree of functional conservation between the orthologs in two plant species, which also indicated the vital role of PLAs in stress signaling and plant development across different plant species. Moreover, sub-cellular localization of a few candidates suggests their differential localization and functional role in the lipid signaling. Conclusion/Significance The comprehensive analysis and expression profiling would provide a critical platform for the functional characterization of the candidate PLA genes in crop plants. PMID:22363522

Macro-fingerprint analysis-through-separation of licorice based on FT-IR and 2DCOS-IR

NASA Astrophysics Data System (ADS)

Wang, Yang; Wang, Ping; Xu, Changhua; Yang, Yan; Li, Jin; Chen, Tao; Li, Zheng; Cui, Weili; Zhou, Qun; Sun, Suqin; Li, Huifen

2014-07-01

In this paper, a step-by-step analysis-through-separation method under the navigation of multi-step IR macro-fingerprint (FT-IR integrated with second derivative IR (SD-IR) and 2DCOS-IR) was developed for comprehensively characterizing the hierarchical chemical fingerprints of licorice from entirety to single active components. Subsequently, the chemical profile variation rules of three parts (flavonoids, saponins and saccharides) in the separation process were holistically revealed and the number of matching peaks and correlation coefficients with standards of pure compounds was increasing along the extracting directions. The findings were supported by UPLC results and a verification experiment of aqueous separation process. It has been demonstrated that the developed multi-step IR macro-fingerprint analysis-through-separation approach could be a rapid, effective and integrated method not only for objectively providing comprehensive chemical characterization of licorice and all its separated parts, but also for rapidly revealing the global enrichment trend of the active components in licorice separation process.

Comprehensive NMR analysis of compositional changes of black garlic during thermal processing.

PubMed

Liang, Tingfu; Wei, Feifei; Lu, Yi; Kodani, Yoshinori; Nakada, Mitsuhiko; Miyakawa, Takuya; Tanokura, Masaru

2015-01-21

Black garlic is a processed food product obtained by subjecting whole raw garlic to thermal processing that causes chemical reactions, such as the Maillard reaction, which change the composition of the garlic. In this paper, we report a nuclear magnetic resonance (NMR)-based comprehensive analysis of raw garlic and black garlic extracts to determine the compositional changes resulting from thermal processing. (1)H NMR spectra with a detailed signal assignment showed that 38 components were altered by thermal processing of raw garlic. For example, the contents of 11 l-amino acids increased during the first step of thermal processing over 5 days and then decreased. Multivariate data analysis revealed changes in the contents of fructose, glucose, acetic acid, formic acid, pyroglutamic acid, cycloalliin, and 5-(hydroxymethyl)furfural (5-HMF). Our results provide comprehensive information on changes in NMR-detectable components during thermal processing of whole garlic.

Psycholinguistic Correlates of Progress in Literature of Students of Russian Vocational Training School

ERIC Educational Resources Information Center

Nuriakhmetov, Aidar

2012-01-01

The article describes psycholinguistic correlates of progress in literature, discovered on the basis of correlation analysis of grades, and results of several psychological and psycholinguistic tests were taken in the context of comprehensive psycholinguistic research based on one of Russian vocational training schools. Analysis revealed a list of…

How sensory-motor systems impact the neural organization for language: direct contrasts between spoken and signed language

PubMed Central

Emmorey, Karen; McCullough, Stephen; Mehta, Sonya; Grabowski, Thomas J.

2014-01-01

To investigate the impact of sensory-motor systems on the neural organization for language, we conducted an H215O-PET study of sign and spoken word production (picture-naming) and an fMRI study of sign and audio-visual spoken language comprehension (detection of a semantically anomalous sentence) with hearing bilinguals who are native users of American Sign Language (ASL) and English. Directly contrasting speech and sign production revealed greater activation in bilateral parietal cortex for signing, while speaking resulted in greater activation in bilateral superior temporal cortex (STC) and right frontal cortex, likely reflecting auditory feedback control. Surprisingly, the language production contrast revealed a relative increase in activation in bilateral occipital cortex for speaking. We speculate that greater activation in visual cortex for speaking may actually reflect cortical attenuation when signing, which functions to distinguish self-produced from externally generated visual input. Directly contrasting speech and sign comprehension revealed greater activation in bilateral STC for speech and greater activation in bilateral occipital-temporal cortex for sign. Sign comprehension, like sign production, engaged bilateral parietal cortex to a greater extent than spoken language. We hypothesize that posterior parietal activation in part reflects processing related to spatial classifier constructions in ASL and that anterior parietal activation may reflect covert imitation that functions as a predictive model during sign comprehension. The conjunction analysis for comprehension revealed that both speech and sign bilaterally engaged the inferior frontal gyrus (with more extensive activation on the left) and the superior temporal sulcus, suggesting an invariant bilateral perisylvian language system. We conclude that surface level differences between sign and spoken languages should not be dismissed and are critical for understanding the neurobiology of language. PMID:24904497

Time-resolved metabolomics reveals metabolic modulation in rice foliage

PubMed Central

Sato, Shigeru; Arita, Masanori; Soga, Tomoyoshi; Nishioka, Takaaki; Tomita, Masaru

2008-01-01

Background To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed. Results Using capillary electrophoresis mass spectrometry (CE-MS) and capillary electrophoresis diode-array detection (CE-DAD), we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica) at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM) allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N) metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks. Conclusion Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the underlying biochemical functions. The application of discrimination of unidentified metabolites and the identification of bottleneck enzymatic steps even to non-targeted comprehensive analysis promise to facilitate an understanding of large-scale interactions among components in biological systems. PMID:18564421

Comprehensive and integrative analysis identifies microRNA-106 as a novel non-invasive biomarker for detection of gastric cancer.

PubMed

Peng, Qiliang; Shen, Yi; Lin, Kaisu; Zou, Li; Shen, Yuntian; Zhu, Yaqun

2018-05-15

Recently, accumulating evidences have revealed that microRNA-106 (miR-106) may serve as a non-invasive and cost-effective biomarker in gastric cancer (GC) detection. However, inconsistent results have prevented its application to clinical practice. As a result of this, a comprehensive meta-analysis was conducted to evaluate the diagnostic performance of miR-106 alone and miR-106-related combination markers for GC detection. Meanwhile, an integrative bioinformatics analysis was performed to explore the function of miR-106 at the systems biology level. The results in our work showed that sensitivity of 0.71 (95% CI 0.65-0.76) and specificity of 0.82 (0.72-0.88), with the under area AUC (area under the curve) value of 0.80 (0.76-0.83) for miR-106 alone. Prospectively, miR-106-related combination markers improved the combined sensitivity, specificity and AUC, describing the discriminatory ability of 0.78 (0.65-0.87), 0.83 (0.77-0.89) and 0.88 (0.85-0.90) in the present analysis. Furthermore, targets of miR-106 were obtained and enriched by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, revealing their associations with the occurrence and development of GC. Hub genes and significant modules were identified from the protein-protein interaction networks constructed by miR-106 targets and found closely associated with the initiation and progression of GC again. Our comprehensive and integrative analysis revealed that miR-106 may be suitable as a diagnostic biomarker for GC while microRNA combination biomarkers may provide a new alternative for clinical application. However, it is necessary to conduct large-scale population-based studies and biological experiments to further investigate the diagnostic value of miR-106.

Optimizing estimation of hemispheric dominance for language using magnetic source imaging

PubMed Central

Passaro, Antony D.; Rezaie, Roozbeh; Moser, Dana C.; Li, Zhimin; Dias, Nadeeka; Papanicolaou, Andrew C.

2011-01-01

The efficacy of magnetoencephalography (MEG) as an alternative to invasive methods for investigating the cortical representation of language has been explored in several studies. Recently, studies comparing MEG to the gold standard Wada procedure have found inconsistent and often less-than accurate estimates of laterality across various MEG studies. Here we attempted to address this issue among normal right-handed adults (N=12) by supplementing a well-established MEG protocol involving word recognition and the single dipole method with a sentence comprehension task and a beamformer approach localizing neural oscillations. Beamformer analysis of word recognition and sentence comprehension tasks revealed a desynchronization in the 10–18 Hz range, localized to the temporo-parietal cortices. Inspection of individual profiles of localized desynchronization (10–18 Hz) revealed left hemispheric dominance in 91.7% and 83.3% of individuals during the word recognition and sentence comprehension tasks, respectively. In contrast, single dipole analysis yielded lower estimates, such that activity in temporal language regions was left-lateralized in 66.7% and 58.3% of individuals during word recognition and sentence comprehension, respectively. The results obtained from the word recognition task and localization of oscillatory activity using a beamformer appear to be in line with general estimates of left hemispheric dominance for language in normal right-handed individuals. Furthermore, the current findings support the growing notion that changes in neural oscillations underlie critical components of linguistic processing. PMID:21890118

[Text Comprehensibility of Hospital Report Cards].

PubMed

Sander, U; Kolb, B; Christoph, C; Emmert, M

2016-12-01

Objectives: Recently, the number of hospital report cards that compare quality of hospitals and present information from German quality reports has greatly increased. Objectives of this study were to a) identify suitable methods for measuring the readability and comprehensibility of hospital report cards, b) to obtain reliable information on the comprehensibility of texts for laymen, c) to give recommendations for improvements and d) to recommend public health actions. Methods: The readability and comprehensibility of the texts were tested with a) a computer-aided evaluation of formal text characteristics (readability indices Flesch (German formula) and 1. Wiener Sachtextformel formula), b) an expert-based heuristic analysis of readability and comprehensibility of texts (counting technical terms and analysis of text simplicity as well as brevity and conciseness using the Hamburg intelligibility model) and c) a survey of subjects about the comprehensibility of individual technical terms, the assessment of the comprehensibility of the presentations and the subjects' decisions in favour of one of the 5 presented clinics due to the better quality of data. In addition, the correlation between the results of the text analysis with the results from the survey of subjects was tested. Results: The assessment of texts with the computer-aided evaluations showed poor comprehensibility values. The assessment of text simplicity using the Hamburg intelligibility model showed poor comprehensibility values (-0.3). On average, 6.8% of the words used were technical terms. A review of 10 technical terms revealed that in all cases only a minority of respondents (from 4.4% to 39.1%) exactly knew what was meant by each of them. Most subjects (62.4%) also believed that unclear terms worsened their understanding of the information offered. The correlation analysis showed that presentations with a lower frequency of technical terms and better values for the text simplicity were better understood. Conclusion: The determination of the frequency of technical terms and the assessment of text simplicity using the Hamburg intelligibility model were suitable methods to determine the readability and comprehensibility of presentations of quality indicators. The analysis showed predominantly poor comprehensibility values and indicated the need to improve the texts of report cards. © Georg Thieme Verlag KG Stuttgart · New York.

Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity

PubMed Central

Anastassiadis, Theonie; Deacon, Sean W.; Devarajan, Karthik; Ma, Haiching; Peterson, Jeffrey R.

2011-01-01

Small-molecule protein kinase inhibitors are central tools for elucidating cellular signaling pathways and are promising therapeutic agents. Due to evolutionary conservation of the ATP-binding site, most kinase inhibitors that target this site promiscuously inhibit multiple kinases. Interpretation of experiments utilizing these compounds is confounded by a lack of data on the comprehensive kinase selectivity of most inhibitors. Here we profiled the activity of 178 commercially available kinase inhibitors against a panel of 300 recombinant protein kinases using a functional assay. Quantitative analysis revealed complex and often unexpected kinase-inhibitor interactions, with a wide spectrum of promiscuity. Many off-target interactions occur with seemingly unrelated kinases, revealing how large-scale profiling can be used to identify multi-targeted inhibitors of specific, diverse kinases. The results have significant implications for drug development and provide a resource for selecting compounds to elucidate kinase function and for interpreting the results of experiments that use them. PMID:22037377

The power of projectomes: genetic mosaic labeling in the larval zebrafish brain reveals organizing principles of sensory circuits.

PubMed

Robles, Estuardo

2017-09-01

In no vertebrate species do we possess an accurate, comprehensive tally of neuron types in the brain. This is in no small part due to the vast diversity of neuronal types that comprise complex vertebrate nervous systems. A fundamental goal of neuroscience is to construct comprehensive catalogs of cell types defined by structure, connectivity, and physiological response properties. This type of information will be invaluable for generating models of how assemblies of neurons encode and distribute sensory information and correspondingly alter behavior. This review summarizes recent efforts in the larval zebrafish to construct sensory projectomes, comprehensive analyses of axonal morphologies in sensory axon tracts. Focusing on the olfactory and optic tract, these studies revealed principles of sensory information processing in the olfactory and visual systems that could not have been directly quantified by other methods. In essence, these studies reconstructed the optic and olfactory tract in a virtual manner, providing insights into patterns of neuronal growth that underlie the formation of sensory axon tracts. Quantitative analysis of neuronal diversity revealed organizing principles that determine information flow through sensory systems in the zebrafish that are likely to be conserved across vertebrate species. The generation of comprehensive cell type classifications based on structural, physiological, and molecular features will lead to testable hypotheses on the functional role of individual sensory neuron subtypes in controlling specific sensory-evoked behaviors.

Comprehensive Gene expression meta-analysis and integrated bioinformatic approaches reveal shared signatures between thrombosis and myeloproliferative disorders

PubMed Central

Jha, Prabhash Kumar; Vijay, Aatira; Sahu, Anita; Ashraf, Mohammad Zahid

2016-01-01

Thrombosis is a leading cause of morbidity and mortality in patients with myeloproliferative disorders (MPDs), particularly polycythemia vera (PV) and essential thrombocythemia (ET). Despite the attempts to establish a link between them, the shared biological mechanisms are yet to be characterized. An integrated gene expression meta-analysis of five independent publicly available microarray data of the three diseases was conducted to identify shared gene expression signatures and overlapping biological processes. Using INMEX bioinformatic tool, based on combined Effect Size (ES) approaches, we identified a total of 1,157 differentially expressed genes (DEGs) (697 overexpressed and 460 underexpressed genes) shared between the three diseases. EnrichR tool’s rich library was used for comprehensive functional enrichment and pathway analysis which revealed “mRNA Splicing” and “SUMO E3 ligases SUMOylate target proteins” among the most enriched terms. Network based meta-analysis identified MYC and FN1 to be the most highly ranked hub genes. Our results reveal that the alterations in biomarkers of the coagulation cascade like F2R, PROS1, SELPLG and ITGB2 were common between the three diseases. Interestingly, the study has generated a novel database of candidate genetic markers, pathways and transcription factors shared between thrombosis and MPDs, which might aid in the development of prognostic therapeutic biomarkers. PMID:27892526

Investigating the value of time and value of reliability for managed lanes.

DOT National Transportation Integrated Search

2015-12-01

This report presents a comprehensive study in Value of Time (VOT) and Value of Reliability (VOR) analysis in : the context of managed lane (ML) facilities. Combined Revealed Preference (RP) and Stated Preference (SP) : data were used to understand tr...

Genome-Wide Identification, Evolution and Expression Analysis of mTERF Gene Family in Maize

PubMed Central

Zhao, Yanxin; Cai, Manjun; Zhang, Xiaobo; Li, Yurong; Zhang, Jianhua; Zhao, Hailiang; Kong, Fei; Zheng, Yonglian; Qiu, Fazhan

2014-01-01

Plant mitochondrial transcription termination factor (mTERF) genes comprise a large family with important roles in regulating organelle gene expression. In this study, a comprehensive database search yielded 31 potential mTERF genes in maize (Zea mays L.) and most of them were targeted to mitochondria or chloroplasts. Maize mTERF were divided into nine main groups based on phylogenetic analysis, and group IX represented the mitochondria and species-specific clade that diverged from other groups. Tandem and segmental duplication both contributed to the expansion of the mTERF gene family in the maize genome. Comprehensive expression analysis of these genes, using microarray data and RNA-seq data, revealed that these genes exhibit a variety of expression patterns. Environmental stimulus experiments revealed differential up or down-regulation expression of maize mTERF genes in seedlings exposed to light/dark, salts and plant hormones, respectively, suggesting various important roles of maize mTERF genes in light acclimation and stress-related responses. These results will be useful for elucidating the roles of mTERF genes in the growth, development and stress response of maize. PMID:24718683

Theory of Mind and Reading Comprehension in Deaf and Hard-of-Hearing Signing Children

PubMed Central

Holmer, Emil; Heimann, Mikael; Rudner, Mary

2016-01-01

Theory of Mind (ToM) is related to reading comprehension in hearing children. In the present study, we investigated progression in ToM in Swedish deaf and hard-of-hearing (DHH) signing children who were learning to read, as well as the association of ToM with reading comprehension. Thirteen children at Swedish state primary schools for DHH children performed a Swedish Sign Language (SSL) version of the Wellman and Liu (2004) ToM scale, along with tests of reading comprehension, SSL comprehension, and working memory. Results indicated that ToM progression did not differ from that reported in previous studies, although ToM development was delayed despite age-appropriate sign language skills. Correlation analysis revealed that ToM was associated with reading comprehension and working memory, but not sign language comprehension. We propose that some factor not investigated in the present study, possibly represented by inference making constrained by working memory capacity, supports both ToM and reading comprehension and may thus explain the results observed in the present study. PMID:27375532

Theory of Mind and Reading Comprehension in Deaf and Hard-of-Hearing Signing Children.

PubMed

Holmer, Emil; Heimann, Mikael; Rudner, Mary

2016-01-01

Theory of Mind (ToM) is related to reading comprehension in hearing children. In the present study, we investigated progression in ToM in Swedish deaf and hard-of-hearing (DHH) signing children who were learning to read, as well as the association of ToM with reading comprehension. Thirteen children at Swedish state primary schools for DHH children performed a Swedish Sign Language (SSL) version of the Wellman and Liu (2004) ToM scale, along with tests of reading comprehension, SSL comprehension, and working memory. Results indicated that ToM progression did not differ from that reported in previous studies, although ToM development was delayed despite age-appropriate sign language skills. Correlation analysis revealed that ToM was associated with reading comprehension and working memory, but not sign language comprehension. We propose that some factor not investigated in the present study, possibly represented by inference making constrained by working memory capacity, supports both ToM and reading comprehension and may thus explain the results observed in the present study.

Methodological Issues and Further Research in the Study of Reading Comprehension with Different Levels of Knowledge.

ERIC Educational Resources Information Center

Qian, Gaoyin

Some methodological issues in the study of levels of knowledge are reviewed, and needs for further research are explored, drawing on an analysis of 12 studies reported since the late 1970s. In the 12 studies, 16 quantitative experiments were conducted. These were assessed for internal and external validity. Analysis revealed some shortcomings in…

Optimizing estimation of hemispheric dominance for language using magnetic source imaging.

PubMed

Passaro, Antony D; Rezaie, Roozbeh; Moser, Dana C; Li, Zhimin; Dias, Nadeeka; Papanicolaou, Andrew C

2011-10-06

The efficacy of magnetoencephalography (MEG) as an alternative to invasive methods for investigating the cortical representation of language has been explored in several studies. Recently, studies comparing MEG to the gold standard Wada procedure have found inconsistent and often less-than accurate estimates of laterality across various MEG studies. Here we attempted to address this issue among normal right-handed adults (N=12) by supplementing a well-established MEG protocol involving word recognition and the single dipole method with a sentence comprehension task and a beamformer approach localizing neural oscillations. Beamformer analysis of word recognition and sentence comprehension tasks revealed a desynchronization in the 10-18Hz range, localized to the temporo-parietal cortices. Inspection of individual profiles of localized desynchronization (10-18Hz) revealed left hemispheric dominance in 91.7% and 83.3% of individuals during the word recognition and sentence comprehension tasks, respectively. In contrast, single dipole analysis yielded lower estimates, such that activity in temporal language regions was left-lateralized in 66.7% and 58.3% of individuals during word recognition and sentence comprehension, respectively. The results obtained from the word recognition task and localization of oscillatory activity using a beamformer appear to be in line with general estimates of left hemispheric dominance for language in normal right-handed individuals. Furthermore, the current findings support the growing notion that changes in neural oscillations underlie critical components of linguistic processing. Published by Elsevier B.V.

A protein interaction network analysis for yeast integral membrane protein.

PubMed

Shi, Ming-Guang; Huang, De-Shuang; Li, Xue-Ling

2008-01-01

Although the yeast Saccharomyces cerevisiae is the best exemplified single-celled eukaryote, the vast number of protein-protein interactions of integral membrane proteins of Saccharomyces cerevisiae have not been characterized by experiments. Here, based on the kernel method of Greedy Kernel Principal Component analysis plus Linear Discriminant Analysis, we identify 300 protein-protein interactions involving 189 membrane proteins and get the outcome of a highly connected protein-protein interactions network. Furthermore, we study the global topological features of integral membrane proteins network of Saccharomyces cerevisiae. These results give the comprehensive description of protein-protein interactions of integral membrane proteins and reveal global topological and robustness of the interactome network at a system level. This work represents an important step towards a comprehensive understanding of yeast protein interactions.

Factor Analysis of the WAIS and Twenty French-Kit Reference Tests.

ERIC Educational Resources Information Center

Ramsey, Philip H.

1979-01-01

The Wechsler Adult Intelligence Scale (WAIS) and 20 tests from the French Kit were administered to over 100 undergraduates. Analyses revealed ten factors: verbal comprehension, visualization, memory span, syllogistic reasoning, general reasoning, induction, mechanical knowledge, number facility, spatial orientation, and associative memory.…

Reading Ability as a Predictor of Academic Procrastination among African American Graduate Students

ERIC Educational Resources Information Center

Collins, Kathleen M. T.; Onwuegbuzie, Anthony J.; Jiao, Qun G.

2008-01-01

The present study examined the relationship between reading ability (i.e., reading comprehension and reading vocabulary) and academic procrastination among 120 African American graduate students. A canonical correlation analysis revealed statistically significant and practically significant multivariate relationships between these two reading…

Relationship Between Speech Intelligibility and Speech Comprehension in Babble Noise.

PubMed

Fontan, Lionel; Tardieu, Julien; Gaillard, Pascal; Woisard, Virginie; Ruiz, Robert

2015-06-01

The authors investigated the relationship between the intelligibility and comprehension of speech presented in babble noise. Forty participants listened to French imperative sentences (commands for moving objects) in a multitalker babble background for which intensity was experimentally controlled. Participants were instructed to transcribe what they heard and obey the commands in an interactive environment set up for this purpose. The former test provided intelligibility scores and the latter provided comprehension scores. Collected data revealed a globally weak correlation between intelligibility and comprehension scores (r = .35, p < .001). The discrepancy tended to grow as noise level increased. An analysis of standard deviations showed that variability in comprehension scores increased linearly with noise level, whereas higher variability in intelligibility scores was found for moderate noise level conditions. These results support the hypothesis that intelligibility scores are poor predictors of listeners' comprehension in real communication situations. Intelligibility and comprehension scores appear to provide different insights, the first measure being centered on speech signal transfer and the second on communicative performance. Both theoretical and practical implications for the use of speech intelligibility tests as indicators of speakers' performances are discussed.

Neural Mechanism Underling Comprehension of Narrative Speech and Its Heritability: Study in a Large Population.

PubMed

Babajani-Feremi, Abbas

2017-09-01

Comprehension of narratives constitutes a fundamental part of our everyday life experience. Although the neural mechanism of auditory narrative comprehension has been investigated in some studies, the neural correlates underlying this mechanism and its heritability remain poorly understood. We investigated comprehension of naturalistic speech in a large, healthy adult population (n = 429; 176/253 M/F; 22-36 years of age) consisting of 192 twin pairs (49 monozygotic and 47 dizygotic pairs) and 237 of their siblings. We used high quality functional MRI datasets from the Human Connectome Project (HCP) in which a story-based paradigm was utilized for the auditory narrative comprehension. Our results revealed that narrative comprehension was associated with activations of the classical language regions including superior temporal gyrus (STG), middle temporal gyrus (MTG), and inferior frontal gyrus (IFG) in both hemispheres, though STG and MTG were activated symmetrically and activation in IFG were left-lateralized. Our results further showed that the narrative comprehension was associated with activations in areas beyond the classical language regions, e.g. medial superior frontal gyrus (SFGmed), middle frontal gyrus (MFG), and supplementary motor area (SMA). Of subcortical structures, only the hippocampus was involved. The results of heritability analysis revealed that the oral reading recognition and picture vocabulary comprehension were significantly heritable (h 2  > 0.56, p < 10 - 13 ). In addition, the extent of activation of five areas in the left hemisphere, i.e. STG, IFG pars opercularis, SFGmed, SMA, and precuneus, and one area in the right hemisphere, i.e. MFG, were significantly heritable (h 2  > 0.33, p < 0.0004). The current study, to the best of our knowledge, is the first to investigate auditory narrative comprehension and its heritability in a large healthy population. Referring to the excellent quality of the HCP data, our results can clarify the functional contributions of linguistic and extra-linguistic cortices during narrative comprehension.

MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

DOE PAGES

Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

2016-08-03

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorialsmore » explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.« less

Effective Teacher Induction and Mentoring: Assessing the Evidence

ERIC Educational Resources Information Center

Strong, Michael

2009-01-01

A well-known authority on teacher induction programs offers the most comprehensive, up-to-date review of all recent research on the effectiveness of mentoring and induction support for new teachers. Michael Strong provides a revealing analysis of teacher induction programs and their consequences for education, teacher quality, teacher…

Impact of aluminum stress on oxalate and other metabolites in Rumex obtusifolius

USDA-ARS?s Scientific Manuscript database

In this study we analyzed metabolite alterations induced by aluminum (Al) stress in Rumex species using the capillary electrophoresis mass spectrometry. Comprehensive metabolome analysis revealed that oxalate and its precursors were up-regulated in leaves of R. obtusifolius by Al3+. Unlike leaves, c...

Pop Culture.

ERIC Educational Resources Information Center

Berger, Arthur Asa

Popular culture in America is comprehensively reviewed in this book. The book is designed for either high school or college level social studies or English courses and includes a variety of graphic illustrations that provide a thread of continuity throughout. Basically the author has developed a method of analysis that reveals how popular culture…

A Comprehensive Needs Assessment To Facilitate Prevention of School Drop Out and Violence.

ERIC Educational Resources Information Center

Hunt, Mary Ellen; Meyers, Joel; Davies, Gwen; Meyers, Barbara; Grogg, Kathryn Rogers; Neel, John

2002-01-01

Study addresses school violence and dropout and proposes that the underlying factor of school connectedness/school climate should guide preventive and intervention efforts. Principal components analysis revealed five distinct factors: school connectedness/positive school climate, causes of violence, causes of school dropout, interventions for drop…

An Analysis of Input and Interaction in the Dialogue Journals of Deaf Community College Students.

ERIC Educational Resources Information Center

Cannon, Beverly; Polio, Charlene

1989-01-01

A study of dialogue journal interaction between an instructor of both deaf and hearing community college students revealed that the instructor individualized journal responses according to individual students' language comprehension ability, motivation, learning style, and interests. (CB) (Adjunct ERIC Clearinghouse on Literacy Education)

Mass Spectrometry Analysis of Spatial Protein Networks by Colocalization Analysis (COLA).

PubMed

Mardakheh, Faraz K

2017-01-01

A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92-105, 2017). As protein localization and function are inherently linked, significant colocalization between two proteins is a strong indication for their functional interaction. COLA uses rapid complete subcellular fractionation, coupled with quantitative proteomics to generate a subcellular localization profile for each protein quantified by the mass spectrometer. Robust clustering is then applied to reveal significant similarities in protein localization profiles, indicative of colocalization.

Cross-Study Differences in the Etiology of Reading Comprehension: a Meta-Analytical Review of Twin Studies.

PubMed

Little, Callie W; Haughbrook, Rasheda; Hart, Sara A

2017-01-01

Numerous twin studies have examined the genetic and environmental etiology of reading comprehension, though it is likely that etiological estimates are influenced by unidentified sample conditions (e.g. Tucker-Drob and Bates, Psychol Sci:0956797615612727, 2015). The purpose of this meta-analysis was to average the etiological influences of reading comprehension and to explore the potential moderators influencing these estimates. Results revealed an average heritability estimate of h 2  = 0.59, with significant variation in estimates across studies, suggesting potential moderation. Moderation results indicated publication year, grade level, project, zygosity methods, and response type moderated heritability estimates. The average shared environmental estimate was c 2  = 0.16, with publication year, grade and zygosity methods acting as significant moderators. These findings support the role of genetics on reading comprehension, and a small significant role of shared environmental influences. The results suggest that our interpretation of how genes and environments influence reading comprehension should reflect aspects of study and sample.

Comprehensive geriatric care reduces acute perioperative delirium in elderly patients with hip fractures: A meta-analysis.

PubMed

Wang, Yiyang; Tang, Jun; Zhou, Feiya; Yang, Lei; Wu, Jianbin

2017-06-01

The aim of the current meta-analysis was to assess the treatment effect of comprehensive geriatric care in reducing acute perioperative delirium in older patients with hip fractures, compared with the effect of a routine orthopedic treatment protocol. We conducted a search of multiple databases to identify randomized controlled trials (RCTs) and quasi-RCTs comparing comprehensive geriatric care and routine orthopedic treatment regarding the following outcomes: incidence of delirium, assessment of cognitive status, and duration of delirium. Odds ratios (ORs) and mean differences (MDs) were pooled using either a fixed-effects or a random-effects model, depending on the heterogeneity of the trials included in the analysis. Six RCTs and 1 quasi-RCT provided data from 1840 patients. These data revealed that comprehensive geriatric care may reduce the incidence of perioperative delirium (OR = 0.71; 95% confidence interval [CI], 0.57-0.89; P = .003) and that it was associated with higher cognitive status during hospitalization or at 1 month postoperatively (MD = 1.03; 95% CI, 0.93-1.13; P ≤ .00001). There was no significant difference in duration of perioperative delirium between the 2 treatment groups (MD = -2.48; 95% CI, -7.36 to 2.40; P = .32). Based on the quality of evidence provided, comprehensive geriatric care may reduce the incidence of perioperative delirium. To obtain evidence regarding the merits of comprehensive geriatric care in reducing severity of delirium and shortening the duration of delirium, there is a need for multicenter RCTs with high methodological quality.

Neural circuit of verbal humor comprehension in schizophrenia - an fMRI study.

PubMed

Adamczyk, Przemysław; Wyczesany, Miroslaw; Domagalik, Aleksandra; Daren, Artur; Cepuch, Kamil; Błądziński, Piotr; Cechnicki, Andrzej; Marek, Tadeusz

2017-01-01

Individuals with schizophrenia exhibit problems with understanding the figurative meaning of language. This study evaluates neural correlates of diminished humor comprehension observed in schizophrenia. The study included chronic schizophrenia (SCH) outpatients (n = 20), and sex, age and education level matched healthy controls (n = 20). The fMRI punchline based humor comprehension task consisted of 60 stories of which 20 had funny, 20 nonsensical and 20 neutral (not funny) punchlines. After the punchlines were presented, the participants were asked to indicate whether the story was comprehensible and how funny it was. Three contrasts were analyzed in both groups reflecting stages of humor processing: abstract vs neutral stories - incongruity detection; funny vs abstract - incongruity resolution and elaboration; and funny vs neutral - complete humor processing. Additionally, parametric modulation analysis was performed using both subjective ratings separately. Between-group comparisons revealed that the SCH subjects had attenuated activation in the right posterior superior temporal gyrus (BA 41) in case of irresolvable incongruity processing of nonsensical puns; in the left dorsomedial middle and superior frontal gyri (BA 8/9) in case of incongruity resolution and elaboration processing of funny puns; and in the interhemispheric dorsal anterior cingulate cortex (BA 24) in case of complete processing of funny puns. Additionally, during comprehensibility ratings the SCH group showed a suppressed activity in the left dorsomedial middle and superior frontal gyri (BA 8/9) and revealed weaker activation during funniness ratings in the left dorsal anterior cingulate cortex (BA 24). Interestingly, these differences in the SCH group were accompanied behaviorally by a protraction of time in both types of rating responses and by indicating funny punchlines less comprehensible. Summarizing, our results indicate neural substrates of humor comprehension processing impairments in schizophrenia, which is accompanied by fronto-temporal hypoactivation.

Transcriptome analysis reveals a comprehensive insect resistance response mechanism in cotton to infestation by the phloem feeding insect Bemisia tabaci (whitefly)

USDA-ARS?s Scientific Manuscript database

The whitefly (Bemisia tabaci) causes tremendous damage to cotton production worldwide. However, very limited information is available about how plants perceive and defend themselves from this destructive pest. In this study, the transcriptomics differences between two cotton cultivars that exhibit e...

Information Theoretical Analysis of a Bovine Gene Atlas Reveals Chromosomal Regions with Tissue Specific Gene Expression.

USDA-ARS?s Scientific Manuscript database

An essential step to understanding the genomic biology of any organism is to comprehensively survey its transcriptome. We present the Bovine Gene Atlas (BGA) a compendium of over 7.2 million unique 20 base Illumina DGE tags representing 100 tissue transcriptomes collected primarily from L1 Dominette...

Principal component analysis study of visual and verbal metaphoric comprehension in children with autism and learning disabilities.

PubMed

Mashal, Nira; Kasirer, Anat

2012-01-01

This research extends previous studies regarding the metaphoric competence of autistic and learning disable children on different measures of visual and verbal non-literal language comprehension, as well as cognitive abilities that include semantic knowledge, executive functions, similarities, and reading fluency. Thirty seven children with autism (ASD), 20 children with learning disabilities (LD), and 21 typically developed (TD) children participated in the study. Principal components analysis was used to examine the interrelationship among the various tests in each group. Results showed different patterns in the data according to group. In particular, the results revealed that there is no dichotomy between visual and verbal metaphors in TD children but rather metaphor are classified according to their familiarity level. In the LD group visual metaphors were classified independently of the verbal metaphors. Verbal metaphoric understanding in the ASD group resembled the LD group. In addition, our results revealed the relative weakness of the ASD and LD children in suppressing irrelevant information. Copyright © 2011 Elsevier Ltd. All rights reserved.

Comprehensive two-dimensional liquid chromatographic analysis of poloxamers.

PubMed

Malik, Muhammad Imran; Lee, Sanghoon; Chang, Taihyun

2016-04-15

Poloxamers are low molar mass triblock copolymers of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO), having number of applications as non-ionic surfactants. Comprehensive one and two-dimensional liquid chromatographic (LC) analysis of these materials is proposed in this study. The separation of oligomers of both types (PEO and PPO) is demonstrated for several commercial poloxamers. This is accomplished at the critical conditions for one of the block while interaction for the other block. Reversed phase LC at CAP of PEO allowed for oligomeric separation of triblock copolymers with regard to PPO block whereas normal phase LC at CAP of PPO renders oligomeric separation with respect to PEO block. The oligomeric separation with regard to PEO and PPO are coupled online (comprehensive 2D-LC) to reveal two-dimensional contour plots by unconventional 2D IC×IC (interaction chromatography) coupling. The study provides chemical composition mapping of both PEO and PPO, equivalent to combined molar mass and chemical composition mapping for several commercial poloxamers. Copyright © 2016 Elsevier B.V. All rights reserved.

Morphological Awareness in Literacy Acquisition of Chinese Second Graders: A Path Analysis.

PubMed

Zhang, Haomin

2016-02-01

The present study tested a path diagram regarding the contribution of morphological awareness (MA) to early literacy acquisition among Chinese-speaking second graders ([Formula: see text]). Three facets of MA were addressed, namely derivational awareness, compound awareness and compound structure awareness. The model aimed to test a theory of causal order among measures of MA and literacy outcomes. Drawing upon multivariate path analysis, direct and indirect effects of MA were analyzed to identify their role in literacy performance among young children. Results revealed that all three facets of MA made significant contributions to lexical inference ability. In addition, compound awareness showed a unique and significant contribution to vocabulary knowledge. It was also observed that lexical inference ability had a mediating effect predictive of both vocabulary knowledge and reading comprehension. Moreover, vocabulary knowledge mediated the effect of MA on reading comprehension. However, no significant contribution of MA to reading comprehension was found after controlling for lexical inference ability and vocabulary knowledge.

Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

PubMed Central

2009-01-01

Background The maintenance of internal pH in bacterial cells is challenged by natural stress conditions, during host infection or in biotechnological production processes. Comprehensive transcriptomic and proteomic analyses has been conducted in several bacterial model systems, yet questions remain as to the mechanisms of pH homeostasis. Results Here we present the comprehensive analysis of pH homeostasis in C. glutamicum, a bacterium of industrial importance. At pH values between 6 and 9 effective maintenance of the internal pH at 7.5 ± 0.5 pH units was found. By DNA microarray analyses differential mRNA patterns were identified. The expression profiles were validated and extended by 1D-LC-ESI-MS/MS based quantification of soluble and membrane proteins. Regulators involved were identified and thereby participation of numerous signaling modules in pH response was found. The functional analysis revealed for the first time the occurrence of oxidative stress in C. glutamicum cells at neutral and low pH conditions accompanied by activation of the iron starvation response. Intracellular metabolite pool analysis unraveled inhibition of the TCA and other pathways at low pH. Methionine and cysteine synthesis were found to be activated via the McbR regulator, cysteine accumulation was observed and addition of cysteine was shown to be toxic under acidic conditions. Conclusions Novel limitations for C. glutamicum at non-optimal pH values were identified by a comprehensive analysis on the level of the transcriptome, proteome, and metabolome indicating a functional link between pH acclimatization, oxidative stress, iron homeostasis, and metabolic alterations. The results offer new insights into bacterial stress physiology and new starting points for bacterial strain design or pathogen defense. PMID:20025733

A Systematic, Intensive Statistical Investigation of Data from the Comprehensive Analysis of Reported Drugs (CARD) for Compliance and Illicit Opioid Abstinence in Substance Addiction Treatment with Buprenorphine/naloxone.

PubMed

Blum, Kenneth; Han, David; Modestino, Edward J; Saunders, Scott; Roy, A Kennison; Jacobs, W; Inaba, Darryl S; Baron, David; Oscar-Berman, Marlene; Hauser, Mary; Badgaiyan, Rajendra D; Smith, David E; Femino, John; Gold, Mark S

2018-01-28

Buprenorphine and naloxone (bup/nal), a combination partial mu receptor agonist and low-dose delta mu antagonist, is presently recommended and used to treat opioid-use disorder. However, a literature review revealed a paucity of research involving data from urine drug tests that looked at compliance and abstinence in one sample. Statistical analysis of data from the Comprehensive Analysis of Reported Drugs (CARD) was used to assess compliance and abstinence during treatment in a large cohort of bup/nal patients attending chemical-dependency programs from eastern USA in 2010 and 2011. Part 1: Bup/nal was present in 93.4% of first (n = 1,282; p <.0001) and 92.4% of last (n = 1,268; p <.0001) urine samples. Concomitantly, unreported illicit drugs were present in 47.7% (n = 655, p =.0261) of samples. Patients who were compliant to the bup/nal prescription were more likely than noncompliant patients to be abstinent during treatment (p =.0012; odds ratio = 1.69 with 95% confidence interval (1.210, 2.354). Part 2: An analysis of all samples collected in 2011 revealed a significant improvement in both compliance (p < 2.2 × 10 -16 ) and abstinence (p < 2.2 × 10 -16 ) during treatment. Conclusion/Importance: While significant use of illicit opioids during treatment with bup/nal is present, improvements in abstinence and high compliance during maintenance-assisted therapy programs may ameliorate fears of diversion in comprehensive programs. Expanded clinical datasets, the treatment modality, location, and year of sampling are important covariates, for further studies. The potential for long-term antireward effects from bup/nal use requires consideration in future investigations.

Sentence comprehension following moderate closed head injury in adults.

PubMed

Leikin, Mark; Ibrahim, Raphiq; Aharon-Peretz, Judith

2012-09-01

The current study explores sentence comprehension impairments among adults following moderate closed head injury. It was hypothesized that if the factor of syntactic complexity significantly affects sentence comprehension in these patients, it would testify to the existence of syntactic processing deficit along with working-memory problems. Thirty-six adults (18 closed head injury patients and 18 healthy controls matched in age, gender, and IQ) participated in the study. A picture-sentence matching task together with various tests for memory, language, and reading abilities were used to explore whether sentence comprehension impairments exist as a result of a deficit in syntactic processing or of working-memory dysfunction. Results indicate significant impairment in sentence comprehension among adults with closed head injury compared with their non-head-injured peers. Results also reveal that closed head injury patients demonstrate considerable decline in working memory, short-term memory, and semantic knowledge. Analysis of the results shows that memory impairment and syntactic complexity contribute significantly to sentence comprehension difficulties in closed head injury patients. At the same time, the presentation mode (spoken or written language) was found to have no effect on comprehension among adults with closed head injury, and their reading abilities appear to be relatively intact.

Comprehensive Lipidome-Wide Profiling Reveals Dynamic Changes of Tea Lipids during Manufacturing Process of Black Tea.

PubMed

Li, Jia; Hua, Jinjie; Zhou, Qinghua; Dong, Chunwang; Wang, Jinjin; Deng, Yuliang; Yuan, Haibo; Jiang, Yongwen

2017-11-22

As important biomolecules in Camellia sinensis L., lipids undergo substantial changes during black tea manufacture, which is considered to contribute to tea sensory quality. However, limited by analytical capacity, detailed lipid composition and its dynamic changes during black tea manufacture remain unclear. Herein, we performed tea lipidome profiling using high resolution liquid chromatography coupled to mass spectrometry (LC-MS), which allows simultaneous and robust analysis of 192 individual lipid species in black tea, covering 17 (sub)classes. Furthermore, dynamic changes of tea lipids during black tea manufacture were investigated. Significant alterations of lipid pattern were revealed, involved with chlorophyll degradation, metabolic pathways of glycoglycerolipids, and other extraplastidial membrane lipids. To our knowledge, this report presented most comprehensive coverage of lipid species in black tea. This study provides a global and in-depth metabolic map of tea lipidome during black tea manufacture.

Is Learning Styles-Based Instruction Effective? A Comprehensive Analysis of Recent Research on Learning Styles

ERIC Educational Resources Information Center

Cuevas, Joshua

2015-01-01

In an influential publication in 2009, a group of cognitive psychologists revealed that there was a lack of empirical evidence supporting the concept of learning styles-based instruction and provided guidelines for the type of research design necessary to verify the learning styles hypothesis. This article examined the literature since 2009 to…

Analysis of Mycobacterium avium subsp. paratuberculosis mutant libraries reveals loci-dependent transcription biases and strategies to novel mutant discovery

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne’s disease in ruminants and it has been implicated as a cause of Crohn’s disease in humans. The generation of comprehensive random mutant banks by transposon mutagenesis is a fundamental wide genomic technology utilized...

Educational Policy Transfer in an Era of Globalization: Theory--History--Comparison. Comparative Studies Series. Volume 23

ERIC Educational Resources Information Center

Rappleye, Jeremy

2012-01-01

As education becomes increasingly global, the processes and politics of transfer have become a central focus of research. This study provides a comprehensive analysis of contemporary theoretical and analytical work aimed at exploring international educational reform and reveals the myriad ways that globalization is now fundamentally altering our…

Unraveling the Link between Trauma and Male Delinquency: The Cumulative Versus Differential Risk Perspectives

ERIC Educational Resources Information Center

Maschi, Tina

2006-01-01

This study examined how the cumulative (additive) versus differential (individual) effects of trauma influenced male delinquency. Using a comprehensive measure of trauma, a secondary data analysis was conducted on a nationally representative sample of male youths between the ages of 12 and 17. Logistic regression analyses revealed that all three…

Examining and Dealing with the Issue of Reading Strategy Use by Iranian EFL Learners

ERIC Educational Resources Information Center

Naeini, Ma'ssoumeh Bemani; Rezaei, Reyhaneh

2015-01-01

This study investigated the relationship between Iranian EFL learners' performance on a reading comprehension test and their pattern of using cognitive and metacognitive learning strategies. Analysis of the data obtained from 190 Iranian intermediate EFL learners (70 males and 120 females, aged 17-25) revealed a strong relationship between reading…

The Use of Mobile Learning in Science: A Systematic Review

ERIC Educational Resources Information Center

Crompton, Helen; Burke, Diane; Gregory, Kristen H.; Gräbe, Catharina

2016-01-01

The use of mobile learning in education is growing at an exponential rate. To best understand how mobile learning is being used, it is crucial to gain a collective understanding of the research that has taken place. This systematic review reveals the trends in mobile learning in science with a comprehensive analysis and synthesis of studies from…

Multiple Paths to Success: Degree Completion of 4-Year Starters Taking Various Pathways

ERIC Educational Resources Information Center

Li, Dai

2016-01-01

With the use of data from the institutional research office at a comprehensive public 4-year university, this chapter describes an in-depth analysis of the institutional attendance, transfer, and graduation of three first-time student cohorts, revealing that not all types of multi-institutional attendance hurt degree completion, and strategic…

A Qualitative Study on the Use of Summarizing Strategies in Elementary Education

ERIC Educational Resources Information Center

Susar Kirmizi, Fatma; Akkaya, Nevin

2011-01-01

The objective of this study is to reveal how well summarizing strategies are used by Grade 4 and Grade 5 students as a reading comprehension strategy. This study was conducted in Buca, Izmir and the document analysis method, a qualitative research strategy, was employed. The study used a text titled "Environmental Pollution" and an…

Age, Ageing and Skills: Results from the Survey of Adult Skills. OECD Education Working Papers, No. 132

ERIC Educational Resources Information Center

Paccagnella, Marco

2016-01-01

This paper presents a comprehensive analysis of the link between age and proficiency in information-processing skills, based on information drawn from the Survey of Adult Skills (PIAAC). The data reveal significant age-related differences in proficiencies, strongly suggesting that proficiency tends to "naturally" decline with age. Age…

Comprehensive analysis of miRNAs expression profiles revealed potential key miRNA/mRNAs regulating colorectal cancer stem cell self-renewal.

PubMed

Xu, Peng; Wang, Junhua; Sun, Bo; Xiao, Zhongdang

2018-05-20

Self-renewal is essential for the malignant biological behaviors of colorectal cancer stem cells. While the self-renewal molecular mechanisms of colorectal cancer stem cells are not yet fully understood. Recently, miRNAs are reported to be relevant to the self-renewal ability of cancer stem cells. In this study, we first isolated colorectal cancer stem cell from colorectal cancer cell line HCT-116 by 1% low serum culture. Then we conducted a comprehensive analysis based on the miRNAs profiles data of both colorectal cancer stem cells and normal cultured colorectal cancer cells. Pathway analysis revealed multiple pathways including Jak-STAT, TGF-beta, PI3K-Akt and MAPK signaling pathway that are correlated to colorectal cancer. Further, we constructed a miRNA-mRNA network, based on which, several miRNA/mRNA pairs were ranked according to their impact index to the self-renewal of colorectal cancer stem cells. Further biological experiment showed that up-regulation of miR-92a-3p led to cell cycle arrest and reduced colony formation. This work provides clues to find the new potential biomarkers for colorectal cancer stem cell diagnosis and select effective miRNAs for targeted therapy. Copyright © 2018 Elsevier B.V. All rights reserved.

CGCI Investigators Reveal Comprehensive Landscape of Diffuse Large B-Cell Lymphoma (DLBCL) Genomes | Office of Cancer Genomics

Cancer.gov

Researchers from British Columbia Cancer Agency used whole genome sequencing to analyze 40 DLBCL cases and 13 cell lines in order to fill in the gaps of the complex landscape of DLBCL genomes. Their analysis, “Mutational and structural analysis of diffuse large B-cell lymphoma using whole genome sequencing,” was published online in Blood on May 22. The authors are Ryan Morin, Marco Marra, and colleagues.  

Comprehensive transcriptome analysis reveals distinct regulatory programs during vernalization and floral bud development of orchardgrass (Dactylis glomerata L.).

PubMed

Feng, Guangyan; Huang, Linkai; Li, Ji; Wang, Jianping; Xu, Lei; Pan, Ling; Zhao, Xinxin; Wang, Xia; Huang, Ting; Zhang, Xinquan

2017-11-22

Vernalization and the transition from vegetative to reproductive growth involve multiple pathways, vital for controlling floral organ formation and flowering time. However, little transcription information is available about the mechanisms behind environmental adaption and growth regulation. Here, we used high-throughput sequencing to analyze the comprehensive transcriptome of Dactylis glomerata L. during six different growth periods. During vernalization, 4689 differentially expressed genes (DEGs) significantly increased in abundance, while 3841 decreased. Furthermore, 12,967 DEGs were identified during booting stage and flowering stage, including 7750 up-regulated and 5219 down-regulated DEGs. Pathway analysis indicated that transcripts related to circadian rhythm, photoperiod, photosynthesis, flavonoid biosynthesis, starch, and sucrose metabolism changed significantly at different stages. Coexpression and weighted correlation network analysis (WGCNA) analysis linked different stages to transcriptional changes and provided evidence of inner relation modules associated with signal transduction, stress responses, cell division, and hormonal transport. We found enrichment in transcription factors (TFs) related to WRKY, NAC, AP2/EREBP, AUX/IAA, MADS-BOX, ABI3/VP1, bHLH, and the CCAAT family during vernalization and floral bud development. TFs expression patterns revealed intricate temporal variations, suggesting relatively separate regulatory programs of TF modules. Further study will unlock insights into the ability of the circadian rhythm and photoperiod to regulate vernalization and flowering time in perennial grass.

Cross-study differences in the etiology of reading comprehension: A meta-analytical review of twin studies

PubMed Central

Little, Callie W; Haughbrook, Rasheda; Hart, Sara A

2016-01-01

Numerous twin studies have been published examining the genetic and environmental etiology of reading comprehension, though the etiological estimates may be influenced currently unidentified sample conditions (e.g., Tucker-Drob & Bates, 2015). The purpose of the current meta-analysis was to average the etiological influences of reading comprehension and to explore the potential moderators that may be influencing these estimates. Results revealed an average heritability estimate of h2 = .59, with significant variation in estimates across studies, suggesting potential moderation. Heritability was moderated by publication year, grade level, project, zygosity determination method, and response type. The average shared environmental estimate was c2 = .16, with publication year, grade and zygosity determination method acting as significant moderators. These findings support the large role of genetic influences on reading comprehension, and a small but significant role of shared environmental influences. The significant moderators of etiological influences within the current synthesis suggest our interpretation of how genes and environment influence reading comprehension should reflect aspects of study and sample. PMID:27630039

Development and validation of a reading-related assessment battery in Malay for the purpose of dyslexia assessment.

PubMed

Lee, Lay Wah

2008-06-01

Malay is an alphabetic language with transparent orthography. A Malay reading-related assessment battery which was conceptualised based on the International Dyslexia Association definition of dyslexia was developed and validated for the purpose of dyslexia assessment. The battery consisted of ten tests: Letter Naming, Word Reading, Non-word Reading, Spelling, Passage Reading, Reading Comprehension, Listening Comprehension, Elision, Rapid Letter Naming and Digit Span. Content validity was established by expert judgment. Concurrent validity was obtained using the schools' language tests as criterion. Evidence of predictive and construct validity was obtained through regression analyses and factor analyses. Phonological awareness was the most significant predictor of word-level literacy skills in Malay, with rapid naming making independent secondary contributions. Decoding and listening comprehension made separate contributions to reading comprehension, with decoding as the more prominent predictor. Factor analysis revealed four factors: phonological decoding, phonological naming, comprehension and verbal short-term memory. In conclusion, despite differences in orthography, there are striking similarities in the theoretical constructs of reading-related tasks in Malay and in English.

Comprehensiveness of care from the patient perspective: comparison of primary healthcare evaluation instruments.

PubMed

Haggerty, Jeannie L; Beaulieu, Marie-Dominique; Pineault, Raynald; Burge, Frederick; Lévesque, Jean-Frédéric; Santor, Darcy A; Bouharaoui, Fatima; Beaulieu, Christine

2011-12-01

Comprehensiveness relates both to scope of services offered and to a whole-person clinical approach. Comprehensive services are defined as "the provision, either directly or indirectly, of a full range of services to meet most patients' healthcare needs"; whole-person care is "the extent to which a provider elicits and considers the physical, emotional and social aspects of a patient's health and considers the community context in their care." Among instruments that evaluate primary healthcare, two had subscales that mapped to comprehensive services and to the community component of whole-person care: the Primary Care Assessment Tool - Short Form (PCAT-S) and the Components of Primary Care Index (CPCI, a limited measure of whole-person care). To examine how well comprehensiveness is captured in validated instruments that evaluate primary healthcare from the patient's perspective. 645 adults with at least one healthcare contact in the previous 12 months responded to six instruments that evaluate primary healthcare. Scores were normalized for descriptive comparison. Exploratory and confirmatory (structural equation modelling) factor analysis examined fit to operational definition, and item response theory analysis examined item performance on common constructs. Over one-quarter of respondents had missing responses on services offered or doctor's knowledge of the community. The subscales did not load on a single factor; comprehensive services and community orientation were examined separately. The community orientation subscales did not perform satisfactorily. The three comprehensive services subscales fit very modestly onto two factors: (1) most healthcare needs (from one provider) (CPCI Comprehensive Care, PCAT-S First-Contact Utilization) and (2) range of services (PCAT-S Comprehensive Services Available). Individual item performance revealed several problems. Measurement of comprehensiveness is problematic, making this attribute a priority for measure development. Range of services offered is best obtained from providers. Whole-person care is not addressed as a separate construct, but some dimensions are covered by attributes such as interpersonal communication and relational continuity.

Ontological analysis of SNOMED CT.

PubMed

Héja, Gergely; Surján, György; Varga, Péter

2008-10-27

SNOMED CT is the most comprehensive medical terminology. However, its use for intelligent services based on formal reasoning is questionable. The analysis of the structure of SNOMED CT is based on the formal top-level ontology DOLCE. The analysis revealed several ontological and knowledge-engineering errors, the most important are errors in the hierarchy (mostly from an ontological point of view, but also regarding medical aspects) and the mixing of subsumption relations with other types (mostly 'part of'). The found errors impede formal reasoning. The paper presents a possible way to correct these problems.

Emotion comprehension: the impact of nonverbal intelligence.

PubMed

Albanese, Ottavia; De Stasio, Simona; Di Chiacchio, Carlo; Fiorilli, Caterina; Pons, Francisco

2010-01-01

A substantial body of research has established that emotion understanding develops throughout early childhood and has identified three hierarchical developmental phases: external, mental, and reflexive. The authors analyzed nonverbal intelligence and its effect on children's improvement of emotion understanding and hypothesized that cognitive level is a consistent predictor of emotion comprehension. In all, 366 children (182 girls, 184 boys) between the ages of 3 and 10 years were tested using the Test of Emotion Comprehension and the Coloured Progressive Matrices. The data obtained by using the path analysis model revealed that nonverbal intelligence was statistically associated with the ability to recognize emotions in the 3 developmental phases. The use of this model showed the significant effect that cognitive aspect plays on the reflexive phase. The authors aim to contribute to the debate about the influence of cognitive factors on emotion understanding.

THE EFFECT OF PLAUSIBILITY ON SENTENCE COMPREHENSION AMONG OLDER ADULTS AND ITS RELATION TO COGNITIVE FUNCTIONS

PubMed Central

Yoon, Jungmee; Campanelli, Luca; Goral, Mira; Marton, Klara; Eichorn, Naomi; Obler, Loraine K.

2016-01-01

Background/Study Context Older adults show age-related decline in complex-sentence comprehension. This has been attributed to a decrease in cognitive abilities that may support language processing, such as working memory (e.g., Caplan, DeDe, Waters, & Michaud, 2011,Psychology and Aging, 26, 439–450). The authors examined whether older adults have difficulty comprehending semantically implausible sentences and whether specific executive functions contribute to their comprehension performance. Methods Forty-two younger adults (aged 18–35) and 42 older adults (aged 55–75) were tested on two experimental tasks: a multiple negative comprehension task and an information processing battery. Results Both groups, older and younger adults, showed poorer performance for implausible sentences than for plausible sentences; however, no interaction was found between plausibility and age group. A regression analysis revealed that inhibition efficiency, as measured by a task that required resistance to proactive interference, predicted comprehension of implausible sentences in older adults only. Consistent with the compensation hypothesis, the older adults with better inhibition skills showed better comprehension than those with poor inhibition skills. Conclusion The findings suggest that semantic implausibility, along with syntactic complexity, increases linguistic and cognitive processing loads on auditory sentence comprehension. Moreover, the contribution of inhibitory control to the processing of semantic plausibility, particularly among older adults, suggests that the relationship between cognitive ability and language comprehension is strongly influenced by age. PMID:25978447

The effect of plausibility on sentence comprehension among older adults and its relation to cognitive functions.

PubMed

Yoon, Jungmee; Campanelli, Luca; Goral, Mira; Marton, Klara; Eichorn, Naomi; Obler, Loraine K

2015-01-01

BACKGROUND/STUDY CONTEXT: Older adults show age-related decline in complex-sentence comprehension. This has been attributed to a decrease in cognitive abilities that may support language processing, such as working memory (e.g., Caplan, DeDe, Waters, & Michaud, 2011,Psychology and Aging, 26, 439-450). The authors examined whether older adults have difficulty comprehending semantically implausible sentences and whether specific executive functions contribute to their comprehension performance. Forty-two younger adults (aged 18-35) and 42 older adults (aged 55-75) were tested on two experimental tasks: a multiple negative comprehension task and an information processing battery. Both groups, older and younger adults, showed poorer performance for implausible sentences than for plausible sentences; however, no interaction was found between plausibility and age group. A regression analysis revealed that inhibition efficiency, as measured by a task that required resistance to proactive interference, predicted comprehension of implausible sentences in older adults only. Consistent with the compensation hypothesis, the older adults with better inhibition skills showed better comprehension than those with poor inhibition skills. The findings suggest that semantic implausibility, along with syntactic complexity, increases linguistic and cognitive processing loads on auditory sentence comprehension. Moreover, the contribution of inhibitory control to the processing of semantic plausibility, particularly among older adults, suggests that the relationship between cognitive ability and language comprehension is strongly influenced by age.

Quantifying the Variability in Species' Vulnerability to Ocean Acidification

NASA Astrophysics Data System (ADS)

Kroeker, K. J.; Kordas, R. L.; Crim, R.; Gattuso, J.; Hendriks, I.; Singh, G. G.

2012-12-01

Ocean acidification represents a threat to marine species and ecosystems worldwide. As such, understanding the potential ecological impacts of acidification is a high priority for science, management, and policy. As research on the biological impacts of ocean acidification continues to expand at an exponential rate, a comprehensive understanding of the generalities and/or variability in organisms' responses and the corresponding levels of certainty of these potential responses is essential. Meta-analysis is a quantitative technique for summarizing the results of primary research studies and provides a transparent method to examine the generalities and/or variability in scientific results across numerous studies. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining the biological impacts of ocean acidification. Our results reveal decreased survival, calcification, growth, reproduction and development in response to acidification across a broad range of marine organisms, as well as significant trait-mediated variation among taxonomic groups and enhanced sensitivity among early life history stages. In addition, our results reveal a pronounced sensitivity of molluscs to acidification, especially among the larval stages, and enhanced vulnerability to acidification with concurrent exposure to increased seawater temperatures across a diversity of organisms.

Comprehensive geriatric care reduces acute perioperative delirium in elderly patients with hip fractures

PubMed Central

Wang, Yiyang; Tang, Jun; Zhou, Feiya; Yang, Lei; Wu, Jianbin

2017-01-01

Abstract Background: The aim of the current meta-analysis was to assess the treatment effect of comprehensive geriatric care in reducing acute perioperative delirium in older patients with hip fractures, compared with the effect of a routine orthopedic treatment protocol. Methods: We conducted a search of multiple databases to identify randomized controlled trials (RCTs) and quasi-RCTs comparing comprehensive geriatric care and routine orthopedic treatment regarding the following outcomes: incidence of delirium, assessment of cognitive status, and duration of delirium. Odds ratios (ORs) and mean differences (MDs) were pooled using either a fixed-effects or a random-effects model, depending on the heterogeneity of the trials included in the analysis. Results: Six RCTs and 1 quasi-RCT provided data from 1840 patients. These data revealed that comprehensive geriatric care may reduce the incidence of perioperative delirium (OR = 0.71; 95% confidence interval [CI], 0.57–0.89; P = .003) and that it was associated with higher cognitive status during hospitalization or at 1 month postoperatively (MD = 1.03; 95% CI, 0.93–1.13; P ≤ .00001). There was no significant difference in duration of perioperative delirium between the 2 treatment groups (MD = −2.48; 95% CI, −7.36 to 2.40; P = .32). Conclusion: Based on the quality of evidence provided, comprehensive geriatric care may reduce the incidence of perioperative delirium. To obtain evidence regarding the merits of comprehensive geriatric care in reducing severity of delirium and shortening the duration of delirium, there is a need for multicenter RCTs with high methodological quality. PMID:28658156

Eye-Tracking Evidence that Happy Faces Impair Verbal Message Comprehension: The Case of Health Warnings in Direct-to-Consumer Pharmaceutical Television Commercials

PubMed Central

Russell, Cristel Antonia; Swasy, John L.; Russell, Dale Wesley; Engel, Larry

2017-01-01

Risk warning or disclosure information in advertising is only effective in correcting consumers’ judgments if enough cognitive capacity is available to process that information. Hence, comprehension of verbal warnings in TV commercials may suffer if accompanied by positive visual elements. This research addresses this concern about cross-modality interference in the context of direct-to-consumer (DTC) pharmaceutical commercials in the United States by experimentally testing whether positive facial expressions reduce consumers’ understanding of the mandated health warning. A content analysis of a sample of DTC commercials reveals that positive facial expressions are more prevalent during the verbal warning act of the commercials than during the other acts. An eye-tracking experiment conducted with specially produced DTC commercials, which vary the valence of characters’ facial expressions during the health warning, provides evidence that happy faces reduce objective comprehension of the warning. PMID:29269979

Working memory and proverb comprehension in adolescents with traumatic brain injury: a preliminary investigation.

PubMed

Moran, Catherine A; Nippold, Marilyn A; Gillon, Gail T

2006-04-01

This study investigated the relationship between working memory and comprehension of low-familiarity proverbs in adolescents with traumatic brain injury (TBI). Ten adolescents, aged 12-21 years who had suffered a TBI prior to the age of 10 years and 10 individually age-matched peers with typical development participated in the study. The participants listened to short paragraphs containing a proverb and interpreted the meaning of the proverb using a forced-choice task. In addition, participants engaged in a task that evaluated working memory ability. Analysis revealed that individuals with TBI differed from their non-injured peers in their understanding of proverbs. In addition, working memory capacity influenced performance for all participants. The importance of considering working memory when evaluating figurative language comprehension in adolescents with TBI is highlighted. Implications for future research, particularly with regard to varying working memory and task demands, are considered.

Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity

NASA Astrophysics Data System (ADS)

Corcoran, Martin M.; Phad, Ganesh E.; Bernat, Néstor Vázquez; Stahl-Hennig, Christiane; Sumida, Noriyuki; Persson, Mats A. A.; Martin, Marcel; Hedestam, Gunilla B. Karlsson

2016-12-01

Comprehensive knowledge of immunoglobulin genetics is required to advance our understanding of B cell biology. Validated immunoglobulin variable (V) gene databases are close to completion only for human and mouse. We present a novel computational approach, IgDiscover, that identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species. Further, we describe a novel human IGHV3-21 allele and confirm significant gene differences between Balb/c and C57BL6 mouse strains, demonstrating the power of IgDiscover as a germline V gene discovery tool.

Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity

PubMed Central

Corcoran, Martin M.; Phad, Ganesh E.; Bernat, Néstor Vázquez; Stahl-Hennig, Christiane; Sumida, Noriyuki; Persson, Mats A.A.; Martin, Marcel; Hedestam, Gunilla B. Karlsson

2016-01-01

Comprehensive knowledge of immunoglobulin genetics is required to advance our understanding of B cell biology. Validated immunoglobulin variable (V) gene databases are close to completion only for human and mouse. We present a novel computational approach, IgDiscover, that identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species. Further, we describe a novel human IGHV3-21 allele and confirm significant gene differences between Balb/c and C57BL6 mouse strains, demonstrating the power of IgDiscover as a germline V gene discovery tool. PMID:27995928

Comprehensive Analysis of Large Sets of Age-Related Physiological Indicators Reveals Rapid Aging around the Age of 55 Years.

PubMed

Lixie, Erin; Edgeworth, Jameson; Shamir, Lior

2015-01-01

While many studies show a correlation between chronological age and physiological indicators, the nature of this correlation is not fully understood. To perform a comprehensive analysis of the correlation between chronological age and age-related physiological indicators. Physiological aging scores were deduced using principal component analysis from a large dataset of 1,227 variables measured in a cohort of 4,796 human subjects, and the correlation between the physiological aging scores and chronological age was assessed. Physiological age does not progress linearly or exponentially with chronological age: a more rapid physiological change is observed around the age of 55 years, followed by a mild decline until around the age of 70 years. These findings provide evidence that the progression of physiological age is not linear with that of chronological age, and that periods of mild change in physiological age are separated by periods of more rapid aging. © 2015 S. Karger AG, Basel.

Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.

PubMed

Yang, Chao; He, Zengyou; Yu, Weichuan

2009-01-06

In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorithms is yet available. The main objective of this paper is to provide such a survey and to compare the performance of single spectrum based peak detection methods. In general, we can decompose a peak detection procedure into three consequent parts: smoothing, baseline correction and peak finding. We first categorize existing peak detection algorithms according to the techniques used in different phases. Such a categorization reveals the differences and similarities among existing peak detection algorithms. Then, we choose five typical peak detection algorithms to conduct a comprehensive experimental study using both simulation data and real MALDI MS data. The results of comparison show that the continuous wavelet-based algorithm provides the best average performance.

How have health promotion frameworks considered gender?

PubMed

Gelb, Karen; Pederson, Ann; Greaves, Lorraine

2012-12-01

This paper provides an overview of five key internationally recognized health promotion frameworks and assesses their consideration of gender. This analysis was conducted as part of the Promoting Health in Women project, a Canadian initiative focused on generating a framework for effective health promotion for women. To date, no review of health promotion frameworks has specifically focused on assessing the treatment of gender. This analysis draws on a comprehensive literature review that covered available literature on gender and health promotion frameworks published internationally between 1974 and 2010. Analysis of five key health promotion frameworks revealed that although gender was at times mentioned as a determinant of health, gender was never identified and integrated as a factor critical to successful health promotion. This superficial attention to the role of gender in health promotion is problematic as it limits our capacity to understand how gender influences health, health contexts and health promotion, as well as our ability to integrate gender into future comprehensive health promotion strategies.

Comprehensive analysis of structure and temperature, frequency and concentration-dependent dielectric properties of lithium-substituted cobalt ferrites (Li x Co1- x Fe2O4)

NASA Astrophysics Data System (ADS)

Anjum, Safia; Nisa, Mehru; Sabah, Aneeqa; Rafique, M. S.; Zia, Rehana

2017-08-01

This paper has been dedicated to the synthesis and characterization of a series of lithium-substituted cobalt ferrites Li x Co1- x Fe2O4 ( x = 0, 0.2, 0.4, 0.6, 0.8, 1). These samples have been prepared using simple ball milling machine through powder metallurgy route. The structural analysis is carried out using X-ray diffractometer and their 3D vitalization is simulated using diamond software. The frequency and temperature-dependent dielectric properties of prepared samples have been measured using inductor capacitor resistor (LCR) meter. The structural analysis confirms that all the prepared samples have inverse cubic spinel structure. It is also revealed that the crystallite size and lattice parameter decrease with the increasing concentration of lithium (Li+1) ions, it is due to the smaller ionic radii of lithium ions. The comprehensive analysis of frequency, concentration and temperature-dependent dielectric properties of prepared samples is described in this paper. It is observed that the dielectric constant and tangent loss have decreased and conductivity increased as the frequency increases. It is also revealed that the dielectric constant, tangent loss and AC conductivity increase as the concentration of lithium increases due to its lower electronegativity value. Temperature plays a vital role in enhancing the dielectric constant, tangent loss and AC conductivity because the mobility of ions increases as the temperature increases.

The Effect of Drama-Based Pedagogy on PreK-16 Outcomes: A Meta-Analysis of Research from 1985 to 2012

ERIC Educational Resources Information Center

Lee, Bridget Kiger; Patall, Erika A.; Cawthon, Stephanie W.; Steingut, Rebecca R.

2015-01-01

The President's Committee on the Arts and Humanities report heartily supported arts integration. However, the President's Committee called for a better understanding of the dimensions of quality and best practices. One promising arts integration method is drama-based pedagogy (DBP). A comprehensive search of the literature revealed 47…

Linguistic and Cognitive Profiles of 8- to 15-Year-Old Children With Specific Reading Comprehension Difficulties.

PubMed

Potocki, Anna; Sanchez, Monique; Ecalle, Jean; Magnan, Annie

This article presents two studies investigating the role of executive functioning in written text comprehension in children and adolescents. In a first study, the involvement of executive functions in reading comprehension performance was examined in normally developing children in fifth grade. Two aspects of text comprehension were differentiated: literal and inferential processes. The results demonstrated that while three aspects of executive functioning (working memory, planning, and inhibition processes) were significantly predictive of the performance on the inferential questions of the comprehension test, these factors did not predict the scores on the literal tasks of the test. In a second experiment, the linguistic and cognitive profiles of children in third/fifth and seventh/ninth grades with a specific reading comprehension deficit were examined. This analysis revealed that the deficits experienced by the less skilled comprehenders in both the linguistic and the executive domains could evolve over time. As a result, linguistic factors do not make it possible to distinguish between good and poor comprehenders among the group of older children, whereas the difficulties relating to executive processing remain stable over development. These findings are discussed in the context of the need to take account of the executive difficulties that characterize less skilled comprehenders of any age, especially for remediation purposes.

Comprehensive meta-analysis reveals association between multiple imprinting disorders and conception by assisted reproductive technology.

PubMed

Cortessis, Victoria K; Azadian, Moosa; Buxbaum, James; Sanogo, Fatimata; Song, Ashley Y; Sriprasert, Intira; Wei, Pengxiao C; Yu, Jing; Chung, Karine; Siegmund, Kimberly D

2018-04-25

To determine whether a history of conception by assisted reproductive technology (ART) is associated with occurrence of one or more imprinting disorders of either maternal or paternal origin. We implemented a systematic review of scholarly literature followed by comprehensive meta-analysis to quantitatively synthesize data from reports relating to use of ART to occurrence of any imprinting disorder of humans, including Beckwith-Wiedemann (BWS), Angelman (AS), Prader-Willi (PWS), and Silver-Russell (SRS) syndromes, as well as transient neonatal diabetes mellitus (TNDB) and sporadic retinoblasoma (RB). The systematic review identified 13 reports presenting unique data from 23 studies that related conception following ART to occurrence of imprinting disorders. Multiple studies of four disorder were identified, for which meta-analysis yielded the following summary estimates of associations with a history of ART: AS, summary odds ratio (sOR) = 4.7 (95% confidence interval (CI) 2.6-8.5, 4 studies); BWS, sOR = 5.8 (95% CI 3.1-11.1, 8 studies); PWS, sOR = 2.2 (95% CI 1.6-3.0, 6 studies); SRS, sOR = 11.3 (95% CI 4.5-28.5, 3 studies). Only one study reported on each of TNDB and RB. Published data reveal positive associations between history of ART conception and each of four imprinting disorders. Reasons for these associations warrant further investigation.

Comprehensive Analysis of ABA Effects on Ethylene Biosynthesis and Signaling during Tomato Fruit Ripening.

PubMed

Mou, Wangshu; Li, Dongdong; Bu, Jianwen; Jiang, Yuanyuan; Khan, Zia Ullah; Luo, Zisheng; Mao, Linchun; Ying, Tiejin

2016-01-01

ABA has been widely acknowledged to regulate ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism underlying the interaction between these two hormones are largely unexplored. In the present study, exogenous ABA treatment obviously promoted fruit ripening as well as ethylene emission, whereas NDGA (Nordihydroguaiaretic acid, an inhibitor of ABA biosynthesis) application showed the opposite biological effects. Combined RNA-seq with time-course RT-PCR analysis, our study not only helped to illustrate how ABA regulated itself at the transcription level, but also revealed that ABA can facilitate ethylene production and response probably by regulating some crucial genes such as LeACS4, LeACO1, GR and LeETR6. In addition, investigation on the fruits treated with 1-MCP immediately after ABA exposure revealed that ethylene might be essential for the induction of ABA biosynthesis and signaling at the onset of fruit ripening. Furthermore, some specific transcription factors (TFs) known as regulators of ethylene synthesis and sensibility (e.g. MADS-RIN, TAGL1, CNR and NOR) were also observed to be ABA responsive, which implied that ABA influenced ethylene action possibly through the regulation of these TFs expression. Our comprehensive physiological and molecular-level analysis shed light on the mechanism of cross-talk between ABA and ethylene during the process of tomato fruit ripening.

Comprehensive Analysis of ABA Effects on Ethylene Biosynthesis and Signaling during Tomato Fruit Ripening

PubMed Central

Bu, Jianwen; Jiang, Yuanyuan; Khan, Zia Ullah; Luo, Zisheng; Mao, Linchun; Ying, Tiejin

2016-01-01

ABA has been widely acknowledged to regulate ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism underlying the interaction between these two hormones are largely unexplored. In the present study, exogenous ABA treatment obviously promoted fruit ripening as well as ethylene emission, whereas NDGA (Nordihydroguaiaretic acid, an inhibitor of ABA biosynthesis) application showed the opposite biological effects. Combined RNA-seq with time-course RT-PCR analysis, our study not only helped to illustrate how ABA regulated itself at the transcription level, but also revealed that ABA can facilitate ethylene production and response probably by regulating some crucial genes such as LeACS4, LeACO1, GR and LeETR6. In addition, investigation on the fruits treated with 1-MCP immediately after ABA exposure revealed that ethylene might be essential for the induction of ABA biosynthesis and signaling at the onset of fruit ripening. Furthermore, some specific transcription factors (TFs) known as regulators of ethylene synthesis and sensibility (e.g. MADS-RIN, TAGL1, CNR and NOR) were also observed to be ABA responsive, which implied that ABA influenced ethylene action possibly through the regulation of these TFs expression. Our comprehensive physiological and molecular-level analysis shed light on the mechanism of cross-talk between ABA and ethylene during the process of tomato fruit ripening. PMID:27100326

Trophic Mode-Dependent Proteomic Analysis Reveals Functional Significance of Light-Independent Chlorophyll Synthesis in Synechocystis sp. PCC 6803.

PubMed

Fang, Longfa; Ge, Haitao; Huang, Xiahe; Liu, Ye; Lu, Min; Wang, Jinlong; Chen, Weiyang; Xu, Wu; Wang, Yingchun

2017-01-09

The photosynthetic model organism Synechocystis sp. PCC 6803 can grow in different trophic modes, depending on the availability of light and exogenous organic carbon source. However, how the protein profile changes to facilitate the cells differentially propagate in different modes has not been comprehensively investigated. Using isobaric labeling-based quantitative proteomics, we simultaneously identified and quantified 45% Synechocystis proteome across four different trophic modes, i.e., autotrophic, heterotrophic, photoheterotrophic, and mixotrophic modes. Among the 155 proteins that are differentially expressed across four trophic modes, proteins involved in nitrogen assimilation and light-independent chlorophyll synthesis are dramatically upregulated in the mixotrophic mode, concomitant with a dramatic increase of P II phosphorylation that senses carbon and nitrogen assimilation status. Moreover, functional study using a mutant defective in light-independent chlorophyll synthesis revealed that this pathway is important for chlorophyll accumulation under a cycled light/dark illumination regime, a condition mimicking day/night cycles in certain natural habitats. Collectively, these results provide the most comprehensive information on trophic mode-dependent protein expression in cyanobacterium, and reveal the functional significance of light-independent chlorophyll synthesis in trophic growth. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

Shallow and deep orthographies in Hebrew: the role of vowelization in reading development for unvowelized scripts.

PubMed

Schiff, Rachel

2012-12-01

The present study explored the speed, accuracy, and reading comprehension of vowelized versus unvowelized scripts among 126 native Hebrew speaking children in second, fourth, and sixth grades. Findings indicated that second graders read and comprehended vowelized scripts significantly more accurately and more quickly than unvowelized scripts, whereas among fourth and sixth graders reading of unvowelized scripts developed to a greater degree than the reading of vowelized scripts. An analysis of the mediation effect for children's mastery of vowelized reading speed and accuracy on their mastery of unvowelized reading speed and comprehension revealed that in second grade, reading accuracy of vowelized words mediated the reading speed and comprehension of unvowelized scripts. In the fourth grade, accuracy in reading both vowelized and unvowelized words mediated the reading speed and comprehension of unvowelized scripts. By sixth grade, accuracy in reading vowelized words offered no mediating effect, either on reading speed or comprehension of unvowelized scripts. The current outcomes thus suggest that young Hebrew readers undergo a scaffolding process, where vowelization serves as the foundation for building initial reading abilities and is essential for successful and meaningful decoding of unvowelized scripts.

[Application of target restoration space quantity and quantitative relation in precise esthetic prosthodontics].

PubMed

Haiyang, Yu; Tian, Luo

2016-06-01

Target restoration space (TRS) is the most precise space required for designing optimal prosthesis. TRS consists of an internal or external tooth space to confirm the esthetics and function of the final restoration. Therefore, assisted with quantitive analysis transfer, TRS quantitative analysis is a significant improvement for minimum tooth preparation. This article presents TRS quantity-related measurement, analysis, transfer, and internal relevance of three TR. classifications. Results reveal the close bond between precision and minimally invasive treatment. This study can be used to improve the comprehension and execution of precise esthetic prosthodontics.

Comprehensive Chemical Fingerprinting of High-Quality Cocoa at Early Stages of Processing: Effectiveness of Combined Untargeted and Targeted Approaches for Classification and Discrimination.

PubMed

Magagna, Federico; Guglielmetti, Alessandro; Liberto, Erica; Reichenbach, Stephen E; Allegrucci, Elena; Gobino, Guido; Bicchi, Carlo; Cordero, Chiara

2017-08-02

This study investigates chemical information of volatile fractions of high-quality cocoa (Theobroma cacao L. Malvaceae) from different origins (Mexico, Ecuador, Venezuela, Columbia, Java, Trinidad, and Sao Tomè) produced for fine chocolate. This study explores the evolution of the entire pattern of volatiles in relation to cocoa processing (raw, roasted, steamed, and ground beans). Advanced chemical fingerprinting (e.g., combined untargeted and targeted fingerprinting) with comprehensive two-dimensional gas chromatography coupled with mass spectrometry allows advanced pattern recognition for classification, discrimination, and sensory-quality characterization. The entire data set is analyzed for 595 reliable two-dimensional peak regions, including 130 known analytes and 13 potent odorants. Multivariate analysis with unsupervised exploration (principal component analysis) and simple supervised discrimination methods (Fisher ratios and linear regression trees) reveal informative patterns of similarities and differences and identify characteristic compounds related to sample origin and manufacturing step.

Comprehensive Quantitative Analysis on Privacy Leak Behavior

PubMed Central

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

Comprehensive quantitative analysis on privacy leak behavior.

PubMed

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects.

Comprehensive analysis of "bath salts" purchased from California stores and the internet.

PubMed

Schneir, A; Ly, B T; Casagrande, K; Darracq, M; Offerman, S R; Thornton, S; Smollin, C; Vohra, R; Rangun, C; Tomaszewski, C; Gerona, R R

2014-08-01

To analyze the contents of "bath salt" products purchased from California stores and the Internet qualitatively and quantitatively in a comprehensive manner. A convenience sample of "bath salt" products were purchased in person by multiple authors at retail stores in six California cities and over the Internet (U.S. sites only), between August 11, 2011 and December 15, 2011. Liquid chromatography-time-of-flight mass spectrometry was utilized to identify and quantify all substances in the purchased products. Thirty-five "bath salt" products were purchased and analyzed. Prices ranged from $9.95 to 49.99 (U.S. dollars). Most products had a warning against use. The majority (32/35, 91%) had one (n = 15) or multiple cathinones (n = 17) present. Fourteen different cathinones were identified, 3,4-methylenedioxypyrovalerone (MDPV) being the most common. Multiple drugs found including cathinones (buphedrone, ethcathinone, ethylone, MDPBP, and PBP), other designer amines (ethylamphetamine, fluoramphetamine, and 5-IAI), and the antihistamine doxylamine had not been previously identified in U.S. "bath salt" products. Quantification revealed high stimulant content and in some cases dramatic differences in either total cathinone or synthetic stimulant content between products with the same declared weight and even between identically named and outwardly appearing products. Comprehensive analysis of "bath salts" purchased from California stores and the Internet revealed the products to consistently contain cathinones, alone, or in different combinations, sometimes in high quantity. Multiple cathinones and other drugs found had not been previously identified in U.S. "bath salt" products. High total stimulant content in some products and variable qualitative and quantitative composition amongst products were demonstrated.

Brain structure differences between Chinese and Caucasian cohorts: A comprehensive morphometry study.

PubMed

Tang, Yuchun; Zhao, Lu; Lou, Yunxia; Shi, Yonggang; Fang, Rui; Lin, Xiangtao; Liu, Shuwei; Toga, Arthur

2018-05-01

Numerous behavioral observations and brain function studies have demonstrated that neurological differences exist between East Asians and Westerners. However, the extent to which these factors relate to differences in brain structure is still not clear. As the basis of brain functions, the anatomical differences in brain structure play a primary and critical role in the origination of functional and behavior differences. To investigate the underlying differences in brain structure between the two cultural/ethnic groups, we conducted a comparative study on education-matched right-handed young male adults (age = 22-29 years) from two cohorts, Han Chinese (n = 45) and Caucasians (n = 45), using high-dimensional structural magnetic resonance imaging (MRI) data. Using two well-validated imaging analysis techniques, surface-based morphometry (SBM) and voxel-based morphometry (VBM), we performed a comprehensive vertex-wise morphometric analysis of the brain structures between Chinese and Caucasian cohorts. We identified consistent significant between-group differences in cortical thickness, volume, and surface area in the frontal, temporal, parietal, occipital, and insular lobes as well as the cingulate cortices. The SBM analyses revealed that compared with Caucasians, the Chinese population showed larger cortical structures in the temporal and cingulate regions, and smaller structural measures in the frontal and parietal cortices. The VBM data of the same sample was well-aligned with the SBM findings. Our findings systematically revealed comprehensive brain structural differences between young male Chinese and Caucasians, and provided new neuroanatomical insights to the behavioral and functional distinctions in the two cultural/ethnic populations. © 2018 Wiley Periodicals, Inc.

Adaptive significance of right hemisphere activation in aphasic language comprehension

PubMed Central

Meltzer, Jed A.; Wagage, Suraji; Ryder, Jennifer; Solomon, Beth; Braun, Allen R.

2013-01-01

Aphasic patients often exhibit increased right hemisphere activity during language tasks. This may represent takeover of function by regions homologous to the left-hemisphere language networks, maladaptive interference, or adaptation of alternate compensatory strategies. To distinguish between these accounts, we tested language comprehension in 25 aphasic patients using an online sentence-picture matching paradigm while measuring brain activation with MEG. Linguistic conditions included semantically irreversible (“The boy is eating the apple”) and reversible (“The boy is pushing the girl”) sentences at three levels of syntactic complexity. As expected, patients performed well above chance on irreversible sentences, and at chance on reversible sentences of high complexity. Comprehension of reversible non-complex sentences ranged from nearly perfect to chance, and was highly correlated with offline measures of language comprehension. Lesion analysis revealed that comprehension deficits for reversible sentences were predicted by damage to the left temporal lobe. Although aphasic patients activated homologous areas in the right temporal lobe, such activation was not correlated with comprehension performance. Rather, patients with better comprehension exhibited increased activity in dorsal fronto-parietal regions. Correlations between performance and dorsal network activity occurred bilaterally during perception of sentences, and in the right hemisphere during a post-sentence memory delay. These results suggest that effortful reprocessing of perceived sentences in short-term memory can support improved comprehension in aphasia, and that strategic recruitment of alternative networks, rather than homologous takeover, may account for some findings of right hemisphere language activation in aphasia. PMID:23566891

The business process management software for successful quality management and organization: A case study from the University of Split School of Medicine.

PubMed

Sapunar, Damir; Grković, Ivica; Lukšić, Davor; Marušić, Matko

2016-05-01

Our aim was to describe a comprehensive model of internal quality management (QM) at a medical school founded on the business process analysis (BPA) software tool. BPA software tool was used as the core element for description of all working processes in our medical school, and subsequently the system served as the comprehensive model of internal QM. The quality management system at the University of Split School of Medicine included the documentation and analysis of all business processes within the School. The analysis revealed 80 weak points related to one or several business processes. A precise analysis of medical school business processes allows identification of unfinished, unclear and inadequate points in these processes, and subsequently the respective improvements and increase of the QM level and ultimately a rationalization of the institution's work. Our approach offers a potential reference model for development of common QM framework allowing a continuous quality control, i.e. the adjustments and adaptation to contemporary educational needs of medical students. Copyright © 2016 by Academy of Sciences and Arts of Bosnia and Herzegovina.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorialsmore » explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. In conclusion, this computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.« less

Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine.

PubMed

Fang, Han; Wu, Yiyang; Yang, Hui; Yoon, Margaret; Jiménez-Barrón, Laura T; Mittelman, David; Robison, Reid; Wang, Kai; Lyon, Gholson J

2017-02-23

Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants. We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader-Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms. A comprehensive WGS pipeline was used to ensure reliable detection of genomic variants. Beyond variant filtering, we pursued phenotypic prioritization of candidate genes using Phenolyzer. Regarding PWS, WGS confirmed a 5.5 Mb de novo deletion of the parental allele at 15q11.2 to 15q13.1. Phenolyzer successfully returned the diagnosis of PWS, and pinpointed clinically relevant genes in the deletion. Further, Phenolyzer revealed how each of the genes is linked with the phenotypes represented by HPO terms. For HH, WGS identified a known disease variant (p.C282Y) in HFE of an affected female. Analysis of HPO terms alone fails to provide a correct diagnosis, but Phenolyzer successfully revealed the phenotype-genotype relationship using a disease-centric approach. Finally, Phenolyzer also revealed the complexity behind dysautonomia-like symptoms, and seven variants that might be associated with the phenotypes were identified by manual filtering based on a dominant inheritance model. The integration of WGS and HPO can inform comprehensive molecular diagnosis for patients, eliminate false positives and reveal novel insights into undiagnosed diseases. Due to extreme heterogeneity and insufficient knowledge of human diseases, it is also important that phenotypic and genomic data are standardized and shared simultaneously.

Genomewide Clonal Analysis of Lethal Mutations in the Drosophila melanogaster Eye: Comparison of the X Chromosome and Autosomes

PubMed Central

Call, Gerald B.; Olson, John M.; Chen, Jiong; Villarasa, Nikki; Ngo, Kathy T.; Yabroff, Allison M.; Cokus, Shawn; Pellegrini, Matteo; Bibikova, Elena; Bui, Chris; Cespedes, Albert; Chan, Cheryl; Chan, Stacy; Cheema, Amrita K.; Chhabra, Akanksha; Chitsazzadeh, Vida; Do, Minh-Tu; Fang, Q. Angela; Folick, Andrew; Goodstein, Gelsey L.; Huang, Cheng R.; Hung, Tony; Kim, Eunha; Kim, William; Kim, Yulee; Kohan, Emil; Kuoy, Edward; Kwak, Robert; Lee, Eric; Lee, JiEun; Lin, Henry; Liu, H-C. Angela; Moroz, Tatiana; Prasad, Tharani; Prashad, Sacha L.; Patananan, Alexander N.; Rangel, Alma; Rosselli, Desiree; Sidhu, Sohrab; Sitz, Daniel; Taber, Chelsea E.; Tan, Jingwen; Topp, Kasey; Tran, PhuongThao; Tran, Quynh-Minh; Unkovic, Mary; Wells, Maggie; Wickland, Jessica; Yackle, Kevin; Yavari, Amir; Zaretsky, Jesse M.; Allen, Christopher M.; Alli, Latifat; An, Ju; Anwar, Abbas; Arevalo, Sonia; Ayoub, Danny; Badal, Shawn S.; Baghdanian, Armonde; Baghdanian, Arthur H.; Baumann, Sara A.; Becerra, Vivian N.; Chan, Hei J.; Chang, Aileen E.; Cheng, Xibin A.; Chin, Mabel; Chong, Fleurette; Crisostomo, Carlyn; Datta, Sanjit; Delosreyes, Angela; Diep, Francie; Ekanayake, Preethika; Engeln, Mark; Evers, Elizabeth; Farshidi, Farzin; Fischer, Katrina; Formanes, Arlene J.; Gong, Jun; Gupta, Riju; Haas, Blake E.; Hahm, Vicky; Hsieh, Michael; Hui, James Z.; Iao, Mei L.; Jin, Sophia D.; Kim, Angela Y.; Kim, Lydia S-H.; King, Megan; Knudsen-Robbins, Chloe; Kohanchi, David; Kovshilovskaya, Bogdana; Ku, Amy; Kung, Raymond W.; Landig, Mark E. L.; Latterman, Stephanie S.; Lauw, Stephanie S.; Lee, Daniel S.; Lee, Joann S.; Lei, Kai C.; Leung, Lesley L.; Lerner, Renata; Lin, Jian-ya; Lin, Kathleen; Lim, Bryon C.; Lui, Crystal P. Y.; Liu, Tiffany Q.; Luong, Vincent; Makshanoff, Jacob; Mei, An-Chi; Meza, Miguel; Mikhaeil, Yara A.; Moarefi, Majid; Nguyen, Long H.; Pai, Shekhar S.; Pandya, Manish; Patel, Aadit R.; Picard, Paul D.; Safaee, Michael M.; Salame, Carol; Sanchez, Christian; Sanchez, Nina; Seifert, Christina C.; Shah, Abhishek; Shilgevorkyan, Oganes H.; Singh, Inderroop; Soma, Vanessa; Song, Junia J.; Srivastava, Neetika; Sta.Ana, Jennifer L.; Sun, Christie; Tan, Diane; Teruya, Alison S.; Tikia, Robyn; Tran, Trinh; Travis, Emily G.; Trinh, Jennifer D.; Vo, Diane; Walsh, Thomas; Wong, Regan S.; Wu, Katherine; Wu, Ya-Whey; Yang, Nkau X. V.; Yeranosian, Michael; Yu, James S.; Zhou, Jennifer J.; Zhu, Ran X.; Abrams, Anna; Abramson, Amanda; Amado, Latiffe; Anderson, Jenny; Bashour, Keenan; Beyer, Elsa; Bookatz, Allen; Brewer, Sarah; Buu, Natalie; Calvillo, Stephanie; Cao, Joseph; Chan, Amy; Chan, Jenny; Chang, Aileen; Chang, Daniel; Chang, Yuli; Chen, YiBing; Choi, Joo; Chou, Jeyling; Dang, Peter; Datta, Sumit; Davarifar, Ardy; Deravanesian, Artemis; Desai, Poonam; Fabrikant, Jordan; Farnad, Shahbaz; Fu, Katherine; Garcia, Eddie; Garrone, Nick; Gasparyan, Srpouhi; Gayda, Phyllis; Go, Sherrylene; Goffstein, Chad; Gonzalez, Courtney; Guirguis, Mariam; Hassid, Ryan; Hermogeno, Brenda; Hong, Julie; Hong, Aria; Hovestreydt, Lindsay; Hu, Charles; Huff, Devon; Jamshidian, Farid; Jen, James; Kahen, Katrin; Kao, Linda; Kelley, Melissa; Kho, Thomas; Kim, Yein; Kim, Sarah; Kirkpatrick, Brian; Langenbacher, Adam; Laxamana, Santino; Lee, Janet; Lee, Chris; Lee, So-Youn; Lee, ToHang S.; Lee, Toni; Lewis, Gemma; Lezcano, Sheila; Lin, Peter; Luu, Thanh; Luu, Julie; Marrs, Will; Marsh, Erin; Marshall, Jamie; Min, Sarah; Minasian, Tanya; Minye, Helena; Misra, Amit; Morimoto, Miles; Moshfegh, Yasaman; Murray, Jessica; Nguyen, Kha; Nguyen, Cynthia; Nodado, Ernesto; O'Donahue, Amanda; Onugha, Ndidi; Orjiakor, Nneka; Padhiar, Bhavin; Paul, Eric; Pavel-Dinu, Mara; Pavlenko, Alex; Paz, Edwin; Phaklides, Sarah; Pham, Lephong; Poulose, Preethi; Powell, Russell; Pusic, Aya; Ramola, Divi; Regalia, Kirsten; Ribbens, Meghann; Rifai, Bassel; Saakyan, Manyak; Saarikoski, Pamela; Segura, Miriam; Shadpour, Farnaz; Shemmassian, Aram; Singh, Ramnik; Singh, Vivek; Skinner, Emily; Solomin, Daniel; Soneji, Kosha; Spivey, Kristin; Stageberg, Erika; Stavchanskiy, Marina; Tekchandani, Leena; Thai, Leo; Thiyanaratnam, Jayantha; Tong, Maurine; Toor, Aneet; Tovar, Steve; Trangsrud, Kelly; Tsang, Wah-Yung; Uemura, Marc; Vollmer, Emily; Weiss, Emily; Wood, Damien; Wu, Joy; Wu, Sophia; Wu, Winston; Xu, Qing; Yamauchi, Yuki; Yarosh, Will; Yee, Laura; Yen, George; Banerjee, Utpal

2007-01-01

Using a large consortium of undergraduate students in an organized program at the University of California, Los Angeles (UCLA), we have undertaken a functional genomic screen in the Drosophila eye. In addition to the educational value of discovery-based learning, this article presents the first comprehensive genomewide analysis of essential genes involved in eye development. The data reveal the surprising result that the X chromosome has almost twice the frequency of essential genes involved in eye development as that found on the autosomes. PMID:17720911

Comparative Genomic Analysis MERS CoV Isolated from Humans and Camels with Special Reference to Virus Encoded Helicase.

PubMed

Alnazawi, Mohamed; Altaher, Abdallah; Kandeel, Mahmoud

2017-01-01

Middle East Respiratory Syndrome Coronavirus (MERS CoV) is a new emerging viral disease characterized by high fatality rate. Understanding MERS CoV genetic aspects and codon usage pattern is important to understand MERS CoV survival, adaptation, evolution, resistance to innate immunity, and help in finding the unique aspects of the virus for future drug discovery experiments. In this work, we provide comprehensive analysis of 238 MERS CoV full genomes comprised of human (hMERS) and camel (cMERS) isolates of the virus. MERS CoV genome shaping seems to be under compositional and mutational bias, as revealed by preference of A/T over G/C nucleotides, preferred codons, nucleotides at the third position of codons (NT3s), relative synonymous codon usage, hydropathicity (Gravy), and aromaticity (Aromo) indices. Effective number of codons (ENc) analysis reveals a general slight codon usage bias. Codon adaptation index reveals incomplete adaptation to host environment. MERS CoV showed high ability to resist the innate immune response by showing lower CpG frequencies. Neutrality evolution analysis revealed a more significant role of mutation pressure in cMERS over hMERS. Correspondence analysis revealed that MERS CoV genomes have three genetic clusters, which were distinct in their codon usage, host, and geographic distribution. Additionally, virtual screening and binding experiments were able to identify three new virus-encoded helicase binding compounds. These compounds can be used for further optimization of inhibitors.

Comprehensive treatments for social cognitive deficits in schizophrenia: A critical review and effect-size analysis of controlled studies.

PubMed

Kurtz, Matthew M; Gagen, Emily; Rocha, Nuno B F; Machado, Sergio; Penn, David L

2016-02-01

Recent advances in psychosocial treatments for schizophrenia have targeted social cognitive deficits. A critical literature review and effect-size (ES) analysis was conducted to investigate the efficacy of comprehensive programs of social cognitive training in schizophrenia. Results revealed 16 controlled studies consisting of seven models of comprehensive treatment with only three of these treatment models investigated in more than one study. The effects of social cognitive training were reported in 11/15 studies that included facial affect recognition skills (ES=.84) and 10/13 studies that included theory-of-mind (ES=.70) as outcomes. Less than half (4/9) of studies that measured attributional style as an outcome reported effects of treatment, but effect sizes across studies were significant (ESs=.30-.52). The effect sizes for symptoms were modest, but, with the exception of positive symptoms, significant (ESs=.32-.40). The majority of trials were randomized (13/16), selected active control conditions (11/16) and included at least 30 participants (12/16). Concerns for this area of research include the absence of blinded outcome raters in more than 50% of trials and low rates of utilization of procedures for maintaining treatment fidelity. These findings provide preliminary support for the broader use of comprehensive social cognitive training procedures as a psychosocial intervention for schizophrenia. Copyright © 2015 Elsevier Ltd. All rights reserved.

Combined Occurrence of Autosomal Dominant Aniridia and Autosomal Recessive Albinism in Several Members of a Family.

PubMed

Yahalom, Claudia; Sharon, Dror; Dalia, Eli; Simhon, Shiran Ben; Shemesh, Efrat; Blumenfeld, Anat

2015-06-01

To characterize clinical and genetic aspects of a family with a unique combination of two hereditary blinding eye diseases. Comprehensive eye examination of proband and family members. Molecular analyses of the TYR and PAX6 genes. A young couple, both legally blind, requested genetic counselling regarding their ocular condition. The female was previously diagnosed with oculocutaneous albinism (OCA1A) and her spouse was diagnosed with Peters anomaly. A comprehensive clinical examination revealed that the female had OCA1A combined with signs of another ocular disease, showing some similarity to aniridia. A complete ocular examination of her family members revealed that her brother also suffered from the same combined phenotype, her father had typical OCA1A signs, and her mother and sister had aniridia-like phenotype, without clinical diagnosis until the time of presentation. Molecular analysis identified two compound heterozygous TYR mutations known to cause OCAIA and cosegregate with oculocutaneous albinism. In addition, we identified a novel heterozygous PAX6 mutation confirming the atypical aniridia phenotype. We report here a unique and rare clinical phenotype that is explained by the segregation of two severe inherited eye diseases. The clinical and genetic analysis in this family allowed them to receive accurate genetic counseling.

A comprehensive, genome-wide analysis of autophagy-related genes identified in tobacco suggests a central role of autophagy in plant response to various environmental cues

PubMed Central

Zhou, Xue-mei; Zhao, Peng; Wang, Wei; Zou, Jie; Cheng, Tian-he; Peng, Xiong-bo; Sun, Meng-xiang

2015-01-01

Autophagy is an evolutionarily conserved mechanism in both animals and plants, which has been shown to be involved in various essential developmental processes in plants. Nicotiana tabacum is considered to be an ideal model plant and has been widely used for the study of the roles of autophagy in the processes of plant development and in the response to various stresses. However, only a few autophagy-related genes (ATGs) have been identified in tobacco up to now. Here, we identified 30 ATGs belonging to 16 different groups in tobacco through a genome-wide survey. Comprehensive expression profile analysis reveals an abroad expression pattern of these ATGs, which could be detected in all tissues tested under normal growth conditions. Our series tests further reveal that majority of ATGs are sensitive and responsive to different stresses including nutrient starvation, plant hormones, heavy metal and other abiotic stresses, suggesting a central role of autophagy, likely as an effector, in plant response to various environmental cues. This work offers a detailed survey of all ATGs in tobacco and also suggests manifold functions of autophagy in both normal plant growth and plant response to environmental stresses. PMID:26205094

Cryosurgery would be An Effective Option for Clinically Localized Prostate Cancer: A Meta-analysis and Systematic Review

PubMed Central

Gao, Liang; Yang, Lu; Qian, Shengqiang; Tang, Zhuang; Qin, Feng; Wei, Qiang; Han, Ping; Yuan, Jiuhong

2016-01-01

Cryosurgery (CS) has been used on patients with clinically localized PCa for more than 10 years. However, clinical studies evaluating its effectiveness and safety have reported conflicting results. This systematic assessment was performed to obtain comprehensive evidence regarding the potential benefits and safety of CS compared with those of radiotherapy (RT) and radical prostatectomy (RP), respectively. All controlled trials comparing CS with RT or RP and single-arm studies reporting results of CS therapy were identified through comprehensive searches of PubMed, the Cochrane Library and Embase. Ten publications from seven trials, with totally 1252 patients, were included in the meta-analysis, which revealed no significant differences in comparisons of CS vs RT and CS vs RP for overall survival and disease specific survival. However, a significantly lower disease-free survival could be observed for CS than RP. Moreover, a systematic review of literature focusing on comparative data of databases and materials of single-arm trials revealed satisfactory survival results in both primary and salvage CS. Our results showed that cryosurgery would be a relatively effective method for clinically localized prostate cancer with survival results comparable to radiotherapy and radical prostatectomy. However, the large percentage of complications caused by cryosurgery should be carefully monitored. PMID:27271239

Syntactic processing as a marker for cognitive impairment in amyotrophic lateral sclerosis

PubMed Central

Tsermentseli, Stella; Leigh, P. Nigel; Taylor, Lorna J.; Radunovic, Aleksandar; Catani, Marco; Goldstein, Laura H.

2016-01-01

Despite recent interest in cognitive changes in patients with amyotrophic lateral sclerosis (ALS), investigations of language function looking at the level of word, sentence and discourse processing are relatively scarce. Data were obtained from 26 patients with sporadic ALS and 26 healthy controls matched for age, education, gender, anxiety, depression and executive function performance. Standardized language tasks included confrontation naming, semantic access, and syntactic comprehension. Quantitative production analysis (QPA) was used to analyse connected speech samples of the Cookie Theft picture description task. Results showed that the ALS patients were impaired on standardized measures of grammatical comprehension and action/verb semantics. At the level of discourse, ALS patients were impaired on measures of syntactic complexity and fluency; however, the latter could be better explained by disease related factors. Discriminant analysis revealed that syntactic measures differentiated ALS patients from controls. In conclusion, patients with ALS exhibit deficits in receptive and expressive language on tasks of comprehension and connected speech production, respectively. Our findings suggest that syntactic processing deficits seem to be the predominant feature of language impairment in ALS and that these deficits can be detected by relatively simple language tests. PMID:26312952

Syntactic processing as a marker for cognitive impairment in amyotrophic lateral sclerosis.

PubMed

Tsermentseli, Stella; Leigh, P Nigel; Taylor, Lorna J; Radunovic, Aleksandar; Catani, Marco; Goldstein, Laura H

2015-01-01

Despite recent interest in cognitive changes in patients with amyotrophic lateral sclerosis (ALS), investigations of language function looking at the level of word, sentence and discourse processing are relatively scarce. Data were obtained from 26 patients with sporadic ALS and 26 healthy controls matched for age, education, gender, anxiety, depression and executive function performance. Standardized language tasks included confrontation naming, semantic access, and syntactic comprehension. Quantitative production analysis (QPA) was used to analyse connected speech samples of the Cookie Theft picture description task. Results showed that the ALS patients were impaired on standardized measures of grammatical comprehension and action/verb semantics. At the level of discourse, ALS patients were impaired on measures of syntactic complexity and fluency; however, the latter could be better explained by disease related factors. Discriminant analysis revealed that syntactic measures differentiated ALS patients from controls. In conclusion, patients with ALS exhibit deficits in receptive and expressive language on tasks of comprehension and connected speech production, respectively. Our findings suggest that syntactic processing deficits seem to be the predominant feature of language impairment in ALS and that these deficits can be detected by relatively simple language tests.

Dimensional Model for Estimating Factors influencing Childhood Obesity: Path Analysis Based Modeling

PubMed Central

Kheirollahpour, Maryam; Shohaimi, Shamarina

2014-01-01

The main objective of this study is to identify and develop a comprehensive model which estimates and evaluates the overall relations among the factors that lead to weight gain in children by using structural equation modeling. The proposed models in this study explore the connection among the socioeconomic status of the family, parental feeding practice, and physical activity. Six structural models were tested to identify the direct and indirect relationship between the socioeconomic status and parental feeding practice general level of physical activity, and weight status of children. Finally, a comprehensive model was devised to show how these factors relate to each other as well as to the body mass index (BMI) of the children simultaneously. Concerning the methodology of the current study, confirmatory factor analysis (CFA) was applied to reveal the hidden (secondary) effect of socioeconomic factors on feeding practice and ultimately on the weight status of the children and also to determine the degree of model fit. The comprehensive structural model tested in this study suggested that there are significant direct and indirect relationships among variables of interest. Moreover, the results suggest that parental feeding practice and physical activity are mediators in the structural model. PMID:25097878

Does Guiding Toward Task-Relevant Information Help Improve Graph Processing and Graph Comprehension of Individuals with Low or High Numeracy? An Eye-Tracker Experiment.

PubMed

Keller, Carmen; Junghans, Alex

2017-11-01

Individuals with low numeracy have difficulties with understanding complex graphs. Combining the information-processing approach to numeracy with graph comprehension and information-reduction theories, we examined whether high numerates' better comprehension might be explained by their closer attention to task-relevant graphical elements, from which they would expect numerical information to understand the graph. Furthermore, we investigated whether participants could be trained in improving their attention to task-relevant information and graph comprehension. In an eye-tracker experiment ( N = 110) involving a sample from the general population, we presented participants with 2 hypothetical scenarios (stomach cancer, leukemia) showing survival curves for 2 treatments. In the training condition, participants received written instructions on how to read the graph. In the control condition, participants received another text. We tracked participants' eye movements while they answered 9 knowledge questions. The sum constituted graph comprehension. We analyzed visual attention to task-relevant graphical elements by using relative fixation durations and relative fixation counts. The mediation analysis revealed a significant ( P < 0.05) indirect effect of numeracy on graph comprehension through visual attention to task-relevant information, which did not differ between the 2 conditions. Training had a significant main effect on visual attention ( P < 0.05) but not on graph comprehension ( P < 0.07). Individuals with high numeracy have better graph comprehension due to their greater attention to task-relevant graphical elements than individuals with low numeracy. With appropriate instructions, both groups can be trained to improve their graph-processing efficiency. Future research should examine (e.g., motivational) mediators between visual attention and graph comprehension to develop appropriate instructions that also result in higher graph comprehension.

Genomic analysis of Meckel–Gruber syndrome in Arabs reveals marked genetic heterogeneity and novel candidate genes

PubMed Central

Shaheen, Ranad; Faqeih, Eissa; Alshammari, Muneera J; Swaid, Abdulrahman; Al-Gazali, Lihadh; Mardawi, Elham; Ansari, Shinu; Sogaty, Sameera; Seidahmed, Mohammed Z; AlMotairi, Muhammed I; Farra, Chantal; Kurdi, Wesam; Al-Rasheed, Shatha; Alkuraya, Fowzan S

2013-01-01

Meckel–Gruber syndrome (MKS, OMIM #249000) is a multiple congenital malformation syndrome that represents the severe end of the ciliopathy phenotypic spectrum. Despite the relatively common occurrence of this syndrome among Arabs, little is known about its genetic architecture in this population. This is a series of 18 Arab families with MKS, who were evaluated clinically and studied using autozygome-guided mutation analysis and exome sequencing. We show that autozygome-guided candidate gene analysis identified the underlying mutation in the majority (n=12, 71%). Exome sequencing revealed a likely pathogenic mutation in three novel candidate MKS disease genes. These include C5orf42, Ellis–van-Creveld disease gene EVC2 and SEC8 (also known as EXOC4), which encodes an exocyst protein with an established role in ciliogenesis. This is the largest and most comprehensive genomic study on MKS in Arabs and the results, in addition to revealing genetic and allelic heterogeneity, suggest that previously reported disease genes and the novel candidates uncovered by this study account for the overwhelming majority of MKS patients in our population. PMID:23169490

Socioeconomic and clinical factors are key to uncovering disparity in accrual onto therapeutic trials for breast cancer.

PubMed

Behrendt, Carolyn E; Hurria, Arti; Tumyan, Lusine; Niland, Joyce C; Mortimer, Joanne E

2014-11-01

To monitor and address disparity in accrual, patient participation in cancer clinical trials is routinely summarized by race/ethnicity. To investigate whether confounding obscures racial/ethnic disparity in participation, all women with breast cancer treated by medical oncologists at City of Hope Comprehensive Cancer Center from 2004 through 2009 were classified by birthplace and self-reported race/ethnicity, and followed for accrual onto therapeutic trials through 2010. Undetectable on univariate analysis, significantly reduced participation by subjects of African, Asian, Eastern European, Latin American, and Middle Eastern ancestries was revealed after accounting for age, socioeconomic factors, tumor and oncologist characteristics, and intrapractice clustering of patients. Copyright © 2014 by the National Comprehensive Cancer Network.

An exploration of the relationship between metacomprehension strategy awareness and reading comprehension performance with narrative and science texts

NASA Astrophysics Data System (ADS)

York, Kathleen Christine

This mixed method study explored the relationship between metacomprehension strategy awareness and reading comprehension performance with narrative and science texts. Participants, 132 eighth-grade, predominately African American students, attending one middle school in a southeastern state, were administered a narrative and science version of the Metacomprehension Strategy Index (MSI) and asked to identify helpful strategic behaviors from six clustered subcategories (predicting and verifying; previewing; purpose setting; self-questioning; drawing from background knowledge; and summarizing and applying fix-up strategies). Participants also read and answered comprehension questions about narrative and science passages. Findings revealed no statistically significant differences in overall metacomprehension awareness with narrative and science texts. Statistically significant (p<.05) differences were found for two of the six subcategories, indicating students preview and set purpose more often with science than narrative texts. Findings also indicated overall narrative and science metacomprehension awareness and comprehension performance scores were statistically significantly (p<.01) related. Specifically, the category of summarizing and applying fix-up strategies was the strongest predictor of comprehension performance for both narrative and science texts. The qualitative phase of this study explored the relationship between metacomprehension awareness with narrative and science texts and the comprehension performance of six middle school students, three of whom scored high overall on the narrative and science text comprehension assessments in phase one of the study, and three of whom scored low. A qualitative analysis of multiple sources of data, including video-taped interviews and think-alouds, revealed the three high scoring participants engaged in competent school-based, metacognitive conversations infused with goal, self, and narrative talk and demonstrated multi-strategic engagements with narrative and science texts. In stark contrast, the three low scoring participants engaged in dissonant school-based talk infused with disclaimers, over-generalized, decontextualized, and literalized answers and demonstrated robotic, limited (primarily rereading and restating), and frustrated strategic acts when interacting with both narrative and science texts. The educational implications are discussed. This dissertation was funded by the Office of Special Education Programs, Federal Office Grant Award No. 324E031501.

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

PubMed Central

2011-01-01

Background Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking. Results We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8-bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs. Conclusions The comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles. PMID:22189060

Echoic Memory Interference and Comprehension in a Foreign Language.

ERIC Educational Resources Information Center

Greenberg, Seth N.; Roscoe, Suzanne

1988-01-01

Study of echoic memory interference among students in college introductory Spanish and German courses revealed that students with weaker listening comprehension skills depended more upon vulnerable sensory codes in echoic memory, while students with stronger comprehension relied on stable higher-order codes. (Author/CB)

Chapter 11. Community analysis-based methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Y.; Wu, C.H.; Andersen, G.L.

2010-05-01

Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. Inmore » increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.« less

Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree (Olea europaea L.) Cultivars.

PubMed

Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Rebai, Ahmed

2016-12-01

The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation coefficient, indicating the usefulness of the UPGMA method for clustering plant genotypes. Based on principal coordinate analysis using a similarity matrix, the first two coordinates, revealed 54.94 % of the total variance. This work provides a more comprehensive explanation of the diversity available in Tunisia olive cultivars, and an important contribution for olive breeding and olive oil authenticity.

Comprehensive Analysis of Human Endogenous Retrovirus Group HERV-W Locus Transcription in Multiple Sclerosis Brain Lesions by High-Throughput Amplicon Sequencing

PubMed Central

Schmitt, Katja; Richter, Christin; Backes, Christina; Meese, Eckart; Ruprecht, Klemens

2013-01-01

Human endogenous retroviruses (HERVs) of the HERV-W group comprise hundreds of loci in the human genome. Deregulated HERV-W expression and HERV-W locus ERVWE1-encoded Syncytin-1 protein have been implicated in the pathogenesis of multiple sclerosis (MS). However, the actual transcription of HERV-W loci in the MS context has not been comprehensively analyzed. We investigated transcription of HERV-W in MS brain lesions and white matter brain tissue from healthy controls by employing next-generation amplicon sequencing of HERV-W env-specific reverse transcriptase (RT) PCR products, thus revealing transcribed HERV-W loci and the relative transcript levels of those loci. We identified more than 100 HERV-W loci that were transcribed in the human brain, with a limited number of loci being predominantly transcribed. Importantly, relative transcript levels of HERV-W loci were very similar between MS and healthy brain tissue samples, refuting deregulated transcription of HERV-W env in MS brain lesions, including the high-level-transcribed ERVWE1 locus encoding Syncytin-1. Quantitative RT-PCR likewise did not reveal differences in MS regarding HERV-W env general transcript or ERVWE1- and ERVWE2-specific transcript levels. However, we obtained evidence for interindividual differences in HERV-W transcript levels. Reporter gene assays indicated promoter activity of many HERV-W long terminal repeats (LTRs), including structurally incomplete LTRs. Our comprehensive analysis of HERV-W transcription in the human brain thus provides important information on the biology of HERV-W in MS lesions and normal human brain, implications for study design, and mechanisms by which HERV-W may (or may not) be involved in MS. PMID:24109235

Effect of an intervention program on the reading comprehension processes and strategies in 5th and 6th grade students.

PubMed

Gayo, Elena; Deaño, Manuel; Conde, Ángeles; Ribeiro, Iolanda; Cadime, Irene; Alfonso, Sonia

2014-01-01

Various investigations have revealed that the promotion of cognitive and metacognitive strategies can improve reading comprehension and that when readers receive this type of instruction, they can use monitoring processes and regulation strategies adequately. The goal of this work is to analyze the effects of strategic and metacognitive instruction on reading comprehension processes and strategies, using the "Aprender a Comprender" [Learning to Understand] program. Instruction was carried out in the classroom by two teachers during six months. Ninety-four students participated, 49 from 5th grade and 45 from 6th grade. A pretest-intervention-posttest-follow-up design was used with a comparison group by grade. The analysis of variance shows an impact of the intervention and its differential maintenance in each grade. The 5th-grade intervention group scored higher than the comparison group in the reading comprehension test, both at posttest and at follow-up. The 6th-grade intervention group scored higher than the comparison group in the Planning scale, both at posttest and at follow-up. Textual strategy instruction favors reading comprehension and the progressive development of planning, which is necessary for supervision and regulation, and its effects are maintained over time.

Comprehensive analysis of cutaneous T-cell lymphoma (CTCL) incidence and mortality in Canada reveals changing trends and geographic clustering for this malignancy.

PubMed

Ghazawi, Feras M; Netchiporouk, Elena; Rahme, Elham; Tsang, Matthew; Moreau, Linda; Glassman, Steven; Provost, Nathalie; Gilbert, Martin; Jean, Sara-Elizabeth; Pehr, Kevin; Sasseville, Denis; Litvinov, Ivan V

2017-09-15

Previous reports of geographic clustering of cutaneous T-cell lymphoma (CTCL) in Texas, Pittsburgh, and Sweden as well as the occurrence of CTCL in married couples and family members raise a possibility of the existence of an external and potentially preventable trigger(s) for this rare skin cancer. The authors studied CTCL incidence and mortality in Canada using 3 distinct population-based cancer databases. Data on patients' sex, age at the time of diagnosis, subtype of CTCL malignancy, reporting province, city, and postal code were analyzed. CTCL cases were mapped across Canada using geographic information systems software. In total, 6685 patients with CTCL were identified in Canada during 1992 through 2010 (CTCL incidence rate, 11.32 cases per million individuals per year), of which 58% were males. The mean age at diagnosis was 59.4 ± 21.5 years. Geographic analysis of patients revealed increased CTCL incidence on the provincial and city levels in several eastern provinces and in Manitoba. An analysis according to postal codes (Forward Sortation Area [FSA]) identified select communities in which several high-incidence FSAs were contiguous or adjacent. Several of these FSAs were located in industrial regions of Canadian cities. Conversely, 3 of 8 low-incidence FSAs were clustered in Ottawa, Ontario, which has very little industrial presence. An analysis of CTCL mortality in Canada corroborated the current incidence findings. The current results provide a comprehensive analysis of CTCL burden in Canada and highlight several important areas of geographic case clustering. These findings argue that industrial exposures may play an important role in promoting CTCL pathogenesis. Cancer 2017;123:3550-67. © 2017 American Cancer Society. © 2017 American Cancer Society.

Comprehensive profiling and characterization of cellular miRNAs in response to hepatitis A virus infection in human fibroblasts.

PubMed

Shi, Jiandong; Sun, Jing; Wu, Meini; Wang, Haixuan; Hu, Ningzhu; Hu, Yunzhang

2016-11-01

Hepatitis A virus (HAV), the causative agent of acute hepatitis, grows slowly without causing any cytopathic effect (CPE) and lead to a persistent infection in the fibroblasts in vitro. miRNAs play a key role in the viral pathogenesis and virus-host interactions. In this study, the comprehensive miRNA expression profiles of HAV-infected and uninfected fibroblasts were investigated by sRNA-seq and validated by RT-qPCR. The results showed that a total of 94 miRNAs were differentially expressed during HAV infection, including 11 up-regulated miRNAs and 83 down-regulated miRNAs. RT-qPCR analysis showed the expression levels of specific miRNAs were consistent with sRNA-seq data. Further, target prediction analysis showed 729 putative target genes that included many immune-related transcripts were revealed. The GO enrichment analysis and the KEGG pathway analysis of the target genes showed that various biological pathways, including JAK-STAT cascade, type I interferon signaling pathway could be affected by HAV infection by the alteration of host miRNAs. The core regulatory relationship between miRNAs and their targets were revealed by miRNA-gene-network. Collectively, this study provides an overall analysis of miRNA profile in cell culture infected with HAV. The present results imply the alteration of miRNAs expression induced by HAV infection which may be related to the establishment of persistent HAV infection and might provide new clues for understanding the persistent HAV infections in vitro and the unique biological characteristics associated with HAV during infection. Copyright © 2016 Elsevier B.V. All rights reserved.

The Comprehension Problems of Children with Poor Reading Comprehension Despite Adequate Decoding: A Meta-Analysis

ERIC Educational Resources Information Center

Spencer, Mercedes; Wagner, Richard K.

2018-01-01

The purpose of this meta-analysis was to examine the comprehension problems of children who have a specific reading comprehension deficit (SCD), which is characterized by poor reading comprehension despite adequate decoding. The meta-analysis included 86 studies of children with SCD who were assessed in reading comprehension and oral language…

Impact of the roll out of comprehensive emergency obstetric care on institutional birth rate in rural Nepal.

PubMed

Maru, Sheela; Bangura, Alex Harsha; Mehta, Pooja; Bista, Deepak; Borgatta, Lynn; Pande, Sami; Citrin, David; Khanal, Sumesh; Banstola, Amrit; Maru, Duncan

2017-03-04

Increasing institutional births rates and improving access to comprehensive emergency obstetric care are central strategies for reducing maternal and neonatal deaths globally. While some studies show women consider service availability when determining where to deliver, the dynamics of how and why institutional birth rates change as comprehensive emergency obstetric care availability increases are unclear. In this pre-post intervention study, we surveyed two exhaustive samples of postpartum women before and after comprehensive emergency obstetric care implementation at a hospital in rural Nepal. We developed a logistic regression model of institutional birth factors through manual backward selection of all significant covariates within and across periods. Qualitatively, we analyzed birth stories through immersion crystallization. Institutional birth rates increased after comprehensive emergency obstetric care implementation (from 30 to 77%, OR 7.7) at both hospital (OR 2.5) and low-level facilities (OR 4.6, p < 0.01 for all). The logistic regression indicated that comprehensive emergency obstetric care availability (OR 5.6), belief that the hospital is the safest birth location (OR 44.8), safety prioritization in decision-making (OR 7.7), and higher income (OR 1.1) predict institutional birth (p ≤ 0.01 for all). Qualitative analysis revealed comprehensive emergency obstetric care awareness, increased social expectation for institutional birth, and birth planning as important factors. Comprehensive emergency obstetric care expansion appears to have generated significant demand for institutional births through increased safety perceptions and birth planning. Increasing comprehensive emergency obstetric care availability increases birth safety, but it may also be a mechanism for increasing the institutional birth rate in areas of under-utilization.

Association of CLU and PICALM variants with Alzheimer's disease

PubMed Central

Kamboh, M.I.; Minster, R. L.; Demirci, F.Y.; Ganguli, M.; DeKosky, S.T.; Lopez, O.L.; Barmada, M.M.

2010-01-01

Two recent large genome-wide association studies have reported significant associations in the CLU (APOJ), CR1 and PICALM genes. In order to replicate these findings, we examined 7 single nucleotide polymorphisms (SNPs) most significantly implicated by these studies in a large case-control sample comprising of 2,707 individuals. Principle components analysis revealed no population substructure in our sample. While no association was observed with CR1 SNPs (P=0.30–0.457), a trend of association was seen with the PICALM (P=0.071–0.086) and CLU (P=0.148–0.258) SNPs. A meta-analysis of three studies revealed significant associations with all three genes. Our data from an independent and large case-control sample suggest that these gene regions should be followed up by comprehensive resequencing to find functional variants. PMID:20570404

The Comprehensive Snack Parenting Questionnaire (CSPQ): Development and Test-Retest Reliability.

PubMed

Gevers, Dorus W M; Kremers, Stef P J; de Vries, Nanne K; van Assema, Patricia

2018-04-26

The narrow focus of existing food parenting instruments led us to develop a food parenting practices instrument measuring the full range of food practices constructs with a focus on snacking behavior. We present the development of the questionnaire and our research on the test-retest reliability. The developed Comprehensive Snack Parenting Questionnaire (CSPQ) covers 21 constructs. Test-retest reliability was assessed by calculating intra class correlation coefficients and percentage agreement after two administrations of the CSPQ among a sample of 66 Dutch parents. Test-retest reliability analysis revealed acceptable intra class correlation coefficients (≥0.41) or agreement scores (≥0.60) for all items. These results, together with earlier work, suggest sufficient psychometric characteristics. The comprehensive, but brief CSPQ opens up chances for highly essential but unstudied research questions to understand and predict children’s snack intake. Example applications include studying the interactional nature of food parenting practices or interactions of food parenting with general parenting or child characteristics.

High-throughput DNA microarray detection of pathogenic bacteria in shallow well groundwater in the Kathmandu Valley, Nepal.

PubMed

Inoue, Daisuke; Hinoura, Takuji; Suzuki, Noriko; Pang, Junqin; Malla, Rabin; Shrestha, Sadhana; Chapagain, Saroj Kumar; Matsuzawa, Hiroaki; Nakamura, Takashi; Tanaka, Yasuhiro; Ike, Michihiko; Nishida, Kei; Sei, Kazunari

2015-01-01

Because of heavy dependence on groundwater for drinking water and other domestic use, microbial contamination of groundwater is a serious problem in the Kathmandu Valley, Nepal. This study investigated comprehensively the occurrence of pathogenic bacteria in shallow well groundwater in the Kathmandu Valley by applying DNA microarray analysis targeting 941 pathogenic bacterial species/groups. Water quality measurements found significant coliform (fecal) contamination in 10 of the 11 investigated groundwater samples and significant nitrogen contamination in some samples. The results of DNA microarray analysis revealed the presence of 1-37 pathogen species/groups, including 1-27 biosafety level 2 ones, in 9 of the 11 groundwater samples. While the detected pathogens included several feces- and animal-related ones, those belonging to Legionella and Arthrobacter, which were considered not to be directly associated with feces, were detected prevalently. This study could provide a rough picture of overall pathogenic bacterial contamination in the Kathmandu Valley, and demonstrated the usefulness of DNA microarray analysis as a comprehensive screening tool of a wide variety of pathogenic bacteria.

Medical-device risk management and public safety: using cost-benefit as a measurement of effectiveness

NASA Astrophysics Data System (ADS)

Hughes, Allen A.

1994-12-01

Public safety can be enhanced through the development of a comprehensive medical device risk management. This can be accomplished through case studies using a framework that incorporates cost-benefit analysis in the evaluation of risk management attributes. This paper presents a framework for evaluating the risk management system for regulatory Class III medical devices. The framework consists of the following sixteen attributes of a comprehensive medical device risk management system: fault/failure analysis, premarket testing/clinical trials, post-approval studies, manufacturer sponsored hospital studies, product labeling, establishment inspections, problem reporting program, mandatory hospital reporting, medical literature surveillance, device/patient registries, device performance monitoring, returned product analysis, autopsy program, emergency treatment funds/interim compensation, product liability, and alternative compensation mechanisms. Review of performance histories for several medical devices can reveal the value of information for many attributes, and also the inter-dependencies of the attributes in generating risk information flow. Such an information flow network is presented as a starting point for enhancing medical device risk management by focusing on attributes with high net benefit values and potential to spur information dissemination.

Analysis of the mixing processes in the subtropical Advancetown Lake, Australia

NASA Astrophysics Data System (ADS)

Bertone, Edoardo; Stewart, Rodney A.; Zhang, Hong; O'Halloran, Kelvin

2015-03-01

This paper presents an extensive investigation of the mixing processes occurring in the subtropical monomictic Advancetown Lake, which is the main water body supplying the Gold Coast City in Australia. Meteorological, chemical and physical data were collected from weather stations, laboratory analysis of grab samples and an in-situ Vertical Profiling System (VPS), for the period 2008-2012. This comprehensive, high frequency dataset was utilised to develop a one-dimensional model of the vertical transport and mixing processes occurring along the water column. Multivariate analysis revealed that air temperature and rain forecasts enabled a reliable prediction of the strength of the lake stratification. Vertical diffusion is the main process driving vertical mixing, particularly during winter circulation. However, a high reservoir volume and warm winters can limit the degree of winter mixing, causing only partial circulation to occur, as was the case in 2013. This research study provides a comprehensive approach for understanding and predicting mixing processes for similar lakes, whenever high-frequency data are available from VPS or other autonomous water monitoring systems.

Confirmatory factor analysis of the Malay version comprehensive feeding practices questionnaire tested among mothers of primary school children in Malaysia.

PubMed

Shohaimi, Shamarina; Wei, Wong Yoke; Shariff, Zalilah Mohd

2014-01-01

Comprehensive feeding practices questionnaire (CFPQ) is an instrument specifically developed to evaluate parental feeding practices. It has been confirmed among children in America and applied to populations in France, Norway, and New Zealand. In order to extend the application of CFPQ, we conducted a factor structure validation of the translated version of CFPQ (CFPQ-M) using confirmatory factor analysis among mothers of primary school children (N = 397) in Malaysia. Several items were modified for cultural adaptation. Of 49 items, 39 items with loading factors >0.40 were retained in the final model. The confirmatory factor analysis revealed that the final model (twelve-factor model with 39 items and 2 error covariances) displayed the best fit for our sample (Chi-square = 1147; df = 634; P < 0.05; CFI = 0.900; RMSEA = 0.045; SRMR = 0.0058). The instrument with some modifications was confirmed among mothers of school children in Malaysia. The present study extends the usability of the CFPQ and enables researchers and parents to better understand the relationships between parental feeding practices and related problems such as childhood obesity.

The “shape” and “meaning” of the roof arts in Chinese classical architecture

NASA Astrophysics Data System (ADS)

Li, Xianda; liu, Yu

2017-04-01

This paper takes the “roof” in Chinese classical architecture as the research object. The breakthrough point of this paper would be the perspective of design aesthetics. Through the rational and perceptual analysis of the roof art, this paper would reveal that the roof shape has the double artistic features: “beauty of shape” and “beauty of idea”. This paper would have a comprehensive analysis for the following aspects: the rational method of roof construction, the emotional feeling of the roof construction and the implied meaning of beauty in the roof construction.

Comprehensive Identification of Glycated Peptides and Their Glycation Motifs in Plasma and Erythrocytes of Control and Diabetic Subjects

PubMed Central

Zhang, Qibin; Monroe, Matthew E.; Schepmoes, Athena A.; Clauss, Therese R. W.; Gritsenko, Marina A.; Meng, Da; Petyuk, Vladislav A.; Smith, Richard D.; Metz, Thomas O.

2011-01-01

Non-enzymatic glycation of proteins sets the stage for formation of advanced glycation end-products and development of chronic complications of diabetes. In this report, we extended our previous methods on proteomics analysis of glycated proteins to comprehensively identify glycated proteins in control and diabetic human plasma and erythrocytes. Using immunodepletion, enrichment, and fractionation strategies, we identified 7749 unique glycated peptides, corresponding to 3742 unique glycated proteins. Semi-quantitative comparisons showed that glycation levels of a number of proteins were significantly increased in diabetes and that erythrocyte proteins were more extensively glycated than plasma proteins. A glycation motif analysis revealed that some amino acids were favored more than others in the protein primary structures in the vicinity of the glycation sites in both sample types. The glycated peptides and corresponding proteins reported here provide a foundation for potential identification of novel markers for diabetes, hyperglycemia, and diabetic complications in future studies. PMID:21612289

Evaluating the Impact of a Multistrategy Inference Intervention for Middle-Grade Struggling Readers

PubMed Central

Elleman, Amy

2017-01-01

Purpose We examined the effectiveness of a multistrategy inference intervention designed to increase inference making and reading comprehension for middle-grade struggling readers. Method A total of 66 middle-grade struggling readers were randomized to treatment (n = 33) and comparison (n = 33) conditions. Students in the treatment group received explicit instruction in 4 inference strategies (i.e., clarification using text clues; activating and using prior knowledge; understanding character perspectives and author's purpose; answering inferential questions). In addition, narrative and informational texts were carefully chosen and sequenced to build requisite background knowledge to form inferences. Intervention was delivered in small groups of 3 students for 10 days of instruction. Results One-way analysis of covariance models on outcome measures with the respective pretest scores as a covariate revealed significant gains on a proximal measure of Egyptian-content knowledge (g = 1.37) and on a standardized measure of reading comprehension—i.e., Wechsler Individual Achievement Test–Third Edition Reading Comprehension (g = 0.46). Conclusion The moderate effect on a standardized measure of reading comprehension provides preliminary evidence for the effectiveness of this multistrategy inference intervention in improving reading comprehension of middle-grade struggling readers. PMID:27776201

Comprehensive Characterization of Molecular Differences in Cancer between Male and Female Patients

PubMed Central

Yuan, Yuan; Liu, Lingxiang; Chen, Hu; Wang, Yumeng; Xu, Yanxun; Mao, Huzhang; Li, Jun; Mills, Gordon B.; Shu, Yongqian; Li, Liang; Liang, Han

2016-01-01

Summary An individual’s sex has been long recognized as a key factor affecting cancer incidence, prognosis and treatment responses. However, the molecular basis for sex disparities in cancer remains poorly understood. We performed a comprehensive analysis of molecular differences between male and female patients in 13 cancer types of The Cancer Genome Atlas and revealed two sex-effect groups associated with distinct incidence and mortality profiles. One group contains a small number of sex-affected genes, whereas the other shows much more extensive sex-biased molecular signatures. Importantly, 53% of clinically actionable genes (60/114) show sex-biased signatures. Our study provides a systematic molecular-level understanding of sex effects in diverse cancers and suggests a pressing need to develop sex-specific therapeutic strategies in certain cancer types. PMID:27165743

In Search of On-Line Locality Effects in Sentence Comprehension

ERIC Educational Resources Information Center

Bartek, Brian; Lewis, Richard L.; Vasishth, Shravan; Smith, Mason R.

2011-01-01

Many comprehension theories assert that increasing the distance between elements participating in a linguistic relation (e.g., a verb and a noun phrase argument) increases the difficulty of establishing that relation during on-line comprehension. Such "locality effects" are expected to increase reading times and are thought to reveal properties…

Systems cell biology

PubMed Central

Mast, Fred D.; Ratushny, Alexander V.

2014-01-01

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. PMID:25225336

Meteors in Australian Aboriginal Dreamings

NASA Astrophysics Data System (ADS)

Hamacher, Duane W.; Norris, Ray P.

2010-06-01

We present a comprehensive analysis of Australian Aboriginal accounts of meteors. The data used were taken from anthropological and ethnographic literature describing oral traditions, ceremonies, and Dreamings of 97 Aboriginal groups representing all states of modern Australia. This revealed common themes in the way meteors were viewed between Aboriginal groups, focusing on supernatural events, death, omens, and war. The presence of such themes around Australia was probably due to the unpredictable nature of meteors in an otherwise well-ordered cosmos.

Comprehensive Analysis of Tropomyosin Isoforms in Skeletal Muscles by Top-down Proteomics

PubMed Central

Jin, Yutong; Peng, Ying; Lin, Ziqing; Chen, Yi-Chen; Wei, Liming; Hacker, Timothy A.; Larsson, Lars; Ge, Ying

2016-01-01

Mammalian skeletal muscles are heterogeneous in nature and are capable of performing various functions. Tropomyosin (Tpm) is a major component of the thin filament in skeletal muscles and plays an important role in controlling muscle contraction and relaxation. Tpm is known to consist of multiple isoforms resulting from different encoding genes and alternative splicing, along with post-translational modifications. However, a systematic characterization of Tpm isoforms in skeletal muscles is still lacking. Therefore, we employed top-down mass spectrometry (MS) to identify and characterize Tpm isoforms present in different skeletal muscles from multiple species, including swine, rat, and human. Our study revealed that Tpm1.1 and Tpm2.2 are the two major Tpm isoforms in swine and rat skeletal muscles, whereas Tpm1.1, Tpm2.2, and Tpm3.12 are present in human skeletal muscles. Tandem MS was utilized to identify the sequences of the major Tpm isoforms. Furthermore, quantitative analysis revealed muscle-type specific differences in the abundance of un-modified and modified Tpm isoforms in rat and human skeletal muscles. This study represents the first systematic investigation of Tpm isoforms in skeletal muscles, which not only demonstrates the capabilities of top-down MS for the comprehensive characterization of skeletal myofilament proteins but also provides the basis for further studies on these Tpm isoforms in muscle-related diseases. PMID:27090236

Refocusing on physical health: Community psychiatric nurses' perceptions of using enhanced health checks for people with severe mental illness.

PubMed

Bressington, Daniel; Mui, Jolene; Wells, Harvey; Chien, Wai Tong; Lam, Claire; White, Jacquie; Gray, Richard

2016-06-01

In the present qualitative, descriptive study, we explored Hong Kong community psychiatric nurses' (CPN) perceptions of using comprehensive physical health checks for service users diagnosed with severe mental illness (SMI). Research interviews were conducted with a purposive sample of 11 CPN in order to explore their perceptions about the use of the Health Improvement Profile (HIP) over a 1-year period. Interview data were analysed using inductive thematic analysis. The analysis revealed that the majority of CPN appreciated the comprehensive focus on the physical health of their clients and reported positive changes in their clinical practice. Many of them observed an increase in the motivation of their clients to improve their physical health, and also noted observable benefits in service users' well-being. The use of the HIP also helped the CPN identify implementation barriers, and highlighted areas of the tool that required modifications to suit the local cultural and clinical context. To our knowledge, this is the first study conducted in an Asian mental health service that explores nurses' views about using comprehensive health checks for people with SMI. The findings suggest that such approaches are viewed as being acceptable, feasible, and potentially beneficial in the community mental health setting. © 2016 Australian College of Mental Health Nurses Inc.

The concept of health technology assessment. Views of applicants to funding of HTA projects.

PubMed

Lange, M; Jørgensen, T; Kristensen, F B; Stilvén, S

2000-01-01

The purpose of this study is to analyze the perception of the content of health technology assessment (HTA) among health professionals applying for a state grant of DKK 10 million. A total of 113 applications were received and analyzed. When conducting the analysis, it was assumed that the applicants' maximum five-page project description would reflect: a) the applicants' perception of what an HTA is; b) how the assessment was to be conducted; and c) what the results were going to be used for. More than 40% of all applications focused on treatment; in 51% only one or two professional groups were to be involved (thus interdisciplinarity was questionable); only 22% of the HTA cases were intended to form the basis for political/administrative decisions; in general, the HTAs were planned far less comprehensively than was relevant; 76% of the projects did not include a formal synthesis phase; 41% intended to use diffusion as the only method for publication of the HTA result. The analysis reveals several areas where DIHTA has to make an effort in order to secure that HTA in fact constitutes a comprehensive and well-documented basis for decision making. These areas concern the following topics: multidisciplinarity, the objective of HTA, comprehensiveness, the synthesis phase, and publication and utilization of the HTA result.

Task-dependent modulation of regions in the left temporal cortex during auditory sentence comprehension.

PubMed

Zhang, Linjun; Yue, Qiuhai; Zhang, Yang; Shu, Hua; Li, Ping

2015-01-01

Numerous studies have revealed the essential role of the left lateral temporal cortex in auditory sentence comprehension along with evidence of the functional specialization of the anterior and posterior temporal sub-areas. However, it is unclear whether task demands (e.g., active vs. passive listening) modulate the functional specificity of these sub-areas. In the present functional magnetic resonance imaging (fMRI) study, we addressed this issue by applying both independent component analysis (ICA) and general linear model (GLM) methods. Consistent with previous studies, intelligible sentences elicited greater activity in the left lateral temporal cortex relative to unintelligible sentences. Moreover, responses to intelligibility in the sub-regions were differentially modulated by task demands. While the overall activation patterns of the anterior and posterior superior temporal sulcus and middle temporal gyrus (STS/MTG) were equivalent during both passive and active tasks, a middle portion of the STS/MTG was found to be selectively activated only during the active task under a refined analysis of sub-regional contributions. Our results not only confirm the critical role of the left lateral temporal cortex in auditory sentence comprehension but further demonstrate that task demands modulate functional specialization of the anterior-middle-posterior temporal sub-areas. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes.

PubMed

Gao, Fan-Xiang; Wang, Yang; Zhang, Qi-Ya; Mou, Cheng-Yan; Li, Zhi; Deng, Yuan-Sheng; Zhou, Li; Gui, Jian-Fang

2017-07-24

Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their resistances to herpesvirus and the underlying mechanism remain unknown. To reveal their susceptibility differences, we firstly performed herpesvirus challenge experiments in three gynogenetic clones of gibel carp, including the leading variety clone A + , candidate variety clone F and wild clone H. Three clones showed distinct resistances to CaHV. Moreover, 8772, 8679 and 10,982 differentially expressed unigenes (DEUs) were identified from comparative transcriptomes between diseased individuals and control individuals of clone A + , F and H, respectively. Comprehensive analysis of the shared DEUs in all three clones displayed common defense pathways to the herpesvirus infection, activating IFN system and suppressing complements. KEGG pathway analysis of specifically changed DEUs in respective clones revealed distinct immune responses to the herpesvirus infection. The DEU numbers identified from clone H in KEGG immune-related pathways, such as "chemokine signaling pathway", "Toll-like receptor signaling pathway" and others, were remarkably much more than those from clone A + and F. Several IFN-related genes, including Mx1, viperin, PKR and others, showed higher increases in the resistant clone H than that in the others. IFNphi3, IFI44-like and Gig2 displayed the highest expression in clone F and IRF1 uniquely increased in susceptible clone A + . In contrast to strong immune defense in resistant clone H, susceptible clone A + showed remarkable up-regulation of genes related to apoptosis or death, indicating that clone A + failed to resist virus offensive and evidently induced apoptosis or death. Our study is the first attempt to screen distinct resistances and immune responses of three gynogenetic gibel carp clones to herpesvirus infection by comprehensive transcriptomes. These differential DEUs, immune-related pathways and IFN system genes identified from susceptible and resistant clones will be beneficial to marker-assisted selection (MAS) breeding or molecular module-based resistance breeding in gibel carp.

Transcriptome analysis and metabolic profiling of green and red kale (Brassica oleracea var. acephala) seedlings.

PubMed

Jeon, Jin; Kim, Jae Kwang; Kim, HyeRan; Kim, Yeon Jeong; Park, Yun Ji; Kim, Sun Ju; Kim, Changsoo; Park, Sang Un

2018-02-15

Kale (Brassica oleracea var. acephala) is a rich source of numerous health-benefiting compounds, including vitamins, glucosinolates, phenolic compounds, and carotenoids. However, the genetic resources for exploiting the phyto-nutritional traits of kales are limited. To acquire precise information on secondary metabolites in kales, we performed a comprehensive analysis of the transcriptome and metabolome of green and red kale seedlings. Kale transcriptome datasets revealed 37,149 annotated genes and several secondary metabolite biosynthetic genes. HPLC analysis revealed 14 glucosinolates, 20 anthocyanins, 3 phenylpropanoids, and 6 carotenoids in the kale seedlings that were examined. Red kale contained more glucosinolates, anthocyanins, and phenylpropanoids than green kale, whereas the carotenoid contents were much higher in green kale than in red kale. Ultimately, our data will be a valuable resource for future research on kale bio-engineering and will provide basic information to define gene-to-metabolite networks in kale. Copyright © 2017 Elsevier Ltd. All rights reserved.

Isolation and chemical analysis of nanoparticles from English ivy (Hedera helix L.)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lenaghan, Scott C; Burris, Jason N; Chourey, Karuna

It was discovered that adventitious roots of English ivy secreted a high strength adhesive containing uniform nanoparticles. These nanoparticles were hypothesized to be organic in nature. Subsequent studies have revealed several applications for these nanoparticles, but their chemical composition remained unknown. Here, we describe an isolation procedure to obtain gram quantities of ivy nanoparticles from adventitious roots. In addition, ultraviolet/visible (UV/Vis) spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS), elemental analysis, fourier transform infrared spectroscopy (FTIR), and gel electrophoresis were conducted to identify the chemical nature of the ivy nanoparticles. Based on this comprehensive analysis, we conclude that the ivy nanoparticlesmore » are proteinaceous consisting of 51.77% carbon, 4.72% nitrogen, and 0.32% sulfur, without the presence of metals. Liquid chromatography tandem mass spectrometry (LC-MS/MS) based protein profiling revealed the presence of at least 6 proteins, including heat shock proteins and other large molecular weight proteins. Identification of these protein candidates will facilitate gene discovery and bioproduction of ivy nanoparticles.« less

Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis

NASA Astrophysics Data System (ADS)

Kaminski, Naftali; Allard, John D.; Pittet, Jean F.; Zuo, Fengrong; Griffiths, Mark J. D.; Morris, David; Huang, Xiaozhu; Sheppard, Dean; Heller, Renu A.

2000-02-01

The molecular mechanisms of pulmonary fibrosis are poorly understood. We have used oligonucleotide arrays to analyze the gene expression programs that underlie pulmonary fibrosis in response to bleomycin, a drug that causes lung inflammation and fibrosis, in two strains of susceptible mice (129 and C57BL/6). We then compared the gene expression patterns in these mice with 129 mice carrying a null mutation in the epithelial-restricted integrin 6 subunit (6/-), which develop inflammation but are protected from pulmonary fibrosis. Cluster analysis identified two distinct groups of genes involved in the inflammatory and fibrotic responses. Analysis of gene expression at multiple time points after bleomycin administration revealed sequential induction of subsets of genes that characterize each response. The availability of this comprehensive data set should accelerate the development of more effective strategies for intervention at the various stages in the development of fibrotic diseases of the lungs and other organs.

Integration Processes Compared: Cortical Differences for Consistency Evaluation and Passive Comprehension in Local and Global Coherence.

PubMed

Egidi, Giovanna; Caramazza, Alfonso

2016-10-01

This research studies the neural systems underlying two integration processes that take place during natural discourse comprehension: consistency evaluation and passive comprehension. Evaluation was operationalized with a consistency judgment task and passive comprehension with a passive listening task. Using fMRI, the experiment examined the integration of incoming sentences with more recent, local context and with more distal, global context in these two tasks. The stimuli were stories in which we manipulated the consistency of the endings with the local context and the relevance of the global context for the integration of the endings. A whole-brain analysis revealed several differences between the two tasks. Two networks previously associated with semantic processing and attention orienting showed more activation during the judgment than the passive listening task. A network previously associated with episodic memory retrieval and construction of mental scenes showed greater activity when global context was relevant, but only during the judgment task. This suggests that evaluation, more than passive listening, triggers the reinstantiation of global context and the construction of a rich mental model for the story. Finally, a network previously linked to fluent updating of a knowledge base showed greater activity for locally consistent endings than inconsistent ones, but only during passive listening, suggesting a mode of comprehension that relies on a local scope approach to language processing. Taken together, these results show that consistency evaluation and passive comprehension weigh differently on distal and local information and are implemented, in part, by different brain networks.

How Much Comprehensible Input Did Heinrich Schliemann Get?

ERIC Educational Resources Information Center

Krashen, Stephen D.

1991-01-01

Examines Heinrich Schliemann's method of acquiring a second language primarily by means of conscious learning. It is revealed that Schliemann probably obtained a great deal of comprehensible input in English. (nine references) (GLR)

Ripening-dependent metabolic changes in the volatiles of pineapple (Ananas comosus (L.) Merr.) fruit: II. Multivariate statistical profiling of pineapple aroma compounds based on comprehensive two-dimensional gas chromatography-mass spectrometry.

PubMed

Steingass, Christof Björn; Jutzi, Manfred; Müller, Jenny; Carle, Reinhold; Schmarr, Hans-Georg

2015-03-01

Ripening-dependent changes of pineapple volatiles were studied in a nontargeted profiling analysis. Volatiles were isolated via headspace solid phase microextraction and analyzed by comprehensive 2D gas chromatography and mass spectrometry (HS-SPME-GC×GC-qMS). Profile patterns presented in the contour plots were evaluated applying image processing techniques and subsequent multivariate statistical data analysis. Statistical methods comprised unsupervised hierarchical cluster analysis (HCA) and principal component analysis (PCA) to classify the samples. Supervised partial least squares discriminant analysis (PLS-DA) and partial least squares (PLS) regression were applied to discriminate different ripening stages and describe the development of volatiles during postharvest storage, respectively. Hereby, substantial chemical markers allowing for class separation were revealed. The workflow permitted the rapid distinction between premature green-ripe pineapples and postharvest-ripened sea-freighted fruits. Volatile profiles of fully ripe air-freighted pineapples were similar to those of green-ripe fruits postharvest ripened for 6 days after simulated sea freight export, after PCA with only two principal components. However, PCA considering also the third principal component allowed differentiation between air-freighted fruits and the four progressing postharvest maturity stages of sea-freighted pineapples.

Agarra, agarran: Evidence of early comprehension of subject-verb agreement in Spanish.

PubMed

Gonzalez-Gomez, Nayeli; Hsin, Lisa; Barrière, Isabelle; Nazzi, Thierry; Legendre, Géraldine

2017-08-01

Studies across many languages (e.g., Dutch, English, Farsi, Spanish, Xhosa) have failed to show early acquisition of subject-verb (SV) agreement, whereas recent studies on French reveal acquisition by 30months of age. Using a similar procedure as in previous French studies, the current study evaluated whether earlier comprehension of SV agreement in (Mexican) Spanish can be revealed when task demands are lowered. Two experiments using a touch-screen pointing task tested comprehension of SV agreement by monolingual Spanish-speaking children growing up in Mexico City between about 3 and 5years of age. In Experiment 1, the auditory stimuli consisted of a transitive verb+pseudonoun object (e.g., agarra el micho 'he throws the micho' vs. agarran el duco 'they throw the duco'); results failed to show early comprehension of SV agreement, replicating previous findings. In Experiment 2, the same stimuli were used, with the crucial difference that the word objeto 'object' replaced all pseudonouns; results revealed SV agreement comprehension as early as 41 to 50months. Taken together, our findings show that comprehension at this age is facilitated when task demands are lowered, here by not requiring children to process pseudowords (even when these were not critical to the task). Hence, these findings underscore the importance of task-specific/stimulus-specific features when testing early morphosyntactic development and suggest that previous results may have underestimated Spanish-speaking children's competence. Copyright © 2017 Elsevier Inc. All rights reserved.

Comprehensive analysis of commercial willow bark extracts by new technology platform: combined use of metabolomics, high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy and high-resolution radical scavenging assay.

PubMed

Agnolet, Sara; Wiese, Stefanie; Verpoorte, Robert; Staerk, Dan

2012-11-02

Here, proof-of-concept of a new analytical platform used for the comprehensive analysis of a small set of commercial willow bark products is presented, and compared with a traditional standardization solely based on analysis of salicin and salicin derivatives. The platform combines principal component analysis (PCA) of two chemical fingerprints, i.e., HPLC and (1)H NMR data, and a pharmacological fingerprint, i.e., high-resolution 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) radical cation (ABTS(+)) reduction profile, with targeted identification of constituents of interest by hyphenated HPLC-solid-phase extraction-tube transfer NMR, i.e., HPLC-SPE-ttNMR. Score plots from PCA of HPLC and (1)H NMR fingerprints showed the same distinct grouping of preparations formulated as capsules of Salix alba bark and separation of S. alba cortex. Loading plots revealed this to be due to high amount of salicin in capsules and ampelopsin, taxifolin, 7-O-methyltaxifolin-3'-O-glucoside, and 7-O-methyltaxifolin in S. alba cortex, respectively. PCA of high-resolution radical scavenging profiles revealed clear separation of preparations along principal component 1 due to the major radical scavengers (+)-catechin and ampelopsin. The new analytical platform allowed identification of 16 compounds in commercial willow bark extracts, and identification of ampelopsin, taxifolin, 7-O-methyltaxifolin-3'-O-glucoside, and 7-O-methyltaxifolin in S. alba bark extract is reported for the first time. The detection of the novel compound, ethyl 1-hydroxy-6-oxocyclohex-2-enecarboxylate, is also described. Copyright © 2012 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Qibin; Monroe, Matthew E.; Schepmoes, Athena A.

Non-enzymatic glycation of proteins is implicated in diabetes mellitus and its related complications. In this report, we extend our previous development and refinement of proteomics-based methods for the analysis of non-enzymatically glycated proteins to comprehensively identify glycated proteins in normal and diabetic human plasma and erythrocytes. Using immunodepletion, enrichment, and fractionation strategies, we identified 7749 unique glycated peptides, corresponding to 3742 unique glycated proteins. Semi-quantitative comparisons revealed a number of proteins with glycation levels significantly increased in diabetes relative to control samples and that erythrocyte proteins are more extensively glycated than plasma proteins. A glycation motif analysis revealed amino acidsmore » that are favored more than others in the protein primary structures in the vicinity of the glycation sites in both sample types. The glycated peptides and corresponding proteins reported here provide a foundation for the potential identification of novel markers for diabetes, glycemia, or diabetic complications.« less

Proteomic and N-glycoproteomic quantification reveal aberrant changes in the human saliva of oral ulcer patients.

PubMed

Zhang, Ying; Wang, Xi; Cui, Dan; Zhu, Jun

2016-12-01

Human whole saliva is a vital body fluid for studying the physiology and pathology of the oral cavity. As a powerful technique for biomarker discovery, MS-based proteomic strategies have been introduced for saliva analysis and identified hundreds of proteins and N-glycosylation sites. However, there is still a lack of quantitative analysis, which is necessary for biomarker screening and biological research. In this study, we establish an integrated workflow by the combination of stable isotope dimethyl labeling, HILIC enrichment, and high resolution MS for both quantification of the global proteome and N-glycoproteome of human saliva from oral ulcer patients. With the help of advanced bioinformatics, we comprehensively studied oral ulcers at both protein and glycoprotein scales. Bioinformatics analyses revealed that starch digestion and protein degradation activities are inhibited while the immune response is promoted in oral ulcer saliva. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Examining the Psychometric Properties of the Family Accommodation Scale-Parent-Report (FAS-PR)

PubMed Central

Sapyta, Jeffrey; Garcia, Abbe; Freeman, Jennifer B.; Franklin, Martin E.; Foa, Edna; March, John

2011-01-01

Growing research has examined parental accommodation among the families of children with obsessive-compulsive disorder (OCD). However, these studies have utilized a parent-report (PR) version of a measure, the Family Accommodation Scale (FAS) that has never received proper psychometric validation. In turn, previously derived subscales have been developed via clinical rather than empirical evidence. This study aims to conduct a comprehensive psychometric analysis of the FAS-PR utilizing data collected from 96 youths with OCD. Exploratory factors analysis was conducted and revealed a 12-item scale yielding two separate, yet related subscales, Avoidance of Triggers (AT) and Involvement in Compulsions (IC). Subsequent analyses revealed good internal consistency and convergent and discriminant validity. These findings suggest that future research should seek to examine factors that may impact various facets to accommodation as well as the role these facets plays in predicting treatment outcome. Limitations are discussed. PMID:21743772

Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.).

PubMed

Malviya, N; Gupta, S; Singh, V K; Yadav, M K; Bisht, N C; Sarangi, B K; Yadav, D

2015-02-01

The DNA binding with One Finger (Dof) protein is a plant specific transcription factor involved in the regulation of wide range of processes. The analysis of whole genome sequence of pigeonpea has identified 38 putative Dof genes (CcDof) distributed on 8 chromosomes. A total of 17 out of 38 CcDof genes were found to be intronless. A comprehensive in silico characterization of CcDof gene family including the gene structure, chromosome location, protein motif, phylogeny, gene duplication and functional divergence has been attempted. The phylogenetic analysis resulted in 3 major clusters with closely related members in phylogenetic tree revealed common motif distribution. The in silico cis-regulatory element analysis revealed functional diversity with predominance of light responsive and stress responsive elements indicating the possibility of these CcDof genes to be associated with photoperiodic control and biotic and abiotic stress. The duplication pattern showed that tandem duplication is predominant over segmental duplication events. The comparative phylogenetic analysis of these Dof proteins along with 78 soybean, 36 Arabidopsis and 30 rice Dof proteins revealed 7 major clusters. Several groups of orthologs and paralogs were identified based on phylogenetic tree constructed. Our study provides useful information for functional characterization of CcDof genes.

What Oral Text Reading Fluency Can Reveal about Reading Comprehension

ERIC Educational Resources Information Center

Veenendaal, Nathalie J.; Groen, Margriet A.; Verhoeven, Ludo

2015-01-01

Text reading fluency--the ability to read quickly, accurately and with a natural intonation--has been proposed as a predictor of reading comprehension. In the current study, we examined the role of oral text reading fluency, defined as text reading rate and text reading prosody, as a contributor to reading comprehension outcomes in addition to…

Using Higher Order Cognitive Questions in the Primary Classroom To Improve Comprehension.

ERIC Educational Resources Information Center

Coolidge, Susan W.

A teaching team leader and second grade teacher designed and implemented a 10-week practicum intervention meant to improve the inferential comprehension of 105 second graders whose reading scores on the Ginn Mastery Tests revealed a gap between inferential and literal comprehension. It was reasoned that the gap would decrease if teachers were…

Acquisition of Prosodic Focus Marking by English, French, and German Three-, Four-, Five- and Six-Year-Olds

ERIC Educational Resources Information Center

Szendroi, Kriszta; Bernard, Carline; Berger, Frauke; Gervain, Judit; Hohle, Barbara

2018-01-01

Previous research on young children's knowledge of prosodic focus marking has revealed an apparent paradox, with comprehension appearing to lag behind production. Comprehension of prosodic focus is difficult to study experimentally due to its subtle and ambiguous contribution to pragmatic meaning. We designed a novel comprehension task, which…

Improving Reading Comprehension Skills through the SCRATCH Program

ERIC Educational Resources Information Center

Papatga, Erdal; Ersoy, Ali

2016-01-01

The aim of this study was to reveal how reading comprehension skills of elementary fourth graders who have problems in reading comprehension can be improved by means of the SCRATCH program. The study was designed as a participant action research. It was carried out within a 15- week process at an elementary school with middle socio-economic level…

The Neural Basis of Reversible Sentence Comprehension: Evidence from Voxel-Based Lesion Symptom Mapping in Aphasia

ERIC Educational Resources Information Center

Thothathiri, Malathi; Kimberg, Daniel Y.; Schwartz, Myrna F.

2012-01-01

We explored the neural basis of reversible sentence comprehension in a large group of aphasic patients (n = 79). Voxel-based lesion symptom mapping revealed a significant association between damage in temporo-parietal cortex and impaired sentence comprehension. This association remained after we controlled for phonological working memory. We…

Development of endosperm transfer cells in barley.

PubMed

Thiel, Johannes

2014-01-01

Endosperm transfer cells (ETCs) are positioned at the intersection of maternal and filial tissues in seeds of cereals and represent a bottleneck for apoplasmic transport of assimilates into the endosperm. Endosperm cellularization starts at the maternal-filial boundary and generates the highly specialized ETCs. During differentiation barley ETCs develop characteristic flange-like wall ingrowths to facilitate effective nutrient transfer. A comprehensive morphological analysis depicted distinct developmental time points in establishment of transfer cell (TC) morphology and revealed intracellular changes possibly associated with cell wall metabolism. Embedded inside the grain, ETCs are barely accessible by manual preparation. To get tissue-specific information about ETC specification and differentiation, laser microdissection (LM)-based methods were used for transcript and metabolite profiling. Transcriptome analysis of ETCs at different developmental stages by microarrays indicated activated gene expression programs related to control of cell proliferation and cell shape, cell wall and carbohydrate metabolism reflecting the morphological changes during early ETC development. Transporter genes reveal distinct expression patterns suggesting a switch from active to passive modes of nutrient uptake with the onset of grain filling. Tissue-specific RNA-seq of the differentiating ETC region from the syncytial stage until functionality in nutrient transfer identified a high number of novel transcripts putatively involved in ETC differentiation. An essential role for two-component signaling (TCS) pathways in ETC development of barley emerged from this analysis. Correlative data provide evidence for abscisic acid and ethylene influences on ETC differentiation and hint at a crosstalk between hormone signal transduction and TCS phosphorelays. Collectively, the data expose a comprehensive view on ETC development, associated pathways and identified candidate genes for ETC specification.

Development of endosperm transfer cells in barley

PubMed Central

Thiel, Johannes

2014-01-01

Endosperm transfer cells (ETCs) are positioned at the intersection of maternal and filial tissues in seeds of cereals and represent a bottleneck for apoplasmic transport of assimilates into the endosperm. Endosperm cellularization starts at the maternal-filial boundary and generates the highly specialized ETCs. During differentiation barley ETCs develop characteristic flange-like wall ingrowths to facilitate effective nutrient transfer. A comprehensive morphological analysis depicted distinct developmental time points in establishment of transfer cell (TC) morphology and revealed intracellular changes possibly associated with cell wall metabolism. Embedded inside the grain, ETCs are barely accessible by manual preparation. To get tissue-specific information about ETC specification and differentiation, laser microdissection (LM)-based methods were used for transcript and metabolite profiling. Transcriptome analysis of ETCs at different developmental stages by microarrays indicated activated gene expression programs related to control of cell proliferation and cell shape, cell wall and carbohydrate metabolism reflecting the morphological changes during early ETC development. Transporter genes reveal distinct expression patterns suggesting a switch from active to passive modes of nutrient uptake with the onset of grain filling. Tissue-specific RNA-seq of the differentiating ETC region from the syncytial stage until functionality in nutrient transfer identified a high number of novel transcripts putatively involved in ETC differentiation. An essential role for two-component signaling (TCS) pathways in ETC development of barley emerged from this analysis. Correlative data provide evidence for abscisic acid and ethylene influences on ETC differentiation and hint at a crosstalk between hormone signal transduction and TCS phosphorelays. Collectively, the data expose a comprehensive view on ETC development, associated pathways and identified candidate genes for ETC specification. PMID:24723929

Quantitative DNA Methylation Analysis Identifies a Single CpG Dinucleotide Important for ZAP-70 Expression and Predictive of Prognosis in Chronic Lymphocytic Leukemia

PubMed Central

Claus, Rainer; Lucas, David M.; Stilgenbauer, Stephan; Ruppert, Amy S.; Yu, Lianbo; Zucknick, Manuela; Mertens, Daniel; Bühler, Andreas; Oakes, Christopher C.; Larson, Richard A.; Kay, Neil E.; Jelinek, Diane F.; Kipps, Thomas J.; Rassenti, Laura Z.; Gribben, John G.; Döhner, Hartmut; Heerema, Nyla A.; Marcucci, Guido; Plass, Christoph; Byrd, John C.

2012-01-01

Purpose Increased ZAP-70 expression predicts poor prognosis in chronic lymphocytic leukemia (CLL). Current methods for accurately measuring ZAP-70 expression are problematic, preventing widespread application of these tests in clinical decision making. We therefore used comprehensive DNA methylation profiling of the ZAP-70 regulatory region to identify sites important for transcriptional control. Patients and Methods High-resolution quantitative DNA methylation analysis of the entire ZAP-70 gene regulatory regions was conducted on 247 samples from patients with CLL from four independent clinical studies. Results Through this comprehensive analysis, we identified a small area in the 5′ regulatory region of ZAP-70 that showed large variability in methylation in CLL samples but was universally methylated in normal B cells. High correlation with mRNA and protein expression, as well as activity in promoter reporter assays, revealed that within this differentially methylated region, a single CpG dinucleotide and neighboring nucleotides are particularly important in ZAP-70 transcriptional regulation. Furthermore, by using clustering approaches, we identified a prognostic role for this site in four independent data sets of patients with CLL using time to treatment, progression-free survival, and overall survival as clinical end points. Conclusion Comprehensive quantitative DNA methylation analysis of the ZAP-70 gene in CLL identified important regions responsible for transcriptional regulation. In addition, loss of methylation at a specific single CpG dinucleotide in the ZAP-70 5′ regulatory sequence is a highly predictive and reproducible biomarker of poor prognosis in this disease. This work demonstrates the feasibility of using quantitative specific ZAP-70 methylation analysis as a relevant clinically applicable prognostic test in CLL. PMID:22564988

Development of a comprehensive model for stakeholder management in mental healthcare.

PubMed

Bierbooms, Joyce; Van Oers, Hans; Rijkers, Jeroen; Bongers, Inge

2016-06-20

Purpose - Stakeholder management is not yet incorporated into the standard practice of most healthcare providers. The purpose of this paper is to assess the applicability of a comprehensive model for stakeholder management in mental healthcare organization for more evidence-based (stakeholder) management. Design/methodology/approach - The assessment was performed in two research parts: the steps described in the model were executed in a single case study at a mental healthcare organization in the Netherlands; and a process and effect evaluation was done to find the supporting and impeding factors with regard to the applicability of the model. Interviews were held with managers and directors to evaluate the effectiveness of the model with a view to stakeholder management. Findings - The stakeholder analysis resulted in the identification of eight stakeholder groups. Different expectations were identified for each of these groups. The analysis on performance gaps revealed that stakeholders generally find the collaboration with a mental healthcare provider "sufficient." Finally a prioritization showed that five stakeholder groups were seen as "definite" stakeholders by the organization. Practical implications - The assessment of the model showed that it generated useful knowledge for more evidence-based (stakeholder) management. Adaptation of the model is needed to increase its feasibility in practice. Originality/value - Provided that the model is properly adapted for the specific field, the analysis can provide more knowledge on stakeholders and can help integrate stakeholder management as a comprehensive process in policy planning.

A Comprehensive Strategy for Accurate Mutation Detection of the Highly Homologous PMS2.

PubMed

Li, Jianli; Dai, Hongzheng; Feng, Yanming; Tang, Jia; Chen, Stella; Tian, Xia; Gorman, Elizabeth; Schmitt, Eric S; Hansen, Terah A A; Wang, Jing; Plon, Sharon E; Zhang, Victor Wei; Wong, Lee-Jun C

2015-09-01

Germline mutations in the DNA mismatch repair gene PMS2 underlie the cancer susceptibility syndrome, Lynch syndrome. However, accurate molecular testing of PMS2 is complicated by a large number of highly homologous sequences. To establish a comprehensive approach for mutation detection of PMS2, we have designed a strategy combining targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS to simultaneously detect point mutations and copy number changes of PMS2. Exonic deletions (E2 to E9, E5 to E9, E8, E10, E14, and E1 to E15), duplications (E11 to E12), and a nonsense mutation, p.S22*, were identified. Traditional multiplex ligation-dependent probe amplification and Sanger sequencing approaches cannot differentiate the origin of the exonic deletions in the 3' region when PMS2 and PMS2CL share identical sequences as a result of gene conversion. Our approach allows unambiguous identification of mutations in the active gene with a straightforward long-range-PCR/NGS method. Breakpoint analysis of multiple samples revealed that recurrent exon 14 deletions are mediated by homologous Alu sequences. Our comprehensive approach provides a reliable tool for accurate molecular analysis of genes containing multiple copies of highly homologous sequences and should improve PMS2 molecular analysis for patients with Lynch syndrome. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Systems cell biology.

PubMed

Mast, Fred D; Ratushny, Alexander V; Aitchison, John D

2014-09-15

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. © 2014 Mast et al.

Histone hyperacetylation and exon skipping: a calcium-mediated dynamic regulation in cardiomyocytes

PubMed Central

Sharma, Alok; Nguyen, Hieu; Cai, Lu; Lou, Hua

2015-01-01

In contrast to cell type-specific pre-mRNA alternative splicing, mechanisms controlling activity-dependent alternative splicing is under-studied and not well understood. In a recent study, we conducted a comprehensive analysis of calcium-mediated mechanism that regulates alternative exon skipping in mouse cardiomyocytes. Our results reveal a strong link between histone hyperacetylation and skipping of cassette exons, and provide support to the kinetic coupling model of the epigenetic regulation of alternative splicing at the chromatin level. PMID:26325491

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

PubMed Central

Shepard, Peter J.; Choi, Eun-A; Lu, Jente; Flanagan, Lisa A.; Hertel, Klemens J.; Shi, Yongsheng

2011-01-01

Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs. PAS-Seq analyses of human and mouse transcriptomes showed that 40%–50% of all expressed genes produce alternatively polyadenylated mRNAs. Furthermore, our study detected evolutionarily conserved polyadenylation of histone mRNAs and revealed novel features of mitochondrial RNA polyadenylation. Finally, PAS-Seq analyses of mouse embryonic stem (ES) cells, neural stem/progenitor (NSP) cells, and neurons not only identified more poly(A) sites than what was found in the entire mouse EST database, but also detected significant changes in the global APA profile that lead to lengthening of 3′ untranslated regions (UTR) in many mRNAs during stem cell differentiation. Together, our PAS-Seq analyses revealed a complex landscape of RNA polyadenylation in mammalian cells and the dynamic regulation of APA during stem cell differentiation. PMID:21343387

Genome-Wide Investigation and Expression Profiling of HD-Zip Transcription Factors in Foxtail Millet (Setaria italica L.).

PubMed

Chai, Wenbo; Si, Weina; Ji, Wei; Qin, Qianqian; Zhao, Manli; Jiang, Haiyang

2018-01-01

HD-Zip proteins represent the major transcription factors in higher plants, playing essential roles in plant development and stress responses. Foxtail millet is a crop to investigate the systems biology of millet and biofuel grasses and the HD-Zip gene family has not been studied in foxtail millet. For further investigation of the expression profile of the HD-Zip gene family in foxtail millet, a comprehensive genome-wide expression analysis was conducted in this study. We found 47 protein-encoding genes in foxtail millet using BLAST search tools; the putative proteins were classified into four subfamilies, namely, subfamilies I, II, III, and IV. Gene structure and motif analysis indicate that the genes in one subfamily were conserved. Promotor analysis showed that HD-Zip gene was involved in abiotic stress. Duplication analysis revealed that 8 (~17%) hdz genes were tandemly duplicated and 28 (58%) were segmentally duplicated; purifying duplication plays important roles in gene expansion. Microsynteny analysis revealed the maximum relationship in foxtail millet-sorghum and foxtail millet-rice. Expression profiling upon the abiotic stresses of drought and high salinity and the biotic stress of ABA revealed that some genes regulated responses to drought and salinity stresses via an ABA-dependent process, especially sihdz29 and sihdz45. Our study provides new insight into evolutionary and functional analyses of HD-Zip genes involved in environmental stress responses in foxtail millet.

Communication in the second and third year of life: Relationships between nonverbal social skills and language.

PubMed

Cochet, Hélène; Byrne, Richard W

2016-08-01

We aimed to investigate developmental continuities between a range of early social and communicative abilities (including gestural communication) and language acquisition in children aged between 11 and 41 months. Initiation of joint attention and imitation were strongly correlated to language comprehension and production. Moreover, the analysis of different communicative gestures revealed significant relationships between language development and the production of symbolic gestures, declarative pointing (declarative informative pointing in particular), and head nodding. Other gestures such as imperative pointing, showing, and head shaking were not found to correlate with language level. Our results also suggest that distinct processes are involved in the development of language comprehension and production, and highlight the importance of considering various characteristics of children's early communicative skills. Copyright © 2016 Elsevier Inc. All rights reserved.

Examining the Impact of Quickreads' Technology and Print Formats on Fluency, Comprehension, and Vocabulary Development for Elementary Students

ERIC Educational Resources Information Center

Trainin, Guy; Hayden, H. Emily; Wilson, Kathleen; Erickson, Joan

2016-01-01

National reports reveal one third of American fourth graders read below basic level on measures of comprehension. One critical component of comprehension is fluency: rapid, accurate, expressive reading with automaticity and prosody. Many fluency studies and classroom interventions focus only on reading rate, but this alone is not sufficient. This…

Quantitative proteomic analysis of human lung tumor xenografts treated with the ectopic ATP synthase inhibitor citreoviridin.

PubMed

Wu, Yi-Hsuan; Hu, Chia-Wei; Chien, Chih-Wei; Chen, Yu-Ju; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

2013-01-01

ATP synthase is present on the plasma membrane of several types of cancer cells. Citreoviridin, an ATP synthase inhibitor, selectively suppresses the proliferation and growth of lung cancer without affecting normal cells. However, the global effects of targeting ectopic ATP synthase in vivo have not been well defined. In this study, we performed quantitative proteomic analysis using isobaric tags for relative and absolute quantitation (iTRAQ) and provided a comprehensive insight into the complicated regulation by citreoviridin in a lung cancer xenograft model. With high reproducibility of the quantitation, we obtained quantitative proteomic profiling with 2,659 proteins identified. Bioinformatics analysis of the 141 differentially expressed proteins selected by their relative abundance revealed that citreoviridin induces alterations in the expression of glucose metabolism-related enzymes in lung cancer. The up-regulation of enzymes involved in gluconeogenesis and storage of glucose indicated that citreoviridin may reduce the glycolytic intermediates for macromolecule synthesis and inhibit cell proliferation. Using comprehensive proteomics, the results identify metabolic aspects that help explain the antitumorigenic effect of citreoviridin in lung cancer, which may lead to a better understanding of the links between metabolism and tumorigenesis in cancer therapy.

Proteomic analysis of ligamentum flavum from patients with lumbar spinal stenosis.

PubMed

Kamita, Masahiro; Mori, Taiki; Sakai, Yoshihito; Ito, Sadayuki; Gomi, Masahiro; Miyamoto, Yuko; Harada, Atsushi; Niida, Shumpei; Yamada, Tesshi; Watanabe, Ken; Ono, Masaya

2015-05-01

Lumbar spinal stenosis (LSS) is a syndromic degenerative spinal disease and is characterized by spinal canal narrowing with subsequent neural compression causing gait disturbances. Although LSS is a major age-related musculoskeletal disease that causes large decreases in the daily living activities of the elderly, its molecular pathology has not been investigated using proteomics. Thus, we used several proteomic technologies to analyze the ligamentum flavum (LF) of individuals with LSS. Using comprehensive proteomics with strong cation exchange fractionation, we detected 1288 proteins in these LF samples. A GO analysis of the comprehensive proteome revealed that more than 30% of the identified proteins were extracellular. Next, we used 2D image converted analysis of LC/MS to compare LF obtained from individuals with LSS to that obtained from individuals with disc herniation (nondegenerative control). We detected 64 781 MS peaks and identified 1675 differentially expressed peptides derived from 286 proteins. We verified four differentially expressed proteins (fibronectin, serine protease HTRA1, tenascin, and asporin) by quantitative proteomics using SRM/MRM. The present proteomic study is the first to identify proteins from degenerated and hypertrophied LF in LSS, which will help in studying LSS. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative Proteomic Analysis of Human Lung Tumor Xenografts Treated with the Ectopic ATP Synthase Inhibitor Citreoviridin

PubMed Central

Wu, Yi-Hsuan; Hu, Chia-Wei; Chien, Chih-Wei; Chen, Yu-Ju; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

2013-01-01

ATP synthase is present on the plasma membrane of several types of cancer cells. Citreoviridin, an ATP synthase inhibitor, selectively suppresses the proliferation and growth of lung cancer without affecting normal cells. However, the global effects of targeting ectopic ATP synthase in vivo have not been well defined. In this study, we performed quantitative proteomic analysis using isobaric tags for relative and absolute quantitation (iTRAQ) and provided a comprehensive insight into the complicated regulation by citreoviridin in a lung cancer xenograft model. With high reproducibility of the quantitation, we obtained quantitative proteomic profiling with 2,659 proteins identified. Bioinformatics analysis of the 141 differentially expressed proteins selected by their relative abundance revealed that citreoviridin induces alterations in the expression of glucose metabolism-related enzymes in lung cancer. The up-regulation of enzymes involved in gluconeogenesis and storage of glucose indicated that citreoviridin may reduce the glycolytic intermediates for macromolecule synthesis and inhibit cell proliferation. Using comprehensive proteomics, the results identify metabolic aspects that help explain the antitumorigenic effect of citreoviridin in lung cancer, which may lead to a better understanding of the links between metabolism and tumorigenesis in cancer therapy. PMID:23990911

Metabolomics study on the hepatoprotective effect of scoparone using ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry.

PubMed

Zhang, Aihua; Sun, Hui; Dou, Shengshan; Sun, Wenjun; Wu, Xiuhong; Wang, Ping; Wang, Xijun

2013-01-07

Scoparone is an important constituent of Yinchenhao (Artemisia annua L.), a famous medicinal plant, and displayed bright prospects in the prevention and therapy of liver injury. However, the precise molecular mechanism of hepatoprotective effects has not been comprehensively explored. Here, metabolomics techniques are the comprehensive assessment of endogenous metabolites in a biological system and may provide additional insight into the mechanisms. The present investigation was designed to assess the effects and possible mechanisms of scoparone against carbon tetrachloride-induced liver injury. Ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry (UPLC/ESI-Q-TOF/MS) combined with pattern recognition approaches including principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were integrated to discover differentiating metabolites. Results indicate five ions in the positive mode as differentiating metabolites. Functional pathway analysis revealed that the alterations in these metabolites were associated with primary bile acid biosynthesis, pyrimidine metabolism. Of note, scoparone has a potential pharmacological effect through regulating multiple perturbed pathways to the normal state. Our findings also showed that the robust metabolomics techniques are promising for getting biomarkers and clarifying mechanisms of disease, highlighting insights into drug discovery.

HIV Rapid Testing in a VA Emergency Department Setting: Cost Analysis at 5 Years.

PubMed

Knapp, Herschel; Chan, Kee

2015-07-01

To conduct a comprehensive cost-minimization analysis to comprehend the financial attributes of the first 5 years of an implementation wherein emergency department (ED) registered nurses administered HIV oral rapid tests to patients. A health science research implementation team coordinated with ED stakeholders and staff to provide training, implementation guidelines, and support to launch ED registered nurse-administered HIV oral rapid testing. Deidentified quantitative data were gathered from the electronic medical records detailing quarterly HIV rapid test rates in the ED setting spanning the first 5 years. Comprehensive cost analyses were conducted to evaluate the financial impact of this implementation. At 5 years, a total of 2,620 tests were conducted with a quarterly mean of 131 ± 81. Despite quarterly variability in testing rates, regression analysis revealed an average increase of 3.58 tests per quarter. Over the course of this implementation, Veterans Health Administration policy transitioned from written to verbal consent for HIV testing, serving to reduce the time and cost(s) associated with the testing process. Our data indicated salient health outcome benefits for patients with respect to the potential for earlier detection, and associated long-run cost savings. Copyright © 2015. Published by Elsevier Inc.

Confirmatory Factor Analysis of the Malay Version Comprehensive Feeding Practices Questionnaire Tested among Mothers of Primary School Children in Malaysia

PubMed Central

Shohaimi, Shamarina; Yoke Wei, Wong; Mohd Shariff, Zalilah

2014-01-01

Comprehensive feeding practices questionnaire (CFPQ) is an instrument specifically developed to evaluate parental feeding practices. It has been confirmed among children in America and applied to populations in France, Norway, and New Zealand. In order to extend the application of CFPQ, we conducted a factor structure validation of the translated version of CFPQ (CFPQ-M) using confirmatory factor analysis among mothers of primary school children (N = 397) in Malaysia. Several items were modified for cultural adaptation. Of 49 items, 39 items with loading factors >0.40 were retained in the final model. The confirmatory factor analysis revealed that the final model (twelve-factor model with 39 items and 2 error covariances) displayed the best fit for our sample (Chi-square = 1147; df = 634; P < 0.05; CFI = 0.900; RMSEA = 0.045; SRMR = 0.0058). The instrument with some modifications was confirmed among mothers of school children in Malaysia. The present study extends the usability of the CFPQ and enables researchers and parents to better understand the relationships between parental feeding practices and related problems such as childhood obesity. PMID:25538958

Comprehensive investigation of tobacco leaves during natural early senescence via multi-platform metabolomics analyses

NASA Astrophysics Data System (ADS)

Li, Lili; Zhao, Jieyu; Zhao, Yanni; Lu, Xin; Zhou, Zhihui; Zhao, Chunxia; Xu, Guowang

2016-11-01

Senescence is the final stage of leaf growth and development. Many different physiological activities occur during this process. A comprehensive metabolomics analysis of tobacco middle leaves at 5 different developmental stages was implemented through multi-platform methods based on liquid chromatography, capillary electrophoresis and gas chromatography coupled with mass spectrometry. In total, 412 metabolites were identified, including pigments, sterols, lipids, amino acids, polyamines, sugars and secondary metabolites. Dramatic metabolic changes were observed. Firstly, membrane degradation and chlorophyll down-regulation occurred after the 50% flower bud stage. Levels of major membrane lipids decreased, including those of the glycolipids in chloroplast thylakoids and phospholipids in membrane envelopes. Clear decreases in free sterols and acylated sterol glucosides were detected along with the accumulation of sterol esters. The accumulation of alkaloids was found. The amino acid levels were significantly decreased, particularly those of N-rich amino acids (glutamine and asparagine), thus reflecting N translocation. Subsequently, the antioxidant system was activated. Sugar alcohols and polyphenols accumulated when the lower leaves turned yellow. These results comprehensively revealed the metabolic changes that occur during tobacco leaf development and senescence under natural conditions.

Spatial Mapping of Lipids at Cellular Resolution in Embryos of Cotton[W][OA

PubMed Central

Horn, Patrick J.; Korte, Andrew R.; Neogi, Purnima B.; Love, Ebony; Fuchs, Johannes; Strupat, Kerstin; Borisjuk, Ljudmilla; Shulaev, Vladimir; Lee, Young-Jin; Chapman, Kent D.

2012-01-01

Advances in mass spectrometry (MS) have made comprehensive lipidomics analysis of complex tissues relatively commonplace. These compositional analyses, although able to resolve hundreds of molecular species of lipids in single extracts, lose the original cellular context from which these lipids are derived. Recently, high-resolution MS of individual lipid droplets from seed tissues indicated organelle-to-organelle variation in lipid composition, suggesting that heterogeneity of lipid distributions at the cellular level may be prevalent. Here, we employed matrix-assisted laser desorption/ionization–MS imaging (MALDI-MSI) approaches to visualize lipid species directly in seed tissues of upland cotton (Gossypium hirsutum). MS imaging of cryosections of mature cotton embryos revealed a distinct, heterogeneous distribution of molecular species of triacylglycerols and phosphatidylcholines, the major storage and membrane lipid classes in cotton embryos. Other lipids were imaged, including phosphatidylethanolamines, phosphatidic acids, sterols, and gossypol, indicating the broad range of metabolites and applications for this chemical visualization approach. We conclude that comprehensive lipidomics images generated by MALDI-MSI report accurate, relative amounts of lipid species in plant tissues and reveal previously unseen differences in spatial distributions providing for a new level of understanding in cellular biochemistry. PMID:22337917

RISK COMMUNICATION IN COMMUNITY PARTICIPATION: COMPARING REGIONAL PROGRAMS IN SOUTH FLORIDA

EPA Science Inventory

Comparison of the U.S. Environmental Protection Agency’s Superfund Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) and the U.S. Army Corps of Engineers’ Comprehensive Everglades Restoration Plan (CERP) decision-making regimes revealed...

Comprehensive Locoregional Treatment and Systemic Therapy for Postmastectomy Isolated Locoregional Recurrence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuo, S.-H.; Cancer Research Center, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan

2008-12-01

Purpose: To assess the impact of comprehensive locoregional therapy and systemic therapy on disease control and survival for postmastectomy patients with isolated locoregional recurrence (ILRR). Methods and Materials: A total of 115 postmastectomy breast cancer patients treated for ILRR were included. Of the patients, 98 underwent comprehensive locoregional treatment (local tumor excision plus postoperative radiotherapy), and 17 received definitive radiotherapy alone. Involved-field radiotherapy was given to 69 patients, whereas entire-field radiotherapy (both involved-field and elective-field, involving the chest wall and regional lymphatics) was given to 46 patients. Systemic therapy consisting of hormone therapy, chemotherapy, or both was given to 69%more » of patients. Results: Patients treated with comprehensive locoregional treatment had a significantly better 5-year invasive disease-free survival (IDFS) and overall survival (OS) after ILRR than patients treated with definitive radiotherapy alone (IDFS rate, 51% vs. 16%, p = 0.006; OS rate, 62% vs. 37%, p = 0.017). Patients with the most comprehensive locoregional treatment (recurrent tumor excision and entire-field radiotherapy) and systemic therapy had a significantly better 5-year IDFS and OS than patients given either treatment or neither treatment (IDFS rate, 52% vs. 39%, p = 0.011; OS rate, 63% vs. 50%, p = 0.026). Multivariate analysis revealed that positive axillary lymph nodes, Grade III tumor, negative estrogen and progesterone receptor status at primary diagnosis, disease-free interval of less than 2 years, and less comprehensive locoregional treatment were significantly associated with worse IDFS and OS. Conclusions: Use of comprehensive locoregional therapy and systemic therapy can achieve good survival outcome in a substantial proportion of postmastectomy patients with ILRR.« less

Pharmaceutical knowledge governance: a human rights perspective.

PubMed

Lemmens, Trudo

2013-01-01

Industry control over the production and distribution of pharmaceutical safety and efficacy data has become a serious public health and health care funding concern. Various recent scandals, several involving the use of flawed representations of scientific data in the most influential medical journals, highlight the urgency of enhancing pharmaceutical knowledge governance. This paper analyzes why this is a human rights concern and what difference a human rights analysis can make. The paper first identifies the challenges associated with the current knowledge deficit. It then discusses, based on an analysis of case law, how various human rights associated interests can be invoked to support the claim that states have an obligation to actively contribute to independent knowledge governance, for example through ensuring clinical trials transparency. The paper further discusses a conceptual use of human rights, as a methodology which requires a comprehensive analysis of the different interwoven historical, economic, cultural, and social factors that contribute to the problem. Such an analysis reveals that historically grown drug regulations have, in fact, contributed directly to industry control over pharmaceutical knowledge production. This type of finding should inform needed reforms of drug regulation. The paper ends with a recommendation for a comprehensive global response to the problem of pharmaceutical knowledge governance. © 2013 American Society of Law, Medicine & Ethics, Inc.

Speech comprehension aided by multiple modalities: behavioural and neural interactions

PubMed Central

McGettigan, Carolyn; Faulkner, Andrew; Altarelli, Irene; Obleser, Jonas; Baverstock, Harriet; Scott, Sophie K.

2014-01-01

Speech comprehension is a complex human skill, the performance of which requires the perceiver to combine information from several sources – e.g. voice, face, gesture, linguistic context – to achieve an intelligible and interpretable percept. We describe a functional imaging investigation of how auditory, visual and linguistic information interact to facilitate comprehension. Our specific aims were to investigate the neural responses to these different information sources, alone and in interaction, and further to use behavioural speech comprehension scores to address sites of intelligibility-related activation in multifactorial speech comprehension. In fMRI, participants passively watched videos of spoken sentences, in which we varied Auditory Clarity (with noise-vocoding), Visual Clarity (with Gaussian blurring) and Linguistic Predictability. Main effects of enhanced signal with increased auditory and visual clarity were observed in overlapping regions of posterior STS. Two-way interactions of the factors (auditory × visual, auditory × predictability) in the neural data were observed outside temporal cortex, where positive signal change in response to clearer facial information and greater semantic predictability was greatest at intermediate levels of auditory clarity. Overall changes in stimulus intelligibility by condition (as determined using an independent behavioural experiment) were reflected in the neural data by increased activation predominantly in bilateral dorsolateral temporal cortex, as well as inferior frontal cortex and left fusiform gyrus. Specific investigation of intelligibility changes at intermediate auditory clarity revealed a set of regions, including posterior STS and fusiform gyrus, showing enhanced responses to both visual and linguistic information. Finally, an individual differences analysis showed that greater comprehension performance in the scanning participants (measured in a post-scan behavioural test) were associated with increased activation in left inferior frontal gyrus and left posterior STS. The current multimodal speech comprehension paradigm demonstrates recruitment of a wide comprehension network in the brain, in which posterior STS and fusiform gyrus form sites for convergence of auditory, visual and linguistic information, while left-dominant sites in temporal and frontal cortex support successful comprehension. PMID:22266262

Speech comprehension aided by multiple modalities: behavioural and neural interactions.

PubMed

McGettigan, Carolyn; Faulkner, Andrew; Altarelli, Irene; Obleser, Jonas; Baverstock, Harriet; Scott, Sophie K

2012-04-01

Speech comprehension is a complex human skill, the performance of which requires the perceiver to combine information from several sources - e.g. voice, face, gesture, linguistic context - to achieve an intelligible and interpretable percept. We describe a functional imaging investigation of how auditory, visual and linguistic information interact to facilitate comprehension. Our specific aims were to investigate the neural responses to these different information sources, alone and in interaction, and further to use behavioural speech comprehension scores to address sites of intelligibility-related activation in multifactorial speech comprehension. In fMRI, participants passively watched videos of spoken sentences, in which we varied Auditory Clarity (with noise-vocoding), Visual Clarity (with Gaussian blurring) and Linguistic Predictability. Main effects of enhanced signal with increased auditory and visual clarity were observed in overlapping regions of posterior STS. Two-way interactions of the factors (auditory × visual, auditory × predictability) in the neural data were observed outside temporal cortex, where positive signal change in response to clearer facial information and greater semantic predictability was greatest at intermediate levels of auditory clarity. Overall changes in stimulus intelligibility by condition (as determined using an independent behavioural experiment) were reflected in the neural data by increased activation predominantly in bilateral dorsolateral temporal cortex, as well as inferior frontal cortex and left fusiform gyrus. Specific investigation of intelligibility changes at intermediate auditory clarity revealed a set of regions, including posterior STS and fusiform gyrus, showing enhanced responses to both visual and linguistic information. Finally, an individual differences analysis showed that greater comprehension performance in the scanning participants (measured in a post-scan behavioural test) were associated with increased activation in left inferior frontal gyrus and left posterior STS. The current multimodal speech comprehension paradigm demonstrates recruitment of a wide comprehension network in the brain, in which posterior STS and fusiform gyrus form sites for convergence of auditory, visual and linguistic information, while left-dominant sites in temporal and frontal cortex support successful comprehension. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comprehensive assessment of cancer patients' concerns and the association with quality of life.

PubMed

Yokoo, Minori; Akechi, Tatsuo; Takayama, Tomoko; Karato, Atsuya; Kikuuchi, Yuki; Okamoto, Naoyuki; Katayama, Kayoko; Nakanotani, Takako; Ogawa, Asao

2014-07-01

Comprehensive assessment of perceived concerns can be used to guide supportive care appropriate to individual cancer patients. This study sought to determine the prevalence of cancer patients' concerns and the degree to which these concerns contribute to patients' quality of life. Participants were patients with all types of cancer, who completed an Internet survey questionnaire regarding comprehensive concerns about physical, psychological, psychosocial and economic aspects of having cancer. The questionnaire was based on the newly developed Comprehensive Concerns Assessment Tool and the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire. We obtained complete data from 807 patients. Factors related to 'self-management' concerns were the most common (61.2%), followed by concerns about 'psychological symptoms' (48.5%), 'medical information' (46.2%), 'daily living' (29.9%), 'pain' (17.6%), 'constipation' (15.6%) and other 'physical symptoms' (15.2%). Multiple regression analysis revealed that all concerns except those about 'medical information' significantly contributed to quality of life. Cancer patients' concerns were shown to be multidimensional and significantly associated with quality of life. Thus, assessment of patients' concerns should be multidimensional in nature, and a multidisciplinary care team should help patients improve their quality of life. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A bibliometric analysis of the 50 most cited papers in cleft lip and palate.

PubMed

Mahon, Nicola A; Joyce, Cormac W

2015-02-01

Citation analysis is an established bibliometric method which catalogues papers according to the number of times they have been referenced. It is believed that the total number of citations an article receives reflects its importance among its peers. Never before has a bibliometric analysis been performed in the area of Cleft Lip and Palate. Our citation analysis creates a comprehensive list of the 50 most influential papers in this field. Journals specializing in Cleft Palate, Craniofacial, Plastic Surgery, Maxillofacial Surgery, Aesthetics and Radiology were searched to establish which articles most enriched the specialty over the past 70 years. The results show an interesting collection of papers which reveal developing trends in surgical techniques. These landmark papers mould and influence management and decision-making today.

Readers in Adult Basic Education.

PubMed

Barnes, Adrienne E; Kim, Young-Suk; Tighe, Elizabeth L; Vorstius, Christian

The present study explored the reading skills of a sample of 48 adults enrolled in a basic education program in northern Florida, United States. Previous research has reported on reading component skills for students in adult education settings, but little is known about eye movement patterns or their relation to reading skills for this population. In this study, reading component skills including decoding, language comprehension, and reading fluency are reported, as are eye movement variables for connected-text oral reading. Eye movement comparisons between individuals with higher and lower oral reading fluency revealed within- and between-subject effects for word frequency and word length as well as group and word frequency interactions. Bivariate correlations indicated strong relations between component skills of reading, eye movement measures, and both the Test of Adult Basic Education ( Reading subtest) and the Woodcock-Johnson III Diagnostic Reading Battery Passage Comprehension assessments. Regression analyses revealed the utility of decoding, language comprehension, and lexical activation time for predicting achievement on both the Woodcock Johnson III Passage Comprehension and the Test of Adult Basic Education Reading Comprehension.

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells.

PubMed

Guedes, Ana M V; Henrique, Domingos; Abranches, Elsa

2016-01-01

Mouse Embryonic Stem cells (mESCs) show heterogeneous and dynamic expression of important pluripotency regulatory factors. Single-cell analysis has revealed the existence of cell-to-cell variability in the expression of individual genes in mESCs. Understanding how these heterogeneities are regulated and what their functional consequences are is crucial to obtain a more comprehensive view of the pluripotent state.In this chapter we describe how to analyze transcriptional heterogeneity by monitoring gene expression of Nanog, Oct4, and Sox2, using single-molecule RNA FISH in single mESCs grown in different cell culture medium. We describe in detail all the steps involved in the protocol, from RNA detection to image acquisition and processing, as well as exploratory data analysis.

Genome-wide classification, evolutionary analysis and gene expression patterns of the kinome in Gossypium

PubMed Central

Yan, Jun; Li, Guilin; Guo, Xingqi; Li, Yang; Cao, Xuecheng

2018-01-01

The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122–24 subfamilies using software HMMER v3.0 scanning and neighbor-joining (NJ) phylogenetic analysis. Some conserved exon-intron structures were identified not only in cotton species but also in primitive plants, ferns and moss, suggesting the significant function and ancient origination of these PK genes. Collinearity analysis revealed that 16.6 million years ago (Mya) cotton-specific whole genome duplication (WGD) events may have played a partial role in the expansion of the cotton kinomes, whereas tandem duplication (TD) events mainly contributed to the expansion of the cotton RLK group. Synteny analysis revealed that tetraploidization of G. hirsutum and G. barbadense contributed to the expansion of G. hirsutum and G. barbadense PKs. Global expression analysis of cotton PKs revealed stress-specific and fiber development-related expression patterns, suggesting that many cotton PKs might be involved in the regulation of the stress response and fiber development processes. This study provides foundational information for further studies on the evolution and molecular function of cotton PKs. PMID:29768506

Linguistic analysis of discourse in aphasia: A review of the literature.

PubMed

Bryant, Lucy; Ferguson, Alison; Spencer, Elizabeth

This review examined previous research applications of linguistic discourse analysis to assess the language of adults with aphasia. A comprehensive literature search of seven databases identified 165 studies that applied linguistic measures to samples of discourse collected from people with aphasia. Analysis of methodological applications revealed an increase in published research using linguistic discourse analysis over the past 40 years, particularly to measure the generalisation of therapy outcomes to language in use. Narrative language samples were most frequently subject to analysis though all language genres were observed across included studies. A total of 536 different linguistic measures were applied to examine language behaviours. Growth in the research use of linguistic discourse analysis and suggestions that this growth may be reflected in clinical practice requires further investigation. Future research directions are discussed to investigate clinical use of discourse analysis and examine the differences that exist between research and clinical practice.

The Role of Comprehension Monitoring, Theory of Mind, and Vocabulary Depth in Predicting Story Comprehension and Recall of Kindergarten Children

ERIC Educational Resources Information Center

Strasser, Katherine; del Río, Francisca

2014-01-01

Recent studies have revealed that preschoolers' story comprehension is influenced by several basic as well as complex cognitive and linguistic processes. Among the abilities known to be relevant for young children's understanding of stories are the size of their vocabulary, their inference-making ability, and their working memory. In this study,…

The Maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID Gene Family: Phylogeny, Synteny, and Unique Root-Type and Tissue-Specific Expression Patterns during Development

PubMed Central

Ludwig, Yvonne; Zhang, Yanxiang; Hochholdinger, Frank

2013-01-01

The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize Aux/IAA gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues. PMID:24223858

Abundance and Diversity of Bacterial Nitrifiers and Denitrifiers and Their Functional Genes in Tannery Wastewater Treatment Plants Revealed by High-Throughput Sequencing

PubMed Central

Wang, Zhu; Zhang, Xu-Xiang; Lu, Xin; Liu, Bo; Li, Yan; Long, Chao; Li, Aimin

2014-01-01

Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs) due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB) amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment. PMID:25420093

The maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID gene family: phylogeny, synteny, and unique root-type and tissue-specific expression patterns during development.

PubMed

Ludwig, Yvonne; Zhang, Yanxiang; Hochholdinger, Frank

2013-01-01

The plant hormone auxin plays a key role in the coordination of many aspects of growth and development. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes encode instable primary auxin responsive regulators of plant development that display a protein structure with four characteristic domains. In the present study, a comprehensive analysis of the 34 members of the maize Aux/IAA gene family was performed. Phylogenetic reconstructions revealed two classes of Aux/IAA proteins that can be distinguished by alterations in their domain III. Seven pairs of paralogous maize Aux/IAA proteins were discovered. Comprehensive root-type and tissue-specific expression profiling revealed unique expression patterns of the diverse members of the gene family. Remarkably, five of seven pairs of paralogous genes displayed highly correlated expression patterns in roots. All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues.

False-Belief Understanding and Language Ability Mediate the Relationship between Emotion Comprehension and Prosocial Orientation in Preschoolers.

PubMed

Ornaghi, Veronica; Pepe, Alessandro; Grazzani, Ilaria

2016-01-01

Emotion comprehension (EC) is known to be a key correlate and predictor of prosociality from early childhood. In the present study, we examined this relationship within the broad theoretical construct of social understanding which includes a number of socio-emotional skills, as well as cognitive and linguistic abilities. Theory of mind, especially false-belief understanding, has been found to be positively correlated with both EC and prosocial orientation. Similarly, language ability is known to play a key role in children's socio-emotional development. The combined contribution of false-belief understanding and language to explaining the relationship between EC and prosociality has yet to be investigated. Thus, in the current study, we conducted an in-depth exploration of how preschoolers' false-belief understanding and language ability each contribute to modeling the relationship between children's comprehension of emotion and their disposition to act prosocially toward others, after controlling for age and gender. Participants were 101 4- to 6-year-old children (54% boys), who were administered measures of language ability, false-belief understanding, EC and prosocial orientation. Multiple mediation analysis of the data suggested that false-belief understanding and language ability jointly and fully mediated the effect of preschoolers' EC on their prosocial orientation. Analysis of covariates revealed that gender exerted no statistically significant effect, while age had a trivial positive effect. Theoretical and practical implications of the findings are discussed.

A Dynamic Calibration Method for Experimental and Analytical Hub Load Comparison

NASA Technical Reports Server (NTRS)

Kreshock, Andrew R.; Thornburgh, Robert P.; Wilbur, Matthew L.

2017-01-01

This paper presents the results from an ongoing effort to produce improved correlation between analytical hub force and moment prediction and those measured during wind-tunnel testing on the Aeroelastic Rotor Experimental System (ARES), a conventional rotor testbed commonly used at the Langley Transonic Dynamics Tunnel (TDT). A frequency-dependent transformation between loads at the rotor hub and outputs of the testbed balance is produced from frequency response functions measured during vibration testing of the system. The resulting transformation is used as a dynamic calibration of the balance to transform hub loads predicted by comprehensive analysis into predicted balance outputs. In addition to detailing the transformation process, this paper also presents a set of wind-tunnel test cases, with comparisons between the measured balance outputs and transformed predictions from the comprehensive analysis code CAMRAD II. The modal response of the testbed is discussed and compared to a detailed finite-element model. Results reveal that the modal response of the testbed exhibits a number of characteristics that make accurate dynamic balance predictions challenging, even with the use of the balance transformation.

Comprehensive proteomic analysis of the wheat pathogenic fungus Zymoseptoria tritici.

PubMed

Yang, Fen; Yin, Qi

2016-01-01

Zymoseptoria tritici causes Septoria tritici blotch disease of wheat. To obtain a comprehensive protein dataset of this fungal pathogen, proteomes of Z. tritici growing in nutrient-limiting and rich media and in vivo at a late stage of wheat infection were fractionated by 1D gel or strong cation exchange (SCX) chromatography and analyzed by LC-MS/MS. A total of 5731, 5376 and 3168 Z. tritici proteins were confidently identified from these conditions, respectively. Of these in vitro and in planta proteins, 9 and 11% were predicted to contain signal peptides, respectively. Functional classification analysis revealed the proteins were involved in the various cellular activities. Comparison of three distinct protein expression profiles demonstrates the elevated carbohydrate, lipid and secondary metabolisms, transport, protein processing and energy production specifically in the host environment, in contrast to the enhancement of signaling, defense, replication, transcription and cell division in vitro. The data provide useful targets towards a better understanding of the molecular basis of Z. tritici growth, development, stress response and pathogenicity. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comprehensive Screening for Naturally Occurring Hepatitis C Virus Resistance to Direct-Acting Antivirals in the NS3, NS5A, and NS5B Genes in Worldwide Isolates of Viral Genotypes 1 to 6.

PubMed

Patiño-Galindo, Juan Ángel; Salvatierra, Karina; González-Candelas, Fernando; López-Labrador, F Xavier

2016-04-01

There is no comprehensive study available on the natural hepatitis C virus (HCV) polymorphism in sites associated with resistance including all viral genotypes which may present variable susceptibilities to particular direct-acting antivirals (DAAs). This study aimed to analyze the frequencies, genetic barriers, and evolutionary histories of naturally occurring resistance-associated variants (RAVs) in the six main HCV genotypes. A comprehensive analysis of up to 103 RAVs was performed in 2,901, 2,216, and 1,344 HCV isolates for the NS3, NS5A, and NS5B genes, respectively. We report significant intergenotypic differences in the frequencies of natural RAVs for these three HCV genes. In addition, we found a low genetic barrier for the generation of new RAVs, irrespective of the viral genotype. Furthermore, in 1,126 HCV genomes, including sequences spanning the three genes, haplotype analysis revealed a remarkably high frequency of viruses carrying more than one natural RAV to DAAs (53% of HCV-1a, 28.5% of HCV-1b, 67.1% of HCV-6, and 100% of genotype 2, 3, 4, and 5 haplotypes). With the exception of HCV-1a, the most prevalent haplotypes showed RAVs in at least two different viral genes. Finally, evolutionary analyses revealed that, while most natural RAVs appeared recently, others have been efficiently transmitted over time and cluster in well-supported clades. In summary, and despite the observed high efficacy of DAA-based regimens, we show that naturally occurring RAVs are common in all HCV genotypes and that there is an overall low genetic barrier for the selection of resistance mutations. There is a need for natural DAA resistance profiling specific for each HCV genotype. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The role of flower pollen extract in managing patients affected by chronic prostatitis/chronic pelvic pain syndrome: a comprehensive analysis of all published clinical trials.

PubMed

Cai, Tommaso; Verze, Paolo; La Rocca, Roberto; Anceschi, Umberto; De Nunzio, Cosimo; Mirone, Vincenzo

2017-04-21

Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is still a challenge to manage for all physicians. We feel that a summary of the current literature and a systematic review to evaluate the therapeutic efficacy of flower pollen extract would be helpful for physicians who are considering a phytotherapeutic approach to treating patients with CP/CPPS. A comprehensive search of the PubMed and Embase databases up to June 2016 was performed. This comprehensive analysis included both pre-clinical and clinical trials on the role of flower pollen extract in CP/CPPS patients. Moreover, a meta-analysis of available randomized controlled trials (RCTs) was performed. The NIH Chronic Prostatitis Symptom Index (NIH-CPSI) and Quality of Life related questionnaires (QoL) were the most commonly used tools to evaluate the therapeutic efficacy of pollen extract. Pre-clinical studies demonstrated the anti-inflammatory and anti-proliferative role of pollen extract. 6 clinical, non-controlled studies including 206 patients, and 4 RCTs including 384 patients were conducted. The mean response rate in non-controlled studies was 83.6% (62.2%-96.0%). The meta-analysis revealed that flower pollen extract could significantly improve patients' quality of life [OR 0.52 (0.34-.0.81); p = 0.02]. No significant adverse events were reported. Most of these studies presented encouraging results in terms of variations in NIH-CPSI and QoL scores. These studies suggest that the use of flower pollen extract for the management of CP/CPPS patients is beneficial. Future publications of robust evidence from additional RCTs and longer-term follow-up would provide more support encouraging the use of flower pollen extracts for CP/CPPS patients.

Genome-wide identification and expression analysis of glutathione S-transferase gene family in tomato: Gaining an insight to their physiological and stress-specific roles

PubMed Central

Islam, Shiful; Rahman, Iffat Ara; Islam, Tahmina

2017-01-01

Glutathione S-transferase (GST) refers to one of the major detoxifying enzymes that plays an important role in different abiotic and biotic stress modulation pathways of plant. The present study aimed to a comprehensive genome-wide functional characterization of GST genes and proteins in tomato (Solanum lycopersicum L.). The whole genome sequence analysis revealed the presence of 90 GST genes in tomato, the largest GST gene family reported till date. Eight segmental duplicated gene pairs might contribute significantly to the expansion of SlGST gene family. Based on phylogenetic analysis of tomato, rice, and Arabidopsis GST proteins, GST family members could be further divided into ten classes. Members of each orthologous class showed high conservancy among themselves. Tau and lambda are the major classes of tomato; while tau and phi are the major classes for rice and Arabidopsis. Chromosomal localization revealed highly uneven distribution of SlGST genes in 13 different chromosomes, where chromosome 9 possessed the highest number of genes. Based on publicly available microarray data, expression analysis of 30 available SlGST genes exhibited a differential pattern in all the analyzed tissues and developmental stages. Moreover, most of the members showed highly induced expression in response to multiple biotic and abiotic stress inducers that could be harmonized with the increase in total GST enzyme activity under several stress conditions. Activity of tomato GST could be enhanced further by using some positive modulators (safeners) that have been predicted through molecular docking of SlGSTU5 and ligands. Moreover, tomato GST proteins are predicted to interact with a lot of other glutathione synthesizing and utilizing enzymes such as glutathione peroxidase, glutathione reductase, glutathione synthetase and γ-glutamyltransferase. This comprehensive genome-wide analysis and expression profiling would provide a rational platform and possibility to explore the versatile role of GST genes in crop engineering. PMID:29095889

Molecular cloning, structure, phylogeny and expression analysis of the invertase gene family in sugarcane.

PubMed

Wang, Liming; Zheng, Yuexia; Ding, Shihui; Zhang, Qing; Chen, Youqiang; Zhang, Jisen

2017-06-23

Invertases (INVs) are key enzymes regulating sucrose metabolism and are here revealed to be involved in responses to environmental stress in plants. To date, individual members of the invertase gene family and their expression patterns are unknown in sugarcane due to its complex genome despite their significance in sucrose metabolism. In this study, based on comparative genomics, eleven cDNA and twelve DNA sequences belonging to 14 non-redundant members of the invertase gene family were successfully cloned from sugarcane. A comprehensive analysis of the invertase gene family was carried out, including gene structures, phylogenetic relationships, functional domains, conserved motifs of proteins. The results revealed that the 14 invertase members from sugarcane could be clustered into three subfamilies, including 6 neutral/alkaline invertases (ShN/AINVs), and 8 acid invertases (ShAINVs). Faster divergence occurred in acid INVs than in neutral/alkaline INVs after the split of sugarcane and sorghum. At least a one-time gene duplication event was observed to have occurred in the four groups of acid INVs, whereas ShN/AINV1 and ShN/AINV2 in the β8 lineage were revealed to be the most recently duplicated genes among their paralogous genes in the β group of N/AINVs. Furthermore, comprehensive expression analysis of these genes was performed in sugarcane seedlings subjected to five abiotic stresses (drought, low temperature, glucose, fructose, and sucrose) using Quantitative Real-time PCR. The results suggested a functional divergence of INVs and their potential role in response to the five different treatments. Enzymatic activity in sugarcane seedlings was detected under five abiotic stresses treatments, and showed that the activities of all INVs were significantly inhibited in response to five different abiotic stresses, and that the neutral/alkaline INVs played a more prominent role in abiotic stresses than the acid INVs. In this study, we determined the INV gene family members of sugarcane by PCR cloning using sorghum as a reference, providing the first study of the INV gene family in sugarcane. Combining existing INV gene data from 7 plants with a comparative approach including a series of comprehensive analyses to isolate and identify INV gene family members proved to be highly successful. Moreover, the expression levels of INV genes and the variation of enzymatic activities associated with drought, low temperature, glucose, fructose, and sucrose are reported in sugarcane for the first time. The results offered useful foundation and framework for future research for understanding the physiological roles of INVs for sucrose accumulation in sugarcane.

Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice.

PubMed

Wang, Yiyi; Feng, Lin; Zhu, Yuxin; Li, Yuan; Yan, Hanwei; Xiang, Yan

2015-09-08

WRKY III genes have significant functions in regulating plant development and resistance. In plant, WRKY gene family has been studied in many species, however, there still lack a comprehensive analysis of WRKY III genes in the woody plant species poplar, three representative lineages of flowering plant species are incorporated in most analyses: Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots) and Oryza sativa (a model plant for monocots). In this study, we identified 10, 6, 13 and 28 WRKY III genes in the genomes of Populus trichocarpa, grape (Vitis vinifera), Arabidopsis thaliana and rice (Oryza sativa), respectively. Phylogenetic analysis revealed that the WRKY III proteins could be divided into four clades. By microsynteny analysis, we found that the duplicated regions were more conserved between poplar and grape than Arabidopsis or rice. We dated their duplications by Ks analysis of Populus WRKY III genes and demonstrated that all the blocks were formed after the divergence of monocots and dicots. Strong purifying selection has played a key role in the maintenance of WRKY III genes in Populus. Tissue expression analysis of the WRKY III genes in Populus revealed that five were most highly expressed in the xylem. We also performed quantitative real-time reverse transcription PCR analysis of WRKY III genes in Populus treated with salicylic acid, abscisic acid and polyethylene glycol to explore their stress-related expression patterns. This study highlighted the duplication and diversification of the WRKY III gene family in Populus and provided a comprehensive analysis of this gene family in the Populus genome. Our results indicated that the majority of WRKY III genes of Populus was expanded by large-scale gene duplication. The expression pattern of PtrWRKYIII gene identified that these genes play important roles in the xylem during poplar growth and development, and may play crucial role in defense to drought stress. Our results presented here may aid in the selection of appropriate candidate genes for further characterization of their biological functions in poplar.

Peptidome analysis of amniotic fluid from pregnancies with preeclampsia.

PubMed

Qian, Yating; Zhang, Lei; Rui, Can; Ding, Hongjuan; Mao, Pengyuan; Ruan, Hongjie; Jia, Ruizhe

2017-11-01

Preeclampsia (PE), a life‑threatening, complicated pregnancy‑associated disease, has recently become a research focus in obstetrics. However, the peptidome of the amniotic fluid in PE patients has rarely been investigated. The present study used peptidomic profiling to perform a comparative analysis of human amniotic fluid between normal and PE pregnancies. Centrifugal ultrafiltration and liquid chromatography‑tandem mass spectrometry (LC‑MS/MS) was combined with isotopomeric dimethyl labels to gain a deeper understanding of the role of proteins and the peptidome in the onset of PE. Following ultrafiltration and LC‑MS/MS, 352 peptides were identified. Of these, 23 peptides were observed to be significantly differentially expressed (6 downregulated and 17 upregulated; P<0.05). Using Gene Ontology and Blastp analyses, the functions and biological activities of these 23 peptides were identified and revealed to include autophagy, signal transduction, receptor activity, enzymatic activity and nucleic acid binding. In addition, a bibliographic search revealed that some of the identified peptides, including Titin, are crucial to the pathogenesis underlying PE. The present study identified 23 peptides expressed at significantly different levels in the amniotic fluid of PE and normal pregnancies. A comprehensive peptidome analysis is more efficient than a simple biomarker analysis at revealing deficiencies and improving the detection rate in diseases. These analyses therefore provide a substantial advantage in applications aimed at the discovery of disease‑specific biomarkers.

Proteome profiling of early seed development in Cunninghamia lanceolata (Lamb.) Hook

PubMed Central

Shi, Jisen; Zhen, Yan; Zheng, Ren-Hua

2010-01-01

Knowledge of the proteome of the early gymnosperm embryo could provide important information for optimizing plant cloning procedures and for establishing platforms for research into plant development/regulation and in vitro transgenic studies. Compared with angiosperms, it is more difficult to induce somatic embryogenesis in gymnosperms; success in this endeavour could be increased, however, if proteomic information was available on the complex, dynamic, and multistage processes of gymnosperm embryogenesis in vivo. A proteomic analysis of Chinese fir seeds in six developmental stages was carried out during early embryogenesis. Proteins were extracted from seeds dissected from immature cones and separated by two-dimensional difference gel electrophoresis. Analysis with DeCyder 6.5 software revealed 136 spots that differed in kinetics of appearance. Analysis by liquid chromatography coupled to tandem mass spectrometry and MALDI-TOF mass spectrometry identified proteins represented by 71 of the spots. Functional annotation of these seed proteins revealed their involvement in programmed cell death and chromatin modification, indicating that the proteins may play a central role in determining the number of zygotic embryos generated and controlling embryo patterning and shape remodelling. The analysis also revealed other proteins involved in carbon metabolism, methionine metabolism, energy production, protein storage, synthesis and stabilization, disease/defence, the cytoskeleton, and embryo development. The comprehensive protein expression profiles generated by our study provide new insights into the complex developmental processes in the seeds of the Chinese fir. PMID:20363864

Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth*

PubMed Central

Mertz, Joseph; Tan, Haiyan; Pagala, Vishwajeeth; Bai, Bing; Chen, Ping-Chung; Li, Yuxin; Cho, Ji-Hoon; Shaw, Timothy; Wang, Xusheng; Peng, Junmin

2015-01-01

The mind bomb 1 (Mib1) ubiquitin ligase is essential for controlling metazoan development by Notch signaling and possibly the Wnt pathway. It is also expressed in postmitotic neurons and regulates neuronal morphogenesis and synaptic activity by mechanisms that are largely unknown. We sought to comprehensively characterize the Mib1 interactome and study its potential function in neuron development utilizing a novel sequential elution strategy for affinity purification, in which Mib1 binding proteins were eluted under different stringency and then quantified by the isobaric labeling method. The strategy identified the Mib1 interactome with both deep coverage and the ability to distinguish high-affinity partners from low-affinity partners. A total of 817 proteins were identified during the Mib1 affinity purification, including 56 high-affinity partners and 335 low-affinity partners, whereas the remaining 426 proteins are likely copurified contaminants or extremely weak binding proteins. The analysis detected all previously known Mib1-interacting proteins and revealed a large number of novel components involved in Notch and Wnt pathways, endocytosis and vesicle transport, the ubiquitin-proteasome system, cellular morphogenesis, and synaptic activities. Immunofluorescence studies further showed colocalization of Mib1 with five selected proteins: the Usp9x (FAM) deubiquitinating enzyme, alpha-, beta-, and delta-catenins, and CDKL5. Mutations of CDKL5 are associated with early infantile epileptic encephalopathy-2 (EIEE2), a severe form of mental retardation. We found that the expression of Mib1 down-regulated the protein level of CDKL5 by ubiquitination, and antagonized CDKL5 function during the formation of dendritic spines. Thus, the sequential elution strategy enables biochemical characterization of protein interactomes; and Mib1 analysis provides a comprehensive interactome for investigating its role in signaling networks and neuronal development. PMID:25931508

A comprehensive functional analysis of PTEN mutations: implications in tumor- and autism-related syndromes.

PubMed

Rodríguez-Escudero, Isabel; Oliver, María D; Andrés-Pons, Amparo; Molina, María; Cid, Víctor J; Pulido, Rafael

2011-11-01

The PTEN (phosphatase and tensin homolog) phosphatase is unique in mammals in terms of its tumor suppressor activity, exerted by dephosphorylation of the lipid second messenger PIP(3) (phosphatidylinositol 3,4,5-trisphosphate), which activates the phosphoinositide 3-kinase/Akt/mTOR (mammalian target of rapamycin) oncogenic pathway. Loss-of-function mutations in the PTEN gene are frequent in human cancer and in the germline of patients with PTEN hamartoma tumor-related syndromes (PHTSs). In addition, PTEN is mutated in patients with autism spectrum disorders (ASDs), although no functional information on these mutations is available. Here, we report a comprehensive in vivo functional analysis of human PTEN using a heterologous yeast reconstitution system. Ala-scanning mutagenesis at the catalytic loops of PTEN outlined the critical role of residues within the P-catalytic loop for PIP(3) phosphatase activity in vivo. PTEN mutations that mimic the P-catalytic loop of mammalian PTEN-like proteins (TPTE, TPIP, tensins and auxilins) affected PTEN function variably, whereas tumor- or PHTS-associated mutations targeting the PTEN P-loop produced complete loss of function. Conversely, Ala-substitutions, as well as tumor-related mutations at the WPD- and TI-catalytic loops, displayed partial activity in many cases. Interestingly, a tumor-related D92N mutation was partially active, supporting the notion that the PTEN Asp92 residue might not function as the catalytic general acid. The analysis of a panel of ASD-associated hereditary PTEN mutations revealed that most of them did not substantially abrogate PTEN activity in vivo, whereas most of PHTS-associated mutations did. Our findings reveal distinctive functional patterns among PTEN mutations found in tumors and in the germline of PHTS and ASD patients, which could be relevant for therapy.

Methane Metabolizing Microbial Communities in the Cold Seep Areas in the Northern Continental Shelf of South China Sea

NASA Astrophysics Data System (ADS)

Wang, F.; Liang, Q.

2016-12-01

Marine sediment contains large amount of methane, estimated approximately 500-2500 gigatonnes of dissolved and hydrated methane carbon stored therein, mainly in continental margins. In localized specific areas named cold seeps, hydrocarbon (mainly methane) containing fluids rise to the seafloor, and support oases of ecosystem composed of various microorganisms and faunal assemblages. South China Sea (SCS) is surrounded by passive continental margins in the west and north and convergent margins in the south and east. Thick organic-rich sediments have accumulated in the SCS since the late Mesozoic, which are continuing sources to form gas hydrates in the sediments of SCS. Here, Microbial ecosystems, particularly those involved in methane transformations were investigated in the cold seep areas (Qiongdongnan, Shenhu, and Dongsha) in the northern continental shelf of SCS. Multiple interdisciplinary analytic tools such as stable isotope probing, geochemical analysis, and molecular ecology, were applied for a comprehensive understanding of the microbe mediated methane transformation in this project. A variety of sediments cores have been collected, the geochemical profiles and the associated microbial distribution along the sediment cores were recorded. The major microbial groups involved in the methane transformation in these sediment cores were revealed, known methane producing and oxidizing archaea including Methanosarcinales, anaerobic methane oxidizing groups ANME-1, ANME-2 and their niche preference in the SCS sediments were found. In-depth comparative analysis revealed the presence of SCS-specific archaeal subtypes which probably reflected the evolution and adaptation of these methane metabolizing microbes to the SCS environmental conditions. Our work represents the first comprehensive analysis of the methane metabolizing microbial communities in the cold seep areas along the northern continental shelf of South China Sea, would provide new insight into the mechanisms of methane biotransformation.

An investigation of communication patterns and strategies between international teaching assistants and undergraduate students in university-level science labs

NASA Astrophysics Data System (ADS)

Gourlay, Barbara Elas

This research project investigates communication between international teaching assistants and their undergraduate students in university-level chemistry labs. During the fall semester, introductory-level chemistry lab sections of three experienced non-native speaking teaching assistants and their undergraduate students were observed. Digital audio and video recordings documented fifteen hours of lab communication, focusing on the activities and interactions in the first hour of the chemistry laboratory sessions. In follow-up one-on-one semi-structured interviews, the participants (undergraduates, teaching assistants, and faculty member) reviewed interactions and responded to a 10-item, 7-point Likert-scaled interview. Interactions were classified into success categories based on participants' opinions. Quantitative and qualitative data from the observations and interviews guided the analysis of the laboratory interactions, which examined patterns of conversational listening. Analysis of laboratory communication reveals that undergraduates initiated nearly two-thirds of laboratory communication, with three-fourths of interactions less than 30 seconds in duration. Issues of gender and topics of interaction activity were also explored. Interview data identified that successful undergraduate-teaching assistant communication in interactive science labs depends on teaching assistant listening comprehension skills to interpret and respond successfully to undergraduate questions. Successful communication in the chemistry lab depended on the coordination of visual and verbal sources of information. Teaching assistant responses that included explanations and elaborations were also seen as positive features in the communicative exchanges. Interaction analysis focusing on the listening comprehension demands placed on international teaching assistants revealed that undergraduate-initiated questions often employ deixis (exophoric reference), requiring teaching assistants to demonstrate skills at disambiguating undergraduate discourse. Interaction analysis reinforced that successful undergraduate-teaching assistant communication depends on the coordination of verbal and visual channels of communication, with the physical objects of the chemistry lab environment playing a pivotal role in expressing information and in mutual understanding. These results have implications for the evaluation of English proficiency and the preparation of non-native speaking teaching assistants by pointing out that teaching assistant listening comprehension skills and the use of contextual artifacts contribute to successful communication and are areas that, to date, have been underrepresented in the research literature on international teaching assistant communication.

The DNA Methylome of Human Peripheral Blood Mononuclear Cells

PubMed Central

Ye, Mingzhi; Zheng, Hancheng; Yu, Jian; Wu, Honglong; Sun, Jihua; Zhang, Hongyu; Chen, Quan; Luo, Ruibang; Chen, Minfeng; He, Yinghua; Jin, Xin; Zhang, Qinghui; Yu, Chang; Zhou, Guangyu; Sun, Jinfeng; Huang, Yebo; Zheng, Huisong; Cao, Hongzhi; Zhou, Xiaoyu; Guo, Shicheng; Hu, Xueda; Li, Xin; Kristiansen, Karsten; Bolund, Lars; Xu, Jiujin; Wang, Wen; Yang, Huanming; Wang, Jian; Li, Ruiqiang; Beck, Stephan; Wang, Jun; Zhang, Xiuqing

2010-01-01

DNA methylation plays an important role in biological processes in human health and disease. Recent technological advances allow unbiased whole-genome DNA methylation (methylome) analysis to be carried out on human cells. Using whole-genome bisulfite sequencing at 24.7-fold coverage (12.3-fold per strand), we report a comprehensive (92.62%) methylome and analysis of the unique sequences in human peripheral blood mononuclear cells (PBMC) from the same Asian individual whose genome was deciphered in the YH project. PBMC constitute an important source for clinical blood tests world-wide. We found that 68.4% of CpG sites and <0.2% of non-CpG sites were methylated, demonstrating that non-CpG cytosine methylation is minor in human PBMC. Analysis of the PBMC methylome revealed a rich epigenomic landscape for 20 distinct genomic features, including regulatory, protein-coding, non-coding, RNA-coding, and repeat sequences. Integration of our methylome data with the YH genome sequence enabled a first comprehensive assessment of allele-specific methylation (ASM) between the two haploid methylomes of any individual and allowed the identification of 599 haploid differentially methylated regions (hDMRs) covering 287 genes. Of these, 76 genes had hDMRs within 2 kb of their transcriptional start sites of which >80% displayed allele-specific expression (ASE). These data demonstrate that ASM is a recurrent phenomenon and is highly correlated with ASE in human PBMCs. Together with recently reported similar studies, our study provides a comprehensive resource for future epigenomic research and confirms new sequencing technology as a paradigm for large-scale epigenomics studies. PMID:21085693

A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia.

PubMed

Wu, Chung Wah; Evans, Jared M; Huang, Shengbing; Mahoney, Douglas W; Dukek, Brian A; Taylor, William R; Yab, Tracy C; Smyrk, Thomas C; Jen, Jin; Kisiel, John B; Ahlquist, David A

2018-05-25

MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conventional profiling methods, limitations in assay and analysis platforms may compromise isomiR interrogation. We introduce a comprehensive approach to sequence-oriented isomiR annotation (CASMIR) to allow unbiased identification of global isomiRs from small RNA sequencing data. In this approach, small RNA reads are maintained as independent sequences instead of being summarized under miRNA names. IsomiR features are identified through step-wise local alignment against canonical forms and precursor sequences. Through customizing the reference database, CASMIR is applicable to isomiR annotation across species. To demonstrate its application, we investigated isomiR profiles in normal and neoplastic human colorectal epithelia. We also ran miRDeep2, a popular miRNA analysis algorithm to validate isomiRs annotated by CASMIR. With CASMIR, specific and biologically relevant isomiR patterns could be identified. We note that specific isomiRs are often more abundant than their canonical forms. We identify isomiRs that are commonly up-regulated in both colorectal cancer and advanced adenoma, and illustrate advantages in targeting isomiRs as potential biomarkers over canonical forms. Studying miRNAs at the isomiR level could reveal new insight into miRNA biology and inform assay design for specific isomiRs. CASMIR facilitates comprehensive annotation of isomiR features in small RNA sequencing data for isomiR profiling and differential expression analysis.

["Prisms of Perception": multiple readings of mass media health messages in Northeast Brazil].

PubMed

Diógenes, Kátia Castelo Branco Machado; Nations, Marilyn

2011-12-01

This anthropological study from February 2009 to November 2010 revealed the comprehension and cultural critique of three mass media health campaigns in Northeast Brazil. Twenty-four ethnographic interviews were conducted, exploring the iconographic and semantic content of the campaigns in the Dendê community in Fortaleza, Ceará State, Brazil. The authors used Content Analysis; Systems of Signs, Significance, and Actions; and Contextualized Semantic Interpretation. There is a gap between the elaboration and reception of messages. Multiple interpretations occur (proximal reading, kaleidoscope of comprehension, and distant reading), depending on the reader's cognitive proximity to (or detachment from) the message. This "perceptual plasticity" arises from the creativity of popular imagination. Health professionals who hear rather than dismiss the "recipient's" subjective voice, which re-signifies authoritative messages, can penetrate the perception of the recipient's "visual world". In the context of poverty, this re-framing is essential for people to comprehend and proactively defend their own health.

Poor comprehenders in the classroom: teacher ratings of behavior in children with poor reading comprehension and its relationship with individual differences in working memory.

PubMed

Pimperton, Hannah; Nation, Kate

2014-01-01

Differing etiological explanations have been proposed to account for poor comprehenders' difficulties with reading comprehension, with some researchers emphasizing working memory deficits and others arguing for oral language weaknesses playing a key causal role. The authors contrasted these two theoretical accounts using data obtained from direct measures of working memory and from teacher ratings of poor comprehenders' behavior in the classroom. At the group level, poor comprehenders showed weaknesses on verbal but not nonverbal working memory tasks, in keeping with the "language account." However, they also showed evidence of elevated levels of problem behaviors specifically associated with working memory deficits. Further analysis revealed that these group differences in working-memory-related problem behaviors were carried by a small subgroup of poor comprehenders who also displayed domain-general (verbal and nonverbal) working memory problems, argued to be reflective of "genuine" underlying working memory deficits.

Proteomic analysis of extracellular vesicles derived from Propionibacterium acnes.

PubMed

Jeon, Jinseong; Mok, Hyuck Jun; Choi, Youngwoo; Park, Seung Cheol; Jo, Hunho; Her, Jin; Han, Jin-Kwan; Kim, Yoon-Keun; Kim, Kwang Pyo; Ban, Changill

2017-01-01

Extracellular vesicle (EV) has been reported to conduct critical pathophysiological functions as an emerging mode of communication in bacteria. Recently, Propionibacterium acnes, an anaerobic Gram-positive human commensal found in the skin and gastrointestinal tract, has drawn increasing attention as an underestimated pathogen in a variety of diseases. For the comprehensive understanding of P. acnes, here we report the isolation of P. acnes EVs for the first time and identification of 252 vesicular proteins with high confidence using triplicate LC-MS/MS analyses. Comprehensive proteomic profiling reveals that P. acnes EVs harbor various proteins involved in biochemical processes, antibiotic resistance, bacterial competition, cell adherence, virulence, and immunogenicity. We believe that this report will provide valuable information for investigating the biological role of P. acnes EVs and effective targets for developing clinical applications against P. acnes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Separable Processes Before, During, and After the N400 Elicited by Previously Inferred and New Information: Evidence from Time-Frequency Decompositions

PubMed Central

Steele, Vaughn R.; Bernat, Edward M.; van den Broek, Paul; Collins, Paul F.; Patrick, Christopher J.; Marsolek, Chad J.

2012-01-01

Successful comprehension during reading often requires inferring information not explicitly presented. This information is readily accessible when subsequently encountered, and a neural correlate of this is an attenuation of the N400 event-related potential (ERP). We used ERPs and time-frequency (TF) analysis to investigate neural correlates of processing inferred information after a causal coherence inference had been generated during text comprehension. Participants read short texts, some of which promoted inference generation. After each text, they performed lexical decisions to target words that were unrelated or inference-related to the preceding text. Consistent with previous findings, inference-related words elicited an attenuated N400 relative to unrelated words. TF analyses revealed unique contributions to the N400 from activity occurring at 1–6 Hz (theta) and 0–2 Hz (delta), supporting the view that multiple, sequential processes underlie the N400. PMID:23165117

A comprehensive pathway map of epidermal growth factor receptor signaling

PubMed Central

Oda, Kanae; Matsuoka, Yukiko; Funahashi, Akira; Kitano, Hiroaki

2005-01-01

The epidermal growth factor receptor (EGFR) signaling pathway is one of the most important pathways that regulate growth, survival, proliferation, and differentiation in mammalian cells. Reflecting this importance, it is one of the best-investigated signaling systems, both experimentally and computationally, and several computational models have been developed for dynamic analysis. A map of molecular interactions of the EGFR signaling system is a valuable resource for research in this area. In this paper, we present a comprehensive pathway map of EGFR signaling and other related pathways. The map reveals that the overall architecture of the pathway is a bow-tie (or hourglass) structure with several feedback loops. The map is created using CellDesigner software that enables us to graphically represent interactions using a well-defined and consistent graphical notation, and to store it in Systems Biology Markup Language (SBML). PMID:16729045

A strategy for screening antioxidants in Ginkgo biloba extract by comprehensive two-dimensional ultra high performance liquid chromatography.

PubMed

Guo, Ru-Zhou; Liu, Xin-Guang; Gao, Wen; Dong, Xin; Fanali, Salvatore; Li, Ping; Yang, Hua

2015-11-27

Recently, screening of bioactive compounds by on-line ultra-high performance liquid chromatography (UHPLC) draws increasing attentions for the advantages of rapidity and intuition. Nevertheless, most on-line methods were limited to the shortcoming like low resolution and peak capacity, which could interfere the active ingredient identification. Comprehensive two-dimensional UHPLC (LC×LC) has revealed to be a powerful tool to separate complex mixtures. Herein, a strategy based on LC×LC analysis coupled with pre-column 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay was proposed to screen the antioxidants from the extract of Ginkgo biloba (EGB). A total of 61 compounds were identified in EGB, and 25 of them showed appreciable radical scavenging capacity. This work may offer pharmacodynamics base for further research about EGB, also the strategy is likelihood to be applied in screening antioxidant in other herbal medicine. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparative Proteomic and Nutritional Composition Analysis of Independent Transgenic Pigeon Pea Seeds Harboring cry1AcF and cry2Aa Genes and Their Nontransgenic Counterparts.

PubMed

Mishra, Pragya; Singh, Shweta; Rathinam, Maniraj; Nandiganti, Muralimohan; Ram Kumar, Nikhil; Thangaraj, Arulprakash; Thimmegowda, Vinutha; Krishnan, Veda; Mishra, Vagish; Jain, Neha; Rai, Vandna; Pattanayak, Debasis; Sreevathsa, Rohini

2017-02-22

Safety assessment of genetically modified plants is an important aspect prior to deregulation. Demonstration of substantial equivalence of the transgenics compared to their nontransgenic counterparts can be performed using different techniques at various molecular levels. The present study is a first-ever comprehensive evaluation of pigeon pea transgenics harboring two independent cry genes, cry2Aa and cry1AcF. The absence of unintended effects in the transgenic seed components was demonstrated by proteome and nutritional composition profiling. Analysis revealed that no significant differences were found in the various nutritional compositional analyses performed. Additionally, 2-DGE-based proteome analysis of the transgenic and nontransgenic seed protein revealed that there were no major changes in the protein profile, although a minor fold change in the expression of a few proteins was observed. Furthermore, the study also demonstrated that neither the integration of T-DNA nor the expression of the cry genes resulted in the production of unintended effects in the form of new toxins or allergens.

Genome-wide analysis and expression profiling of the Solanum tuberosum aquaporins.

PubMed

Venkatesh, Jelli; Yu, Jae-Woong; Park, Se Won

2013-12-01

Aquaporins belongs to the major intrinsic proteins involved in the transcellular membrane transport of water and other small solutes. A comprehensive genome-wide search for the homologues of Solanum tuberosum major intrinsic protein (MIP) revealed 41 full-length potato aquaporin genes. All potato aquaporins are grouped into five subfamilies; plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), NOD26-like intrinsic proteins (NIPs), small basic intrinsic proteins (SIPs) and x-intrinsic proteins (XIPs). Functional predictions based on the aromatic/arginine (ar/R) selectivity filters and Froger's positions showed a remarkable difference in substrate transport specificity among subfamilies. The expression pattern of potato aquaporins, examined by qPCR analysis, showed distinct expression profiles in various organs and tuber developmental stages. Furthermore, qPCR analysis of potato plantlets, subjected to various abiotic stresses revealed the marked effect of stresses on expression levels of aquaporins. Taken together, the expression profiles of aquaporins imply that aquaporins play important roles in plant growth and development, in addition to maintaining water homeostasis in response to environmental stresses. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Increased plasma proline concentrations are associated with sarcopenia in the elderly.

PubMed

Toyoshima, Kenji; Nakamura, Marie; Adachi, Yusuke; Imaizumi, Akira; Hakamada, Tomomi; Abe, Yasuko; Kaneko, Eiji; Takahashi, Soiciro; Shimokado, Kentaro

2017-01-01

Metabolome analyses have shown that plasma amino acid profiles reflect various pathological conditions, such as cancer and diabetes mellitus. It remains unclear, however, whether plasma amino acid profiles change in patients with sarcopenia. This study therefore aimed to investigate whether sarcopenia-specific changes occur in plasma amino acid profiles. A total of 153 community-dwelling and seven institutionalized elderly individuals (56 men, 104 women; mean age, 77.7±7.0 years) were recruited for this cross-sectional analysis. We performed a comprehensive geriatric assessment, which included an evaluation of hand grip strength, gait speed, muscle mass and blood chemistry, including the concentration of 18 amino acids. Twenty-eight of the 160 participants met the criteria for sarcopenia established by the Asian Working Group on Sarcopenia in Older People. Univariate analysis revealed associations between the presence of sarcopenia and a higher plasma concentration of proline and glutamine, lower concentrations of histidine and tryptophan. Multivariable analysis revealed that a higher concentration of proline was the only variable independently associated with sarcopenia. The plasma concentration of proline may be useful for understanding the underlying pathophysiology of sarcopenia.

Readers select a comprehension mode independent of pronoun: Evidence from fMRI during narrative comprehension.

PubMed

Hartung, Franziska; Hagoort, Peter; Willems, Roel M

2017-07-01

Perspective is a crucial feature for communicating about events. Yet it is unclear how linguistically encoded perspective relates to cognitive perspective taking. Here, we tested the effect of perspective taking with short literary stories. Participants listened to stories with 1st or 3rd person pronouns referring to the protagonist, while undergoing fMRI. When comparing action events with 1st and 3rd person pronouns, we found no evidence for a neural dissociation depending on the pronoun. A split sample approach based on the self-reported experience of perspective taking revealed 3 comprehension preferences. One group showed a strong 1st person preference, another a strong 3rd person preference, while a third group engaged in 1st and 3rd person perspective taking simultaneously. Comparing brain activations of the groups revealed different neural networks. Our results suggest that comprehension is perspective dependent, but not on the perspective suggested by the text, but on the reader's (situational) preference. Copyright © 2017 Elsevier Inc. All rights reserved.

Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes

PubMed Central

Timinskas, Kęstutis; Balvočiūtė, Monika; Timinskas, Albertas; Venclovas, Česlovas

2014-01-01

The analysis of ∼2000 bacterial genomes revealed that they all, without a single exception, encode one or more DNA polymerase III α-subunit (PolIIIα) homologs. Classified into C-family of DNA polymerases they come in two major forms, PolC and DnaE, related by ancient duplication. While PolC represents an evolutionary compact group, DnaE can be further subdivided into at least three groups (DnaE1-3). We performed an extensive analysis of various sequence, structure and surface properties of all four polymerase groups. Our analysis suggests a specific evolutionary pathway leading to PolC and DnaE from the last common ancestor and reveals important differences between extant polymerase groups. Among them, DnaE1 and PolC show the highest conservation of the analyzed properties. DnaE3 polymerases apparently represent an ‘impaired’ version of DnaE1. Nonessential DnaE2 polymerases, typical for oxygen-using bacteria with large GC-rich genomes, have a number of features in common with DnaE3 polymerases. The analysis of polymerase distribution in genomes revealed three major combinations: DnaE1 either alone or accompanied by one or more DnaE2s, PolC + DnaE3 and PolC + DnaE1. The first two combinations are present in Escherichia coli and Bacillus subtilis, respectively. The third one (PolC + DnaE1), found in Clostridia, represents a novel, so far experimentally uncharacterized, set. PMID:24106089

Determinants of underage college student drinking: implications for four major alcohol reduction strategies.

PubMed

Paek, Hye-Jin; Hove, Thomas

2012-01-01

Guided by the assumptions of the social ecological model and the social marketing approach, this study provides a simultaneous and comprehensive assessment of 4 major alcohol reduction strategies for college campuses: school education programs, social norms campaigns, alcohol counter-marketing, and alcohol control policies. Analysis of nationally representative secondary survey data among 5,472 underage students reveals that alcohol marketing seems to be the most formidable risk factor for underage drinking, followed by perceived drinking norms (injunctive norm) and lax policy enforcement. This analysis suggests that, to make social norms campaigns and alcohol control policies more effective, alcohol reduction strategies should be developed to counter the powerful influence of alcohol marketing and promotions.

Genomic characterization and taxonomic position of a rhabdovirus from a hybrid snakehead.

PubMed

Zeng, Weiwei; Wang, Qing; Wang, Yingying; Liu, Cun; Liang, Hongru; Fang, Xiang; Wu, Shuqin

2014-09-01

A new rhabdovirus, tentatively designated as hybrid snakehead rhabdovirus C1207 (HSHRV-C1207), was first isolated from a moribund hybrid snakehead (Channa maculata×Channa argus) in China. We present the complete genome sequence of HSHRV-C1207 and a comprehensive sequence comparison between HSHRV-C1207 and other rhabdoviruses. Sequence alignment and phylogenetic analysis revealed that HSHRV-C1207 shared the highest degree of homology with Monopterus albus rhabdovirus and Siniperca chuatsi rhabdovirus. All three viruses clustered into a single group that was distinct from the recognized genera in the family Rhabdoviridae. Our analysis suggests that HSHRV-C1207, as well as MARV and SCRV, should be assigned to a new rhabdovirus genus.

Graphic organizers and their effects on the reading comprehension of students with LD: a synthesis of research.

PubMed

Kim, Ae-Hwa; Vaughn, Sharon; Wanzek, Jeanne; Wei, Shangjin

2004-01-01

Previous research studies examining the effects of graphic organizers on reading comprehension for students with learning disabilities (LD) are reviewed. An extensive search of the professional literature between 1963 and June 2001 yielded a total of 21 group design intervention studies that met the criteria for inclusion in the synthesis. Using graphic organizers (i.e., semantic organizers, framed outlines, cognitive maps with and without a mnemonic) was associated with improved reading comprehension overall for students with LD. Compared to standardized reading measures, researcher-developed comprehension measures were associated with higher effect sizes. Initial gains demonstrated when using graphic organizers were not revealed during later comprehension tasks or on new comprehension tasks.

Studying hemispheric lateralization during a Stroop task through near-infrared spectroscopy-based connectivity

NASA Astrophysics Data System (ADS)

Zhang, Lei; Sun, Jinyan; Sun, Bailei; Luo, Qingming; Gong, Hui

2014-05-01

Near-infrared spectroscopy (NIRS) is a developing and promising functional brain imaging technology. Developing data analysis methods to effectively extract meaningful information from collected data is the major bottleneck in popularizing this technology. In this study, we measured hemodynamic activity of the prefrontal cortex (PFC) during a color-word matching Stroop task using NIRS. Hemispheric lateralization was examined by employing traditional activation and novel NIRS-based connectivity analyses simultaneously. Wavelet transform coherence was used to assess intrahemispheric functional connectivity. Spearman correlation analysis was used to examine the relationship between behavioral performance and activation/functional connectivity, respectively. In agreement with activation analysis, functional connectivity analysis revealed leftward lateralization for the Stroop effect and correlation with behavioral performance. However, functional connectivity was more sensitive than activation for identifying hemispheric lateralization. Granger causality was used to evaluate the effective connectivity between hemispheres. The results showed increased information flow from the left to the right hemispheres for the incongruent versus the neutral task, indicating a leading role of the left PFC. This study demonstrates that the NIRS-based connectivity can reveal the functional architecture of the brain more comprehensively than traditional activation, helping to better utilize the advantages of NIRS.

The portrayal of Down syndrome in prenatal screening information pamphlets.

PubMed

Lawson, Karen L; Carlson, Kara; Shynkaruk, Jody M

2012-08-01

To examine the information about Down syndrome (DS) provided to pregnant women in Canada through a content analysis of prenatal screening information pamphlets. Prenatal screening information pamphlets were requested from Canadian prenatal testing centres. In total, 17 pamphlets were received (response rate = 65%). Statements presenting information descriptive of DS were identified from the pamphlets, and a content analysis was carried out. Specifically, each statement was analyzed with respect to both the content and the valence of the information presented on the basis of predetermined decision rules. To enhance reliability, four independent raters reviewed each statement, and any differences in coding were resolved through discussion. In total, 158 statements descriptive of DS were extracted from the pamphlets. The categorical analysis revealed that 91% of the extracted statements emphasized medical or clinical information about DS, whereas only 9% of the statements relayed information pertaining to psychosocial issues. The valence analysis revealed that nearly one half of the statements portrayed a negative message pertaining to DS, while only 2.4% of the statements conveyed a positive image of DS. The pamphlets provided to pregnant women do not appear to present a comprehensive, balanced portrayal of DS, which may serve to limit informed decision-making.

Transcriptome-wide identification of salt-responsive members of the WRKY gene family in Gossypium aridum.

PubMed

Fan, Xinqi; Guo, Qi; Xu, Peng; Gong, YuanYong; Shu, Hongmei; Yang, Yang; Ni, Wanchao; Zhang, Xianggui; Shen, Xinlian

2015-01-01

WRKY transcription factors are plant-specific, zinc finger-type transcription factors. The WRKY superfamily is involved in abiotic stress responses in many crops including cotton, a major fiber crop that is widely cultivated and consumed throughout the world. Salinity is an important abiotic stress that results in considerable yield losses. In this study, we identified 109 WRKY genes (GarWRKYs) in a salt-tolerant wild cotton species Gossypium aridum from transcriptome sequencing data to elucidate the roles of these factors in cotton salt tolerance. According to their structural features, the predicted members were divided into three groups (Groups I-III), as previously described for Arabidopsis. Furthermore, 28 salt-responsive GarWRKY genes were identified from digital gene expression data and subjected to real-time quantitative RT-PCR analysis. The expression patterns of most GarWRKY genes revealed by this analysis are in good agreement with those revealed by RNA-Seq analysis. RT-PCR analysis revealed that 27 GarWRKY genes were expressed in roots and one was exclusively expressed in roots. Analysis of gene orthology and motif compositions indicated that WRKY members from Arabidopsis, rice and soybean generally shared the similar motifs within the same subgroup, suggesting they have the similar function. Overexpression-GarWRKY17 and -GarWRKY104 in Arabidopsis revealed that they could positively regulate salt tolerance of transgenic Arabidopsis during different development stages. The comprehensive data generated in this study provide a platform for elucidating the functions of WRKY transcription factors in salt tolerance of G. aridum. In addition, GarWRKYs related to salt tolerance identified in this study will be potential candidates for genetic improvement of cultivated cotton salt stress tolerance.

Effect of cryopreservation on delineation of immune cell subpopulations in tumor specimens as determinated by multiparametric single cell mass cytometry analysis.

PubMed

Kadić, Elma; Moniz, Raymond J; Huo, Ying; Chi, An; Kariv, Ilona

2017-02-02

Comprehensive understanding of cellular immune subsets involved in regulation of tumor progression is central to the development of cancer immunotherapies. Single cell immunophenotyping has historically been accomplished by flow cytometry (FC) analysis, enabling the analysis of up to 18 markers. Recent advancements in mass cytometry (MC) have facilitated detection of over 50 markers, utilizing high resolving power of mass spectrometry (MS). This study examined an analytical and operational feasibility of MC for an in-depth immunophenotyping analysis of the tumor microenvironment, using the commercial CyTOF™ instrument, and further interrogated challenges in managing the integrity of tumor specimens. Initial longitudinal studies with frozen peripheral blood mononuclear cells (PBMCs) showed minimal MC inter-assay variability over nine independent runs. In addition, detection of common leukocyte lineage markers using MC and FC detection confirmed that these methodologies are comparable in cell subset identification. An advanced multiparametric MC analysis of 39 total markers enabled a comprehensive evaluation of cell surface marker expression in fresh and cryopreserved tumor samples. This comparative analysis revealed significant reduction of expression levels of multiple markers upon cryopreservation. Most notably myeloid derived suppressor cells (MDSC), defined by co-expression of CD66b + and CD15 + , HLA-DR dim and CD14 - phenotype, were undetectable in frozen samples. These results suggest that optimization and evaluation of cryopreservation protocols is necessary for accurate biomarker discovery in frozen tumor specimens.

Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins.

PubMed

Waks, Zeev; Weissbrod, Omer; Carmeli, Boaz; Norel, Raquel; Utro, Filippo; Goldschmidt, Yaara

2016-12-23

Compiling a comprehensive list of cancer driver genes is imperative for oncology diagnostics and drug development. While driver genes are typically discovered by analysis of tumor genomes, infrequently mutated driver genes often evade detection due to limited sample sizes. Here, we address sample size limitations by integrating tumor genomics data with a wide spectrum of gene-specific properties to search for rare drivers, functionally classify them, and detect features characteristic of driver genes. We show that our approach, CAnceR geNe similarity-based Annotator and Finder (CARNAF), enables detection of potentially novel drivers that eluded over a dozen pan-cancer/multi-tumor type studies. In particular, feature analysis reveals a highly concentrated pool of known and putative tumor suppressors among the <1% of genes that encode very large, chromatin-regulating proteins. Thus, our study highlights the need for deeper characterization of very large, epigenetic regulators in the context of cancer causality.

Global Analysis of Palmitoylated Proteins in Toxoplasma gondii.

PubMed

Foe, Ian T; Child, Matthew A; Majmudar, Jaimeen D; Krishnamurthy, Shruthi; van der Linden, Wouter A; Ward, Gary E; Martin, Brent R; Bogyo, Matthew

2015-10-14

Post-translational modifications (PTMs) such as palmitoylation are critical for the lytic cycle of the protozoan parasite Toxoplasma gondii. While palmitoylation is involved in invasion, motility, and cell morphology, the proteins that utilize this PTM remain largely unknown. Using a chemical proteomic approach, we report a comprehensive analysis of palmitoylated proteins in T. gondii, identifying a total of 282 proteins, including cytosolic, membrane-associated, and transmembrane proteins. From this large set of palmitoylated targets, we validate palmitoylation of proteins involved in motility (myosin light chain 1, myosin A), cell morphology (PhIL1), and host cell invasion (apical membrane antigen 1, AMA1). Further studies reveal that blocking AMA1 palmitoylation enhances the release of AMA1 and other invasion-related proteins from apical secretory organelles, suggesting a previously unrecognized role for AMA1. These findings suggest that palmitoylation is ubiquitous throughout the T. gondii proteome and reveal insights into the biology of this important human pathogen. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular and cellular organization of taste neurons in adult Drosophila pharynx

PubMed Central

Chen, Yu-Chieh (David); Dahanukar, Anupama

2017-01-01

SUMMARY The Drosophila pharyngeal taste organs are poorly characterized despite their location at important sites for monitoring food quality. Functional analysis of pharyngeal neurons has been hindered by the paucity of molecular tools to manipulate them, as well as their relative inaccessibility for neurophysiological investigations. Here, we generate receptor-to-neuron maps of all three pharyngeal taste organs by performing a comprehensive chemoreceptor-GAL4/LexA expression analysis. The organization of pharyngeal neurons reveals similarities and distinctions in receptor repertoires and neuronal groupings compared to external taste neurons. We validate the mapping results by pinpointing a single pharyngeal neuron required for feeding avoidance of L-canavanine. Inducible activation of pharyngeal taste neurons reveals functional differences between external and internal taste neurons and functional subdivision within pharyngeal sweet neurons. Our results provide road maps of pharyngeal taste organs in an insect model system for probing the role of these understudied neurons in controlling feeding behaviors. PMID:29212040

Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics.

PubMed

Fang, Jing; Nevin, Philip; Kairys, Visvaldas; Venclovas, Česlovas; Engen, John R; Beuning, Penny J

2014-04-08

The relationship between protein sequence, structure, and dynamics has been elusive. Here, we report a comprehensive analysis using an in-solution experimental approach to study how the conservation of tertiary structure correlates with protein dynamics. Hydrogen exchange measurements of eight processivity clamp proteins from different species revealed that, despite highly similar three-dimensional structures, clamp proteins display a wide range of dynamic behavior. Differences were apparent both for structurally similar domains within proteins and for corresponding domains of different proteins. Several of the clamps contained regions that underwent local unfolding with different half-lives. We also observed a conserved pattern of alternating dynamics of the α helices lining the inner pore of the clamps as well as a correlation between dynamics and the number of salt bridges in these α helices. Our observations reveal that tertiary structure and dynamics are not directly correlated and that primary structure plays an important role in dynamics. Copyright © 2014 Elsevier Ltd. All rights reserved.

PIXE analysis of Italian ink drawings of the XVI century

NASA Astrophysics Data System (ADS)

Zucchiatti, A.; Climent-Font, A.; Enguita, O.; Fernandez-Jimenez, M. T.; Finaldi, G.; Garrido, C.; Matillas, J. M.

2005-10-01

The composition of inks in a group of 24 drawings of ten XVI century Italian painters, has been determined by PIXE at the external micro-beam line of the Centro de Micro Análisis de Materiales of the Universidad Autónoma de Madrid. Ink elemental thicknesses have been determined by comparison with a set of certified thin standards. A comprehensive comparison of inks has also been performed by renormalisation of spectra and definition of an ink-to-ink distance. The elemental compositions and the ink-to-ink distances give consistent results that are generally in line with the appearance of the drawings and add relevant instrumental information to the stylistic observation, revealing for example the presence of retouches and additions in different parts of a drawing. Cluster analysis performed on a subgroup of 13 artefacts from the Genoese painter Luca Cambiaso and his school has revealed a partition that separates neatly the work of the master from that of his followers.

Fault Tree Analysis.

PubMed

McElroy, Lisa M; Khorzad, Rebeca; Rowe, Theresa A; Abecassis, Zachary A; Apley, Daniel W; Barnard, Cynthia; Holl, Jane L

The purpose of this study was to use fault tree analysis to evaluate the adequacy of quality reporting programs in identifying root causes of postoperative bloodstream infection (BSI). A systematic review of the literature was used to construct a fault tree to evaluate 3 postoperative BSI reporting programs: National Surgical Quality Improvement Program (NSQIP), Centers for Medicare and Medicaid Services (CMS), and The Joint Commission (JC). The literature review revealed 699 eligible publications, 90 of which were used to create the fault tree containing 105 faults. A total of 14 identified faults are currently mandated for reporting to NSQIP, 5 to CMS, and 3 to JC; 2 or more programs require 4 identified faults. The fault tree identifies numerous contributing faults to postoperative BSI and reveals substantial variation in the requirements and ability of national quality data reporting programs to capture these potential faults. Efforts to prevent postoperative BSI require more comprehensive data collection to identify the root causes and develop high-reliability improvement strategies.

Water conservation behavior in Australia.

PubMed

Dolnicar, Sara; Hurlimann, Anna; Grün, Bettina

2012-08-30

Ensuring a nation's long term water supply requires the use of both supply-sided approaches such as water augmentation through water recycling, and demand-sided approaches such as water conservation. Conservation behavior can only be increased if the key drivers of such behavior are understood. The aim of this study is to reveal the main drivers from a comprehensive pool of hypothesized factors. An empirical study was conducted with 3094 Australians. Data was analyzed using multivariate linear regression analysis and decision trees to determine which factors best predict self-reported water conservation behavior. Two key factors emerge: high level of pro-environmental behavior; and pro-actively seeking out information about water. A number of less influential factors are also revealed. Public communication strategy implications are derived. Copyright © 2012 Elsevier Ltd. All rights reserved.

Referential Strategy Training for Second Language Reading Comprehension of Japanese Texts.

ERIC Educational Resources Information Center

Kitajima, Ryu

1997-01-01

Examines whether strategy training orienting second language (L2) students' attention toward referential processes improves their comprehension of Japanese narrative. Findings revealed that experimental students comprehended the story at the macro level significantly better than control students, suggesting that the strategy training is beneficial…

Most Likely to Succeed: Exploring Predictor Variables for the Counselor Preparation Comprehensive Examination

ERIC Educational Resources Information Center

Hartwig, Elizabeth Kjellstrand; Van Overschelde, James P.

2016-01-01

The authors investigated predictor variables for the Counselor Preparation Comprehensive Examination (CPCE) to examine whether academic variables, demographic variables, and test version were associated with graduate counseling students' CPCE scores. Multiple regression analyses revealed all 3 variables were statistically significant predictors of…

Venturing into Unknown Territory: Using Aesthetic Representations to Understand Reading Comprehension

ERIC Educational Resources Information Center

Cuero, Kimberley K.; Bonner, Jennifer; Smith, Brittaney; Schwartz, Michelle; Touchstone, Rose; Vela, Yvonne

2008-01-01

Based on Elliot Eisner's notions of multiple forms of representation and Rosenblatt's aesthetic/efferent responses to reading, a teacher educator/researcher had her undergraduate students explore their connections, using aesthetic representations, to a course entitled "Reading Comprehension". Each aesthetic representation revealed the complexities…

Genome-wide characterization of pectin methyl esterase genes reveals members differentially expressed in tolerant and susceptible wheats in response to Fusarium graminearum.

PubMed

Zega, Alessandra; D'Ovidio, Renato

2016-11-01

Pectin methyl esterase (PME) genes code for enzymes that are involved in structural modifications of the plant cell wall during plant growth and development. They are also involved in plant-pathogen interaction. PME genes belong to a multigene family and in this study we report the first comprehensive analysis of the PME gene family in bread wheat (Triticum aestivum L.). Like in other species, the members of the TaPME family are dispersed throughout the genome and their encoded products retain the typical structural features of PMEs. qRT-PCR analysis showed variation in the expression pattern of TaPME genes in different tissues and revealed that these genes are mainly expressed in flowering spikes. In our attempt to identify putative TaPME genes involved in wheat defense, we revealed a strong variation in the expression of the TaPME following Fusarium graminearum infection, the causal agent of Fusarium head blight (FHB). Particularly interesting was the finding that the expression profile of some PME genes was markedly different between the FHB-resistant wheat cultivar Sumai3 and the FHB-susceptible cultivar Bobwhite, suggesting a possible involvement of these PME genes in FHB resistance. Moreover, the expression analysis of the TaPME genes during F. graminearum progression within the spike revealed those genes that responded more promptly to pathogen invasion. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

A CS1 pedagogical approach to parallel thinking

NASA Astrophysics Data System (ADS)

Rague, Brian William

Almost all collegiate programs in Computer Science offer an introductory course in programming primarily devoted to communicating the foundational principles of software design and development. The ACM designates this introduction to computer programming course for first-year students as CS1, during which methodologies for solving problems within a discrete computational context are presented. Logical thinking is highlighted, guided primarily by a sequential approach to algorithm development and made manifest by typically using the latest, commercially successful programming language. In response to the most recent developments in accessible multicore computers, instructors of these introductory classes may wish to include training on how to design workable parallel code. Novel issues arise when programming concurrent applications which can make teaching these concepts to beginning programmers a seemingly formidable task. Student comprehension of design strategies related to parallel systems should be monitored to ensure an effective classroom experience. This research investigated the feasibility of integrating parallel computing concepts into the first-year CS classroom. To quantitatively assess student comprehension of parallel computing, an experimental educational study using a two-factor mixed group design was conducted to evaluate two instructional interventions in addition to a control group: (1) topic lecture only, and (2) topic lecture with laboratory work using a software visualization Parallel Analysis Tool (PAT) specifically designed for this project. A new evaluation instrument developed for this study, the Perceptions of Parallelism Survey (PoPS), was used to measure student learning regarding parallel systems. The results from this educational study show a statistically significant main effect among the repeated measures, implying that student comprehension levels of parallel concepts as measured by the PoPS improve immediately after the delivery of any initial three-week CS1 level module when compared with student comprehension levels just prior to starting the course. Survey results measured during the ninth week of the course reveal that performance levels remained high compared to pre-course performance scores. A second result produced by this study reveals no statistically significant interaction effect between the intervention method and student performance as measured by the evaluation instrument over three separate testing periods. However, visual inspection of survey score trends and the low p-value generated by the interaction analysis (0.062) indicate that further studies may verify improved concept retention levels for the lecture w/PAT group.

Single-Cell Sequencing Technologies for Cardiac Stem Cell Studies.

PubMed

Liu, Tiantian; Wu, Hongjin; Wu, Shixiu; Wang, Charles

2017-11-01

Today with the rapid advancements in stem cell studies and the promising potential of using stem cells in clinical therapy, there is an increasing demand for in-depth comprehensive analysis on individual cell transcriptome and epigenome, as they play critical roles in a number of cell functions such as cell differentiation, growth, and reprogramming. The development of single-cell sequencing technologies has helped in revealing some exciting new perspectives in stem cells and regenerative medicine research. Among the various potential applications, single-cell analysis for cardiac stem cells (CSCs) holds tremendous promises in understanding the mechanisms of heart development and regeneration, which might light up the path toward cell therapy for cardiovascular diseases. This review briefly highlights the recent progresses in single-cell sequencing analysis technologies and their applications in CSC research.

Deep functional analysis of synII, a 770 kb synthetic yeast chromosome

PubMed Central

Gao, Feng; Gong, Jianhui; Abramczyk, Dariusz; Walker, Roy; Zhao, Hongcui; Chen, Shihong; Liu, Wei; Luo, Yisha; Müller, Carolin A.; Paul-Dubois-Taine, Adrien; Alver, Bonnie; Stracquadanio, Giovanni; Mitchell, Leslie A.; Luo, Zhouqing; Fan, Yanqun; Zhou, Baojin; Wen, Bo; Tan, Fengji; Wang, Yujia; Zi, Jin; Xie, Zexiong; Li, Bingzhi; Yang, Kun; Richardson, Sarah M.; Jiang, Hui; French, Christopher E.; Nieduszynski, Conrad A.; Koszul, Romain; Marston, Adele L.; Yuan, Yingjin; Wang, Jian; Bader, Joel S.; Dai, Junbiao; Boeke, Jef D.; Xu, Xun; Cai, Yizhi; Yang, Huanming

2017-01-01

Herein we report the successful design, construction and characterization of a 770 kb synthetic yeast chromosome II (synII). Our study incorporates characterization at multiple levels, including phenomics, transcriptomics, proteomics, chromosome segregation and replication analysis to provide a thorough and comprehensive analysis of a synthetic chromosome. Our “Trans-Omics” analyses reveal a modest but potentially significant pervasive up-regulation of translational machinery observed in synII is mainly caused by the deletion of 13 tRNAs. By both complementation assays and SCRaMbLE, we targeted and debuged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the HOG response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain. PMID:28280153

Requirements for Next Generation Comprehensive Analysis of Rotorcraft

NASA Technical Reports Server (NTRS)

Johnson, Wayne; Data, Anubhav

2008-01-01

The unique demands of rotorcraft aeromechanics analysis have led to the development of software tools that are described as comprehensive analyses. The next generation of rotorcraft comprehensive analyses will be driven and enabled by the tremendous capabilities of high performance computing, particularly modular and scaleable software executed on multiple cores. Development of a comprehensive analysis based on high performance computing both demands and permits a new analysis architecture. This paper describes a vision of the requirements for this next generation of comprehensive analyses of rotorcraft. The requirements are described and substantiated for what must be included and justification provided for what should be excluded. With this guide, a path to the next generation code can be found.

Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis.

PubMed

Harper, Marc; Gronenberg, Luisa; Liao, James; Lee, Christopher

2014-01-01

Discovering all the genetic causes of a phenotype is an important goal in functional genomics. We combine an experimental design for detecting independent genetic causes of a phenotype with a high-throughput sequencing analysis that maximizes sensitivity for comprehensively identifying them. Testing this approach on a set of 24 mutant strains generated for a metabolic phenotype with many known genetic causes, we show that this pathway-based phenotype sequencing analysis greatly improves sensitivity of detection compared with previous methods, and reveals a wide range of pathways that can cause this phenotype. We demonstrate our approach on a metabolic re-engineering phenotype, the PEP/OAA metabolic node in E. coli, which is crucial to a substantial number of metabolic pathways and under renewed interest for biofuel research. Out of 2157 mutations in these strains, pathway-phenoseq discriminated just five gene groups (12 genes) as statistically significant causes of the phenotype. Experimentally, these five gene groups, and the next two high-scoring pathway-phenoseq groups, either have a clear connection to the PEP metabolite level or offer an alternative path of producing oxaloacetate (OAA), and thus clearly explain the phenotype. These high-scoring gene groups also show strong evidence of positive selection pressure, compared with strictly neutral selection in the rest of the genome.

In Vitro Evaluation of Glycoengineered RSV-F in the Human Artificial Lymph Node Reactor.

PubMed

Radke, Lars; Sandig, Grit; Lubitz, Annika; Schließer, Ulrike; von Horsten, Hans Henning; Blanchard, Veronique; Keil, Karolin; Sandig, Volker; Giese, Christoph; Hummel, Michael; Hinderlich, Stephan; Frohme, Marcus

2017-08-15

Subunit vaccines often require adjuvants to elicit sustained immune activity. Here, a method is described to evaluate the efficacy of single vaccine candidates in the preclinical stage based on cytokine and gene expression analysis. As a model, the recombinant human respiratory syncytial virus (RSV) fusion protein (RSV-F) was produced in CHO cells. For comparison, wild-type and glycoengineered, afucosylated RSV-F were established. Both glycoprotein vaccines were tested in a commercial Human Artificial Lymph Node in vitro model (HuALN ® ). The analysis of six key cytokines in cell culture supernatants showed well-balanced immune responses for the afucosylated RSV-F, while immune response of wild-type RSV-F was more Th1 accentuated. In particular, stronger and specific secretion of interleukin-4 after each round of re-stimulation underlined higher potency and efficacy of the afucosylated vaccine candidate. Comprehensive gene expression analysis by nCounter gene expression assay confirmed the stronger onset of the immunologic reaction in stimulation experiments with the afucosylated vaccine in comparison to wild-type RSV-F and particularly revealed prominent activation of Th17 related genes, innate immunity, and comprehensive activation of humoral immunity. We, therefore, show that our method is suited to distinguish the potency of two vaccine candidates with minor structural differences.

Detailed analysis of the microbial population in Malaysian spontaneous cocoa pulp fermentations reveals a core and variable microbiota.

PubMed

Meersman, Esther; Steensels, Jan; Mathawan, Melissa; Wittocx, Pieter-Jan; Saels, Veerle; Struyf, Nore; Bernaert, Herwig; Vrancken, Gino; Verstrepen, Kevin J

2013-01-01

The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a "core" and a "variable" part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations ("core" yeasts), and a large number of yeasts that only occur in lower numbers and specific fermentations ("variable" yeasts). Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency.

Comparative analysis of protein interactome networks prioritizes candidate genes with cancer signatures.

PubMed

Li, Yongsheng; Sahni, Nidhi; Yi, Song

2016-11-29

Comprehensive understanding of human cancer mechanisms requires the identification of a thorough list of cancer-associated genes, which could serve as biomarkers for diagnoses and therapies in various types of cancer. Although substantial progress has been made in functional studies to uncover genes involved in cancer, these efforts are often time-consuming and costly. Therefore, it remains challenging to comprehensively identify cancer candidate genes. Network-based methods have accelerated this process through the analysis of complex molecular interactions in the cell. However, the extent to which various interactome networks can contribute to prediction of candidate genes responsible for cancer is still enigmatic. In this study, we evaluated different human protein-protein interactome networks and compared their application to cancer gene prioritization. Our results indicate that network analyses can increase the power to identify novel cancer genes. In particular, such predictive power can be enhanced with the use of unbiased systematic protein interaction maps for cancer gene prioritization. Functional analysis reveals that the top ranked genes from network predictions co-occur often with cancer-related terms in literature, and further, these candidate genes are indeed frequently mutated across cancers. Finally, our study suggests that integrating interactome networks with other omics datasets could provide novel insights into cancer-associated genes and underlying molecular mechanisms.

Detailed Analysis of the Microbial Population in Malaysian Spontaneous Cocoa Pulp Fermentations Reveals a Core and Variable Microbiota

PubMed Central

Mathawan, Melissa; Wittocx, Pieter-Jan; Saels, Veerle; Struyf, Nore; Bernaert, Herwig; Vrancken, Gino; Verstrepen, Kevin J.

2013-01-01

The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a “core” and a “variable” part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations (“core” yeasts), and a large number of yeasts that only occur in lower numbers and specific fermentations (“variable” yeasts). Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency. PMID:24358116

PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species ▿ ‡ #

PubMed Central

Gillespie, Joseph J.; Wattam, Alice R.; Cammer, Stephen A.; Gabbard, Joseph L.; Shukla, Maulik P.; Dalay, Oral; Driscoll, Timothy; Hix, Deborah; Mane, Shrinivasrao P.; Mao, Chunhong; Nordberg, Eric K.; Scott, Mark; Schulman, Julie R.; Snyder, Eric E.; Sullivan, Daniel E.; Wang, Chunxia; Warren, Andrew; Williams, Kelly P.; Xue, Tian; Seung Yoo, Hyun; Zhang, Chengdong; Zhang, Yan; Will, Rebecca; Kenyon, Ronald W.; Sobral, Bruno W.

2011-01-01

Funded by the National Institute of Allergy and Infectious Diseases, the Pathosystems Resource Integration Center (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. Specifically, PATRIC provides scientists with (i) a comprehensive bacterial genomics database, (ii) a plethora of associated data relevant to genomic analysis, and (iii) an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary aim of PATRIC is to advance the knowledge underlying the biology of human pathogens, all publicly available genome-scale data for bacteria are compiled and continually updated, thereby enabling comparative analyses to reveal the basis for differences between infectious free-living and commensal species. Herein we summarize the major features available at PATRIC, dividing the resources into two major categories: (i) organisms, genomes, and comparative genomics and (ii) recurrent integration of community-derived associated data. Additionally, we present two experimental designs typical of bacterial genomics research and report on the execution of both projects using only PATRIC data and tools. These applications encompass a broad range of the data and analysis tools available, illustrating practical uses of PATRIC for the biologist. Finally, a summary of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided. PMID:21896772

The Comprehension Problems of Children with Poor Reading Comprehension despite Adequate Decoding: A Meta-Analysis.

PubMed

Spencer, Mercedes; Wagner, Richard K

2018-06-01

The purpose of this meta-analysis was to examine the comprehension problems of children who have a specific reading comprehension deficit (SCD), which is characterized by poor reading comprehension despite adequate decoding. The meta-analysis included 86 studies of children with SCD who were assessed in reading comprehension and oral language (vocabulary, listening comprehension, storytelling ability, and semantic and syntactic knowledge). Results indicated that children with SCD had deficits in oral language ( d = -0.78, 95% CI [-0.89, -0.68], but these deficits were not as severe as their deficit in reading comprehension ( d = -2.78, 95% CI [-3.01, -2.54]). When compared to reading comprehension age-matched normal readers, the oral language skills of the two groups were comparable ( d = 0.32, 95% CI [-0.49, 1.14]), which suggests that the oral language weaknesses of children with SCD represent a developmental delay rather than developmental deviance. Theoretical and practical implications of these findings are discussed.

Selectivity of lexical-semantic disorders in Polish-speaking patients with aphasia: evidence from single-word comprehension.

PubMed

Jodzio, Krzysztof; Biechowska, Daria; Leszniewska-Jodzio, Barbara

2008-09-01

Several neuropsychological studies have shown that patients with brain damage may demonstrate selective category-specific deficits of auditory comprehension. The present paper reports on an investigation of aphasic patients' preserved ability to perform a semantic task on spoken words despite severe impairment in auditory comprehension, as shown by failure in matching spoken words to pictured objects. Twenty-six aphasic patients (11 women and 15 men) with impaired speech comprehension due to a left-hemisphere ischaemic stroke were examined; all were right-handed and native speakers of Polish. Six narrowly defined semantic categories for which dissociations have been reported are colors, body parts, animals, food, objects (mostly tools), and means of transportation. An analysis using one-way ANOVA with repeated measures in conjunction with the Lambda-Wilks Test revealed significant discrepancies among these categories in aphasic patients, who had much more difficulty comprehending names of colors than they did comprehending names of other objects (F((5,21))=13.15; p<.001). Animals were most often the easiest category to understand. The possibility of a simple explanation in terms of word frequency and/or visual complexity was ruled out. Evidence from the present study support the position that so called "global" aphasia is an imprecise term and should be redefined. These results are discussed within the connectionist and modular perspectives on category-specific deficits in aphasia.

The pterygoalar bar: A meta-analysis of its prevalence, morphology and morphometry.

PubMed

Pękala, Przemysław A; Henry, Brandon Michael; Pękala, Jakub R; Frączek, Paulina A; Taterra, Dominik; Natsis, Konstantinos; Piagkou, Maria; Skrzat, Janusz; Tomaszewska, Iwona M

2017-09-01

The pterygoalar (PA) bar is a bony bridge resulting from the partial or complete ossification of a PA ligament. The aim of this meta-analysis was to systematically analyze and provide the most comprehensive data on the prevalence, morphology and topographical anatomy of the PA bar. A comprehensive search of the major electronic databases (PubMed, Embase, ScienceDirect, SciELO, BIOSIS, and Web of Science) was conducted in order to identify relevant studies. Studies reporting the prevalence, side of occurrence, gender dimorphism and morphometry of the PA bar were included in the current study. A total of 25 articles (n = 16,168 subjects) were included in the meta-analysis. The overall pooled prevalence of the complete PA bar was 4.4% (95% CI: 3.0-6.0) and of the incomplete was 8.4% (95% CI: 4.6-13.3). The PA bar was most often observed unilaterally, on the left side. Analysis of geographical subgroups revealed considerable differences, with the lowest prevalence rates in Europe for both incomplete and complete PA bars. Considering the prevalence and anatomical characteristics of the PA bar, caution is recommended while planning or performing transfacial needle approach to the foramen ovale and when considering a differential diagnosis for nerve compression or entrapment syndromes. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Revealing impaired pathways in the an11 mutant by high-throughput characterization of Petunia axillaris and Petunia inflata transcriptomes.

PubMed

Zenoni, Sara; D'Agostino, Nunzio; Tornielli, Giovanni B; Quattrocchio, Francesca; Chiusano, Maria L; Koes, Ronald; Zethof, Jan; Guzzo, Flavia; Delledonne, Massimo; Frusciante, Luigi; Gerats, Tom; Pezzotti, Mario

2011-10-01

Petunia is an excellent model system, especially for genetic, physiological and molecular studies. Thus far, however, genome-wide expression analysis has been applied rarely because of the lack of sequence information. We applied next-generation sequencing to generate, through de novo read assembly, a large catalogue of transcripts for Petunia axillaris and Petunia inflata. On the basis of both transcriptomes, comprehensive microarray chips for gene expression analysis were established and used for the analysis of global- and organ-specific gene expression in Petunia axillaris and Petunia inflata and to explore the molecular basis of the seed coat defects in a Petunia hybrida mutant, anthocyanin 11 (an11), lacking a WD40-repeat (WDR) transcription regulator. Among the transcripts differentially expressed in an11 seeds compared with wild type, many expected targets of AN11 were found but also several interesting new candidates that might play a role in morphogenesis of the seed coat. Our results validate the combination of next-generation sequencing with microarray analyses strategies to identify the transcriptome of two petunia species without previous knowledge of their genome, and to develop comprehensive chips as useful tools for the analysis of gene expression in P. axillaris, P. inflata and P. hybrida. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

Inference Strategies to Improve Reading Comprehension of Challenging Texts

ERIC Educational Resources Information Center

Attaprechakul, Damrong

2013-01-01

This study aimed to explore inference strategies necessary to successfully read journal articles. Eighty-eight graduate students read a set of texts on education and economic growth and answered comprehension questions. Twenty-four of these participants also volunteered for an in-depth interview. The findings revealed that students usually relied…

Reading for Understanding: Methodist Youths' Shared Scripture-Reading Practices

ERIC Educational Resources Information Center

Rackley, Eric D.

2018-01-01

Informed by reading comprehension and comprehension strategies research, this study explores the Scripture-reading practices of four Methodist youths. Several rounds of inductive thematic analyses of Scripture-reading protocols revealed a set of five strategic reading practices youths used to understand Scripture. They drew inferences about the…

Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development.

PubMed

Beck, Kristen L; Weber, Darren; Phinney, Brett S; Smilowitz, Jennifer T; Hinde, Katie; Lönnerdal, Bo; Korf, Ian; Lemay, Danielle G

2015-05-01

Milk has been well established as the optimal nutrition source for infants, yet there is still much to be understood about its molecular composition. Therefore, our objective was to develop and compare comprehensive milk proteomes for human and rhesus macaques to highlight differences in neonatal nutrition. We developed a milk proteomics technique that overcomes previous technical barriers including pervasive post-translational modifications and limited sample volume. We identified 1606 and 518 proteins in human and macaque milk, respectively. During analysis of detected protein orthologs, we identified 88 differentially abundant proteins. Of these, 93% exhibited increased abundance in human milk relative to macaque and include lactoferrin, polymeric immunoglobulin receptor, alpha-1 antichymotrypsin, vitamin D-binding protein, and haptocorrin. Furthermore, proteins more abundant in human milk compared with macaque are associated with development of the gastrointestinal tract, the immune system, and the brain. Overall, our novel proteomics method reveals the first comprehensive macaque milk proteome and 524 newly identified human milk proteins. The differentially abundant proteins observed are consistent with the perspective that human infants, compared with nonhuman primates, are born at a slightly earlier stage of somatic development and require additional support through higher quantities of specific proteins to nurture human infant maturation.

Systems Biology to Support Nanomaterial Grouping.

PubMed

Riebeling, Christian; Jungnickel, Harald; Luch, Andreas; Haase, Andrea

2017-01-01

The assessment of potential health risks of engineered nanomaterials (ENMs) is a challenging task due to the high number and great variety of already existing and newly emerging ENMs. Reliable grouping or categorization of ENMs with respect to hazards could help to facilitate prioritization and decision making for regulatory purposes. The development of grouping criteria, however, requires a broad and comprehensive data basis. A promising platform addressing this challenge is the systems biology approach. The different areas of systems biology, most prominently transcriptomics, proteomics and metabolomics, each of which provide a wealth of data that can be used to reveal novel biomarkers and biological pathways involved in the mode-of-action of ENMs. Combining such data with classical toxicological data would enable a more comprehensive understanding and hence might lead to more powerful and reliable prediction models. Physico-chemical data provide crucial information on the ENMs and need to be integrated, too. Overall statistical analysis should reveal robust grouping and categorization criteria and may ultimately help to identify meaningful biomarkers and biological pathways that sufficiently characterize the corresponding ENM subgroups. This chapter aims to give an overview on the different systems biology technologies and their current applications in the field of nanotoxicology, as well as to identify the existing challenges.

Comprehensive Analysis of ETS Family Members in Melanoma by Fluorescence In Situ Hybridization Reveals Recurrent ETV1 Amplification

PubMed Central

Mehra, Rohit; Dhanasekaran, Saravana M; Palanisamy, Nallasivam; Vats, Pankaj; Cao, Xuhong; Kim, Jung H; Kim, David SL; Johnson, Timothy; Fullen, Douglas R; Chinnaiyan, Arul M

2013-01-01

E26 transformation-specific (ETS) transcription factors are known to be involved in gene aberrations in various malignancies including prostate cancer; however, their role in melanoma oncogenesis has yet to be fully explored. We have completed a comprehensive fluorescence in situ hybridization (FISH)-based screen for all 27 members of the ETS transcription factor family on two melanoma tissue microarrays, representing 223 melanomas, 10 nevi, and 5 normal skin tissues. None of the melanoma cases demonstrated ETS fusions; however, 6 of 114 (5.3%) melanomas were amplified for ETV1 using a break-apart FISH probe. For the six positive cases, locus-controlled FISH probes revealed that two of six cases were amplified for the ETV1 region, whereas four cases showed copy gains of the entire chromosome 7. The remaining 26 ETS family members showed no chromosomal aberrations by FISH. Quantitative polymerase chain reaction showed an average 3.4-fold (P value = .00218) increased expression of ETV1 in melanomas, including the FISH ETV1-amplified cases, when compared to other malignancies (prostate, breast, and bladder carcinomas). These data suggest that a subset of melanomas overexpresses ETV1 and amplification of ETV1 may be one mechanism for achieving high gene expression. PMID:23908683

Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity

PubMed Central

Westernberg, Luise; Pham, John; Lane, Jerome; Paul, Sinu; Greenbaum, Jason; Stranzl, Thomas; Lund, Gitte; Hoof, Ilka; Holm, Jens; Würtzen, Peter A; Meno, Kåre H.; Frazier, April; Schulten, Veronique; Andersen, Peter S.; Peters, Bjoern; Sette, Alessandro

2016-01-01

BACKGROUND House dust mite (HDM) allergens are a common cause of allergy and allergic asthma. A comprehensive analysis of proteins targeted by T cells, which are implicated in the development and regulation of allergic disease independent of their antibody reactivity, is still lacking. OBJECTIVE To comprehensively analyze the HDM-derived protein targets of T cell responses in HDM-allergic individuals, and investigate their correlation with IgE/IgG responses and protein function. METHODS Proteomic analysis (liquid chromatography tandem mass spectrometry) of HDM extracts identified 90 distinct protein clusters, corresponding to 29 known allergens and 61 novel proteins. Peripheral blood mononuclear cells (PBMC) from 20 HDM-allergic individuals were stimulated with HDM extracts and assayed with a set of ~2500 peptides derived from these 90 protein clusters and predicted to bind the most common HLA class II types. 2D immunoblots were made in parallel to elucidate IgE and IgG reactivity and putative function analyses were performed in silico according to gene ontology (GO) annotations. RESULTS Analysis of T cell reactivity revealed a large number of T cell epitopes. Overall response magnitude and frequency was comparable for known and novel proteins, with 15 antigens (nine of which were novel) dominating the total T cell response. Most of the known allergens that were dominant at the T cell level were also IgE-reactive, as expected, while few novel dominant T cell antigens were IgE reactive. Among known allergens, hydrolase activity and detectable IgE/IgG reactivity are strongly correlated, while no protein function correlates with immunogenicity of novel proteins. A total of 106 epitopes accounted for half of the total T-cell response, underlining the heterogeneity of T cell responses to HDM allergens. CONCLUSIONS AND CLINICAL RELEVANCE Herein, we define the T cell targets for both known allergens and novel proteins, which may inform future diagnostics and immunotherapeutics for allergy to HDM. PMID:27684489

Comprehensive gene expression analysis of canine invasive urothelial bladder carcinoma by RNA-Seq.

PubMed

Maeda, Shingo; Tomiyasu, Hirotaka; Tsuboi, Masaya; Inoue, Akiko; Ishihara, Genki; Uchikai, Takao; Chambers, James K; Uchida, Kazuyuki; Yonezawa, Tomohiro; Matsuki, Naoaki

2018-04-27

Invasive urothelial carcinoma (iUC) is a major cause of death in humans, and approximately 165,000 individuals succumb to this cancer annually worldwide. Comparative oncology using relevant animal models is necessary to improve our understanding of progression, diagnosis, and treatment of iUC. Companion canines are a preferred animal model of iUC due to spontaneous tumor development and similarity to human disease in terms of histopathology, metastatic behavior, and treatment response. However, the comprehensive molecular characterization of canine iUC is not well documented. In this study, we performed transcriptome analysis of tissue samples from canine iUC and normal bladders using an RNA sequencing (RNA-Seq) approach to identify key molecular pathways in canine iUC. Total RNA was extracted from bladder tissues of 11 dogs with iUC and five healthy dogs, and RNA-Seq was conducted. Ingenuity Pathway Analysis (IPA) was used to assign differentially expressed genes to known upstream regulators and functional networks. Differential gene expression analysis of the RNA-Seq data revealed 2531 differentially expressed genes, comprising 1007 upregulated and 1524 downregulated genes, in canine iUC. IPA revealed that the most activated upstream regulator was PTGER2 (encoding the prostaglandin E 2 receptor EP2), which is consistent with the therapeutic efficiency of cyclooxygenase inhibitors in canine iUC. Similar to human iUC, canine iUC exhibited upregulated ERBB2 and downregulated TP53 pathways. Biological functions associated with cancer, cell proliferation, and leukocyte migration were predicted to be activated, while muscle functions were predicted to be inhibited, indicating muscle-invasive tumor property. Our data confirmed similarities in gene expression patterns between canine and human iUC and identified potential therapeutic targets (PTGER2, ERBB2, CCND1, Vegf, and EGFR), suggesting the value of naturally occurring canine iUC as a relevant animal model for human iUC.

Riddle appreciation and reading comprehension in Cantonese-speaking children.

PubMed

Tang, Ivy N Y; To, Carol K S; Weekes, Brendan S

2013-10-01

Inference-making skills are necessary for reading comprehension. Training in riddle appreciation is an effective way to improve reading comprehension among English-speaking children. However, it is not clear whether these methods generalize to other writing systems. The goal of the present study was to investigate the relationship between inference-making skills, as measured by riddle appreciation ability, and reading comprehension performance in typically developing Cantonese-speaking children in the 4th grade. Forty Cantonese-speaking children between the ages of 9;1 (years;months) and 11;0 were given tests of riddle appreciation ability and reading comprehension. Chinese character reading and auditory comprehension abilities were also assessed using tests that had been standardized in Hong Kong. Regression analyses revealed that riddle appreciation ability explained a significant amount of variance in reading comprehension after variance due to character reading skills and auditory comprehension skills were first considered. Orthographic, lexical, morphological, and syntactic riddles were also significantly correlated with reading comprehension. Riddle appreciation ability predicts reading comprehension in Cantonese-speaking 4th-grade children. Therefore, training Cantonese speakers in riddle appreciation should improve their reading comprehension.

Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity.

PubMed

Wei, Feifei; Ito, Kengo; Sakata, Kenji; Date, Yasuhiro; Kikuchi, Jun

2015-03-03

Extracting useful information from high dimensionality and large data sets is a major challenge for data-driven approaches. The present study was aimed at developing novel integrated analytical strategies for comprehensively characterizing seaweed similarities based on chemical diversity. The chemical compositions of 107 seaweed and 2 seagrass samples were analyzed using multiple techniques, including Fourier transform infrared (FT-IR) and solid- and solution-state nuclear magnetic resonance (NMR) spectroscopy, thermogravimetry-differential thermal analysis (TG-DTA), inductively coupled plasma-optical emission spectrometry (ICP-OES), CHNS/O total elemental analysis, and isotope ratio mass spectrometry (IR-MS). The spectral data were preprocessed using non-negative matrix factorization (NMF) and NMF combined with multivariate curve resolution-alternating least-squares (MCR-ALS) methods in order to separate individual component information from the overlapping and/or broad spectral peaks. Integrated analysis of the preprocessed chemical data demonstrated distinct discrimination of differential seaweed species. Further network analysis revealed a close correlation between the heavy metal elements and characteristic components of brown algae, such as cellulose, alginic acid, and sulfated mucopolysaccharides, providing a componential basis for its metal-sorbing potential. These results suggest that this integrated analytical strategy is useful for extracting and identifying the chemical characteristics of diverse seaweeds based on large chemical data sets, particularly complicated overlapping spectral data.

A Discrepancy in Comprehension and Production in Early Language Development in ASD: Is it Clinically Relevant?

PubMed

Davidson, Meghan M; Ellis Weismer, Susan

2017-07-01

This study examined the extent to which a discrepant comprehension-production profile (i.e., relatively more delayed comprehension than production) is characteristic of the early language phenotype in autism spectrum disorders (ASD) and tracked the developmental progression of the profile. Our findings indicated that a discrepant comprehension-production profile distinguished toddlers (30 months) with ASD from late talkers without ASD (91% sensitivity, 100% specificity) in groups that were comparable on expressive language, age, and socioeconomic status. Longitudinal data for children with ASD revealed that the discrepant profile steadily decreased from 30 to 44 months until there was no significant comprehension-production difference at 66 months. In conclusion, results suggest that lower comprehension than production may be an age-specific marker of toddlers with ASD.

UHPLC-LTQ-Orbitrap MS combined with spike-in method for plasma metabonomics analysis of acute myocardial ischemia rats and pretreatment effect of Danqi Tongmai tablet.

PubMed

Yan, Bingpeng; Deng, Yanping; Hou, Jinjun; Bi, Qirui; Yang, Min; Jiang, Baohong; Liu, Xuan; Wu, Wanying; Guo, Dean

2015-02-01

Undoubtedly, metabonomics can reveal the comprehensive efficacies of traditional Chinese medicine (TCM) formulae and its complex mechanism at the molecular biological level. In this study, an attempt was made to address the pretreatment effect of a TCM formula. In this case, as a critical point, we should first know how to really reflect the various endogenous metabolites in a disease status before a TCM formula is employed in a therapeutic procedure. Here, we explored an approach that combined high resolution LTQ-Orbitrap mass spectrometry with a spike-in method to characterize endogenous metabolites in acute myocardial ischemia (AMI) rats. As a result, 19 potential biomarkers in rat plasma were identified and 10 related disturbed pathways were perturbed in the early stages of AMI development. Subsequently, the metabonomics method was applied to investigate the pretreatment effect of the TCM formula named the Danqi Tongmai tablet (DQTM). The results revealed that the DQTM pretreatment could reduce the AMI injury and partially regulate the perturbed TCA cycle and amino and nucleotide metabolism, which were presumable related to energy metabolism and myocardial cells apoptosis/necrosis. In conclusion, UHPLC-LTQ-Orbitrap MS combined with a spike-in method were successfully applied to the metabonomics analysis of DQTM, which demonstrated that not only a comprehensive metabolic profile in the early stages of AMI development was achieved, but also that the underlying holistic efficacies were assessed and it was helpful to understand the possible mechanism of pretreatment with DQTM.

False-Belief Understanding and Language Ability Mediate the Relationship between Emotion Comprehension and Prosocial Orientation in Preschoolers

PubMed Central

Ornaghi, Veronica; Pepe, Alessandro; Grazzani, Ilaria

2016-01-01

Emotion comprehension (EC) is known to be a key correlate and predictor of prosociality from early childhood. In the present study, we examined this relationship within the broad theoretical construct of social understanding which includes a number of socio-emotional skills, as well as cognitive and linguistic abilities. Theory of mind, especially false-belief understanding, has been found to be positively correlated with both EC and prosocial orientation. Similarly, language ability is known to play a key role in children’s socio-emotional development. The combined contribution of false-belief understanding and language to explaining the relationship between EC and prosociality has yet to be investigated. Thus, in the current study, we conducted an in-depth exploration of how preschoolers’ false-belief understanding and language ability each contribute to modeling the relationship between children’s comprehension of emotion and their disposition to act prosocially toward others, after controlling for age and gender. Participants were 101 4- to 6-year-old children (54% boys), who were administered measures of language ability, false-belief understanding, EC and prosocial orientation. Multiple mediation analysis of the data suggested that false-belief understanding and language ability jointly and fully mediated the effect of preschoolers’ EC on their prosocial orientation. Analysis of covariates revealed that gender exerted no statistically significant effect, while age had a trivial positive effect. Theoretical and practical implications of the findings are discussed. PMID:27774075

Comprehensive behavioral analysis of the Cdkl5 knockout mice revealed significant enhancement in anxiety- and fear-related behaviors and impairment in both acquisition and long-term retention of spatial reference memory

PubMed Central

Okuda, Kosuke; Takao, Keizo; Watanabe, Aya; Miyakawa, Tsuyoshi; Mizuguchi, Masashi

2018-01-01

Mutations in the Cyclin-dependent kinase-like 5 (CDKL5) gene cause severe neurodevelopmental disorders. Recently we have generated Cdkl5 KO mice by targeting exon 2 on the C57BL/6N background, and demonstrated postsynaptic overaccumulation of GluN2B-containing N-methyl-D-aspartate (NMDA) receptors in the hippocampus. In the current study, we subjected the Cdkl5 KO mice to a battery of comprehensive behavioral tests, aiming to reveal the effects of loss of CDKL5 in a whole perspective of motor, emotional, social, and cognition/memory functions, and to identify its undetermined roles. The neurological screen, rotarod, hot plate, prepulse inhibition, light/dark transition, open field, elevated plus maze, Porsolt forced swim, tail suspension, one-chamber and three-chamber social interaction, 24-h home cage monitoring, contextual and cued fear conditioning, Barnes maze, and T-maze tests were applied on adult Cdkl5 -/Y and +/Y mice. Cdkl5 -/Y mice showed a mild alteration in the gait. Analyses of emotional behaviors revealed significantly enhanced anxiety-like behaviors of Cdkl5 -/Y mice. Depressive-like behaviors and social interaction of Cdkl5 -/Y mice were uniquely altered. The contextual and cued fear conditioning of Cdkl5 -/Y mice were comparable to control mice; however, Cdkl5 -/Y mice showed a significantly increased freezing time and a significantly decreased distance traveled during the pretone period in the altered context. Both acquisition and long-term retention of spatial reference memory were significantly impaired. The morphometric analysis of hippocampal CA1 pyramidal neurons revealed impaired dendritic arborization and immature spine development in Cdkl5 -/Y mice. These results indicate that CDKL5 plays significant roles in regulating emotional behaviors especially on anxiety- and fear-related responses, and in both acquisition and long-term retention of spatial reference memory, which suggests that focus and special attention should be paid to the specific mechanisms of these deficits in the CDKL5 deficiency disorder. PMID:29702698

Comprehensive behavioral analysis of the Cdkl5 knockout mice revealed significant enhancement in anxiety- and fear-related behaviors and impairment in both acquisition and long-term retention of spatial reference memory.

PubMed

Okuda, Kosuke; Takao, Keizo; Watanabe, Aya; Miyakawa, Tsuyoshi; Mizuguchi, Masashi; Tanaka, Teruyuki

2018-01-01

Mutations in the Cyclin-dependent kinase-like 5 (CDKL5) gene cause severe neurodevelopmental disorders. Recently we have generated Cdkl5 KO mice by targeting exon 2 on the C57BL/6N background, and demonstrated postsynaptic overaccumulation of GluN2B-containing N-methyl-D-aspartate (NMDA) receptors in the hippocampus. In the current study, we subjected the Cdkl5 KO mice to a battery of comprehensive behavioral tests, aiming to reveal the effects of loss of CDKL5 in a whole perspective of motor, emotional, social, and cognition/memory functions, and to identify its undetermined roles. The neurological screen, rotarod, hot plate, prepulse inhibition, light/dark transition, open field, elevated plus maze, Porsolt forced swim, tail suspension, one-chamber and three-chamber social interaction, 24-h home cage monitoring, contextual and cued fear conditioning, Barnes maze, and T-maze tests were applied on adult Cdkl5 -/Y and +/Y mice. Cdkl5 -/Y mice showed a mild alteration in the gait. Analyses of emotional behaviors revealed significantly enhanced anxiety-like behaviors of Cdkl5 -/Y mice. Depressive-like behaviors and social interaction of Cdkl5 -/Y mice were uniquely altered. The contextual and cued fear conditioning of Cdkl5 -/Y mice were comparable to control mice; however, Cdkl5 -/Y mice showed a significantly increased freezing time and a significantly decreased distance traveled during the pretone period in the altered context. Both acquisition and long-term retention of spatial reference memory were significantly impaired. The morphometric analysis of hippocampal CA1 pyramidal neurons revealed impaired dendritic arborization and immature spine development in Cdkl5 -/Y mice. These results indicate that CDKL5 plays significant roles in regulating emotional behaviors especially on anxiety- and fear-related responses, and in both acquisition and long-term retention of spatial reference memory, which suggests that focus and special attention should be paid to the specific mechanisms of these deficits in the CDKL5 deficiency disorder.

Examining the Effects of Classroom Discussion on Students' Comprehension of Text: A Meta-Analysis

ERIC Educational Resources Information Center

Murphy, P. Karen; Wilkinson, Ian A. G.; Soter, Anna O.; Hennessey, Maeghan N.; Alexander, John F.

2009-01-01

The role of classroom discussions in comprehension and learning has been the focus of investigations since the early 1960s. Despite this long history, no syntheses have quantitatively reviewed the vast body of literature on classroom discussions for their effects on students' comprehension and learning. This comprehensive meta-analysis of…

The Effects of Meta-Cognitive Instruction on Students' Reading Comprehension in Computerized Reading Contexts: A Quantitative Meta-Analysis

ERIC Educational Resources Information Center

Lan, Yi-Chin; Lo, Yu-Ling; Hsu, Ying-Shao

2014-01-01

Comprehension is the essence of reading. Finding appropriate and effective reading strategies to support students' reading comprehension has always been a critical issue for educators. This article presents findings from a meta-analysis of 17 studies of metacognitive strategy instruction on students' reading comprehension in computerized…

Cross-language differences in the brain network subserving intelligible speech.

PubMed

Ge, Jianqiao; Peng, Gang; Lyu, Bingjiang; Wang, Yi; Zhuo, Yan; Niu, Zhendong; Tan, Li Hai; Leff, Alexander P; Gao, Jia-Hong

2015-03-10

How is language processed in the brain by native speakers of different languages? Is there one brain system for all languages or are different languages subserved by different brain systems? The first view emphasizes commonality, whereas the second emphasizes specificity. We investigated the cortical dynamics involved in processing two very diverse languages: a tonal language (Chinese) and a nontonal language (English). We used functional MRI and dynamic causal modeling analysis to compute and compare brain network models exhaustively with all possible connections among nodes of language regions in temporal and frontal cortex and found that the information flow from the posterior to anterior portions of the temporal cortex was commonly shared by Chinese and English speakers during speech comprehension, whereas the inferior frontal gyrus received neural signals from the left posterior portion of the temporal cortex in English speakers and from the bilateral anterior portion of the temporal cortex in Chinese speakers. Our results revealed that, although speech processing is largely carried out in the common left hemisphere classical language areas (Broca's and Wernicke's areas) and anterior temporal cortex, speech comprehension across different language groups depends on how these brain regions interact with each other. Moreover, the right anterior temporal cortex, which is crucial for tone processing, is equally important as its left homolog, the left anterior temporal cortex, in modulating the cortical dynamics in tone language comprehension. The current study pinpoints the importance of the bilateral anterior temporal cortex in language comprehension that is downplayed or even ignored by popular contemporary models of speech comprehension.

Cross-language differences in the brain network subserving intelligible speech

PubMed Central

Ge, Jianqiao; Peng, Gang; Lyu, Bingjiang; Wang, Yi; Zhuo, Yan; Niu, Zhendong; Tan, Li Hai; Leff, Alexander P.; Gao, Jia-Hong

2015-01-01

How is language processed in the brain by native speakers of different languages? Is there one brain system for all languages or are different languages subserved by different brain systems? The first view emphasizes commonality, whereas the second emphasizes specificity. We investigated the cortical dynamics involved in processing two very diverse languages: a tonal language (Chinese) and a nontonal language (English). We used functional MRI and dynamic causal modeling analysis to compute and compare brain network models exhaustively with all possible connections among nodes of language regions in temporal and frontal cortex and found that the information flow from the posterior to anterior portions of the temporal cortex was commonly shared by Chinese and English speakers during speech comprehension, whereas the inferior frontal gyrus received neural signals from the left posterior portion of the temporal cortex in English speakers and from the bilateral anterior portion of the temporal cortex in Chinese speakers. Our results revealed that, although speech processing is largely carried out in the common left hemisphere classical language areas (Broca’s and Wernicke’s areas) and anterior temporal cortex, speech comprehension across different language groups depends on how these brain regions interact with each other. Moreover, the right anterior temporal cortex, which is crucial for tone processing, is equally important as its left homolog, the left anterior temporal cortex, in modulating the cortical dynamics in tone language comprehension. The current study pinpoints the importance of the bilateral anterior temporal cortex in language comprehension that is downplayed or even ignored by popular contemporary models of speech comprehension. PMID:25713366

Active engagement in a web-based tutorial to prevent obesity grounded in Fuzzy-Trace Theory predicts higher knowledge and gist comprehension.

PubMed

Brust-Renck, Priscila G; Reyna, Valerie F; Wilhelms, Evan A; Wolfe, Christopher R; Widmer, Colin L; Cedillos-Whynott, Elizabeth M; Morant, A Kate

2017-08-01

We used Sharable Knowledge Objects (SKOs) to create an Intelligent Tutoring System (ITS) grounded in Fuzzy-Trace Theory to teach women about obesity prevention: GistFit, getting the gist of healthy eating and exercise. The theory predicts that reliance on gist mental representations (as opposed to verbatim) is more effective in reducing health risks and improving decision making. Technical information was translated into decision-relevant gist representations and gist principles (i.e., healthy values). The SKO was hypothesized to facilitate extracting these gist representations and principles by engaging women in dialogue, "understanding" their responses, and replying appropriately to prompt additional engagement. Participants were randomly assigned to either the obesity prevention tutorial (GistFit) or a control tutorial containing different content using the same technology. Participants were administered assessments of knowledge about nutrition and exercise, gist comprehension, gist principles, behavioral intentions and self-reported behavior. An analysis of engagement in tutorial dialogues and responses to multiple-choice questions to check understanding throughout the tutorial revealed significant correlations between these conversations and scores on subsequent knowledge tests and gist comprehension. Knowledge and comprehension measures correlated with healthier behavior and greater intentions to perform healthy behavior. Differences between GistFit and control tutorials were greater for participants who engaged more fully. Thus, results are consistent with the hypothesis that active engagement with a new gist-based ITS, rather than a passive memorization of verbatim details, was associated with an array of known psychosocial mediators of preventive health decisions, such as knowledge acquisition, and gist comprehension.

The Cytotoxicity Mechanism of 6-Shogaol-Treated HeLa Human Cervical Cancer Cells Revealed by Label-Free Shotgun Proteomics and Bioinformatics Analysis.

PubMed

Liu, Qun; Peng, Yong-Bo; Qi, Lian-Wen; Cheng, Xiao-Lan; Xu, Xiao-Jun; Liu, Le-Le; Liu, E-Hu; Li, Ping

2012-01-01

Cervical cancer is one of the most common cancers among women in the world. 6-Shogaol is a natural compound isolated from the rhizome of ginger (Zingiber officinale). In this paper, we demonstrated that 6-shogaol induced apoptosis and G2/M phase arrest in human cervical cancer HeLa cells. Endoplasmic reticulum stress and mitochondrial pathway were involved in 6-shogaol-mediated apoptosis. Proteomic analysis based on label-free strategy by liquid chromatography chip quadrupole time-of-flight mass spectrometry was subsequently proposed to identify, in a non-target-biased manner, the molecular changes in cellular proteins in response to 6-shogaol treatment. A total of 287 proteins were differentially expressed in response to 24 h treatment with 15 μM 6-shogaol in HeLa cells. Significantly changed proteins were subjected to functional pathway analysis by multiple analyzing software. Ingenuity pathway analysis (IPA) suggested that 14-3-3 signaling is a predominant canonical pathway involved in networks which may be significantly associated with the process of apoptosis and G2/M cell cycle arrest induced by 6-shogaol. In conclusion, this work developed an unbiased protein analysis strategy by shotgun proteomics and bioinformatics analysis. Data observed provide a comprehensive analysis of the 6-shogaol-treated HeLa cell proteome and reveal protein alterations that are associated with its anticancer mechanism.

The Cytotoxicity Mechanism of 6-Shogaol-Treated HeLa Human Cervical Cancer Cells Revealed by Label-Free Shotgun Proteomics and Bioinformatics Analysis

PubMed Central

Liu, Qun; Peng, Yong-Bo; Qi, Lian-Wen; Cheng, Xiao-Lan; Xu, Xiao-Jun; Liu, Le-Le; Liu, E-Hu; Li, Ping

2012-01-01

Cervical cancer is one of the most common cancers among women in the world. 6-Shogaol is a natural compound isolated from the rhizome of ginger (Zingiber officinale). In this paper, we demonstrated that 6-shogaol induced apoptosis and G2/M phase arrest in human cervical cancer HeLa cells. Endoplasmic reticulum stress and mitochondrial pathway were involved in 6-shogaol-mediated apoptosis. Proteomic analysis based on label-free strategy by liquid chromatography chip quadrupole time-of-flight mass spectrometry was subsequently proposed to identify, in a non-target-biased manner, the molecular changes in cellular proteins in response to 6-shogaol treatment. A total of 287 proteins were differentially expressed in response to 24 h treatment with 15 μM 6-shogaol in HeLa cells. Significantly changed proteins were subjected to functional pathway analysis by multiple analyzing software. Ingenuity pathway analysis (IPA) suggested that 14-3-3 signaling is a predominant canonical pathway involved in networks which may be significantly associated with the process of apoptosis and G2/M cell cycle arrest induced by 6-shogaol. In conclusion, this work developed an unbiased protein analysis strategy by shotgun proteomics and bioinformatics analysis. Data observed provide a comprehensive analysis of the 6-shogaol-treated HeLa cell proteome and reveal protein alterations that are associated with its anticancer mechanism. PMID:23243437

Analysis of underivatised low volatility compounds by comprehensive two-dimensional gas chromatography with a short primary column.

PubMed

Novaes, Fábio Junior Moreira; Kulsing, Chadin; Bizzo, Humberto Ribeiro; de Aquino Neto, Francisco Radler; Rezende, Claudia Moraes; Marriott, Philip John

2018-02-09

Comprehensive two-dimensional gas chromatography (GC×GC) approaches with cryogenic modulation were developed for the qualitative analysis of selected low volatility compounds in raw coffee bean extracts, without derivatisation. The approaches employed short first ( 1 D) and second ( 2 D) dimension columns, specifically a 1 D 65% phenyl methyl siloxane column (11m) and a 2 D 5% phenyl methyl siloxane column (1m), which allowed elution of high molar mass compounds (e.g.>600Da). Solutes included hydrocarbons, fatty acids, diterpenes, tocopherols, sterols, diterpene esters, and di- and triacylglycerides. An oven temperature program up to 370°C was employed. The effects of experimental conditions were investigated, revealing that the GC×GC results strongly depended on the cryogenic trap T, and oven T program. An appropriate condition was selected and further applied for group type analysis of low volatility compounds in green Arabica coffee beans. Retention indices were compiled for 1D GC analysis and were similar for the composite column data in GC×GC. The elution of some compounds was confirmed by use of authentic standards. The approach allowed direct analysis of coffee extract in ethyl acetate solution, with improved analyte peak capacity (approximately 200 compounds were detected) without prior fractionation or pre-treatment of the sample. This avoided potential hydrolysis of high molar mass conjugate esters as well as degradation of thermally labile compounds such as the derivatives of the diterpenes cafestol and kahweol. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome wide identification, phylogeny, and expression of bone morphogenetic protein genes in tetraploidized common carp (Cyprinus carpio).

PubMed

Chen, Lin; Dong, Chuanju; Kong, Shengnan; Zhang, Jiangfan; Li, Xuejun; Xu, Peng

2017-09-05

Bone morphogenetic proteins (Bmps) are a group of signaling molecules known to play important roles during formation and maintenance of various organs, not only bone, but also muscle, blood and so on. Common carp (Cyprinus carpio) is one of the most intensively studied fish due to its economic and environmental importance. Besides, common carp has encountered an additional round of whole genome duplication (WGD) compared with many closely related diploid teleost, which make it one of the most important models for genome evolutionary studies in teleost. Comprehensive genome resources of common carp have been developed recently, which facilitate the thorough characterization of bmp gene family in the tetraploidized common carp genome. We identified a total of 44 bmps from the common carp genome, which are twice as many as that of zebrafish. Phylogenetic analysis revealed that most of bmps are highly conserved. Comparative analysis was performed across six typical vertebrate genomes. It appeared that all the bmp genes in common carp were duplicated. Obviously, the expansion of the bmp gene family in common carp was due to the latest additional round of whole genome duplication and made it more abundant than other diploid teleosts. Expression signatures were assessed in major tissues, including gill, intestine, liver, spleen, skin, heart, gonad, muscle, kidney, head kidney, brain and blood, which demonstrated the comprehensive expression profiles of bmp genes in the tetraploidized genome. Significant gene expression divergences were observed which revealed substantial functional divergences of those duplicated bmp genes post the latest WGD event. The conserved synteny blocks of bmp5s revealed the genome rearrangement of common carp post the 4R WGD. The whole set of bmp gene family in common carp provides insight into gene fate of tetraploidized common carp genome post recent WGD. Copyright © 2017. Published by Elsevier B.V.

Evolution and Diversity of the Antimicrobial Resistance Associated Mobilome in Streptococcus suis: A Probable Mobile Genetic Elements Reservoir for Other Streptococci.

PubMed

Huang, Jinhu; Ma, Jiale; Shang, Kexin; Hu, Xiao; Liang, Yuan; Li, Daiwei; Wu, Zuowei; Dai, Lei; Chen, Li; Wang, Liping

2016-01-01

Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S. suis . Integrative conjugative elements (ICEs), prophages and tandem MGEs were located at different insertion sites, while 86% of the AMR-associated MGEs were inserted at rplL and rum loci. Comprehensive analysis of insertions at rplL and rum loci among four pathogenic Streptococcus species ( Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes , and S. suis ) revealed the existence of different groups of MGEs, including Tn5252, ICE Sp 1108, and TnGBS2 groups ICEs, Φm46.1 group prophage, ICE_ICE and ICE_prophage tandem MGEs. Comparative ICE genomics of ICE Sa 2603 family revealed that module exchange and acquisition/deletion were the main mechanisms in MGEs' expansion and evolution. Furthermore, the observation of tandem MGEs reflected a novel mechanism for MGE diversity. Moreover, an in vitro competition assay showed no visible fitness cost was observed between different MGE-carrying isolates and a conjugation assay revealed the transferability of ICE Sa 2603 family of ICEs. Our statistics further indicated that the prevalence and diversity of MGEs in S. suis is much greater than in other three species which prompted our hypothesis that S. suis is probably a MGEs reservoir for other streptococci. In conclusion, our results showed that acquisition of MGEs confers S. suis not only its capability as a multidrug resistance pathogen, but also represents a paradigm to study the modular evolution and matryoshkas of MGEs.

Evolution and Diversity of the Antimicrobial Resistance Associated Mobilome in Streptococcus suis: A Probable Mobile Genetic Elements Reservoir for Other Streptococci

PubMed Central

Huang, Jinhu; Ma, Jiale; Shang, Kexin; Hu, Xiao; Liang, Yuan; Li, Daiwei; Wu, Zuowei; Dai, Lei; Chen, Li; Wang, Liping

2016-01-01

Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S. suis. Integrative conjugative elements (ICEs), prophages and tandem MGEs were located at different insertion sites, while 86% of the AMR-associated MGEs were inserted at rplL and rum loci. Comprehensive analysis of insertions at rplL and rum loci among four pathogenic Streptococcus species (Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and S. suis) revealed the existence of different groups of MGEs, including Tn5252, ICESp1108, and TnGBS2 groups ICEs, Φm46.1 group prophage, ICE_ICE and ICE_prophage tandem MGEs. Comparative ICE genomics of ICESa2603 family revealed that module exchange and acquisition/deletion were the main mechanisms in MGEs' expansion and evolution. Furthermore, the observation of tandem MGEs reflected a novel mechanism for MGE diversity. Moreover, an in vitro competition assay showed no visible fitness cost was observed between different MGE-carrying isolates and a conjugation assay revealed the transferability of ICESa2603 family of ICEs. Our statistics further indicated that the prevalence and diversity of MGEs in S. suis is much greater than in other three species which prompted our hypothesis that S. suis is probably a MGEs reservoir for other streptococci. In conclusion, our results showed that acquisition of MGEs confers S. suis not only its capability as a multidrug resistance pathogen, but also represents a paradigm to study the modular evolution and matryoshkas of MGEs. PMID:27774436

Integrated web visualizations for protein-protein interaction databases.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Holzinger, Andreas

2015-06-16

Understanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions. Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery. They provide predictions and correlations, indicate possibilities for future experimental research and fill the gaps to complete the picture of biochemical processes. There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. Many computational resources integrate interaction data with additional information on molecular background. However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks. We selected M=10 out of N=53 resources supporting visualization, and we tested against the following set of criteria: interoperability, data integration, quantity of possible interactions, data visualization quality and data coverage. The study reveals differences in usability, visualization features and quality as well as the quantity of interactions. StringDB is the recommended first choice. CPDB presents a comprehensive dataset and IntAct lets the user change the network layout. A comprehensive comparison table is available via web. The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015. Only some web resources featuring graph visualization can be successfully applied to interactive visual analysis of protein-protein interaction. Study results underline the necessity for further enhancements of visualization integration in biochemical analysis tools. Identified challenges are data comprehensiveness, confidence, interactive feature and visualization maturing.

Neural correlates underlying the comprehension of deceitful and ironic communicative intentions.

PubMed

Bosco, Francesca M; Parola, Alberto; Valentini, Maria C; Morese, Rosalba

2017-09-01

Neuroimaging studies have shown that a left fronto-temporo-parietal cerebral network is recruited in the comprehension of both deceitful and ironic speech acts. However, no studies to date have directly compared neural activation during the comprehension of these pragmatic phenomena. We used fMRI to investigate the existence of common and specific neural circuits underlying the comprehension of the same speech act, uttered with different communicative intentions, i.e., of being sincere, deceitful or ironic. In particular, the novelty of the present study is that it explores the existence of a specific cerebral area involved in the recognition of irony versus deceit. We presented 23 healthy participants with 48 context stories each followed by a target sentence. For each story we designed different versions eliciting, respectively, different pragmatic interpretations of the same target sentence - literal, deceitful or ironic-. We kept the semantic and syntactic complexity of the target sentence constant across the conditions. Our results showed that the recognition of ironic communicative intention activated the left temporo-parietal junction (lTPJ), the left inferior frontal gyrus (lIFG), the left middle frontal gyrus (lMFG), the left middle temporal gyrus (lMTG), and the left dorsolateral prefrontal cortex (lDLPFC). Comprehension of deceitful communicative intention activated the lIFG, the lMFG, and the lDLPFC. fMRI analysis revealed that a left fronto-temporal network-including the inferior frontal gyrus (IFG), the dorsolateral prefrontal cortex (DLPFC) and the middle frontal gyrus (MFG)-is activated in both irony and deceit recognition. The original result of the present investigation is that the lMTG was found to be more active in the comprehension of ironic versus deceitful communicative intention, thus suggesting its specific role in irony recognition. To conclude, our results showed that common cerebral areas are recruited in the comprehension of both pragmatic phenomena, while the lMTG has a key role in the recognition of ironic versus deceitful communicative intention. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yingchun; Yang, Feng; Fu, Yi

Abstract - Brain development and spinal cord regeneration require neurite sprouting and growth cone navigation in response to extension and collapsing factors present in the extracellular environment. These external guidance cues control neurite growth cone extension and retraction processes through intracellular protein phosphorylation of numerous cytoskeletal, adhesion, and polarity complex signaling proteins. However, the complex kinase/substrate signaling networks that mediate neuritogenesis have not been investigated. Here, we compare the neurite phosphoproteome under growth and retraction conditions using neurite purification methodology combined with mass spectrometry. More than 4000 non-redundant phosphorylation sites from 1883 proteins have been annotated and mapped to signalingmore » pathways that control kinase/phosphatase networks, cytoskeleton remodeling, and axon/dendrite specification. Comprehensive informatics and functional studies revealed a compartmentalized ERK activation/deactivation cytoskeletal switch that governs neurite growth and retraction, respectively. Our findings provide the first system-wide analysis of the phosphoprotein signaling networks that enable neurite growth and retraction and reveal an important molecular switch that governs neuritogenesis.« less

A Comprehensive Proteomics Analysis Reveals a Secretory Path- and Status-Dependent Signature of Exosomes Released from Tumor-Associated Macrophages.

PubMed

Zhu, Yinghui; Chen, Xianwei; Pan, Qingfei; Wang, Yang; Su, Siyuan; Jiang, Cuicui; Li, Yang; Xu, Ningzhi; Wu, Lin; Lou, Xiaomin; Liu, Siqi

2015-10-02

Exosomes are 30-120 nm-sized membrane vesicles of endocytic origin that are released into the extracellular environment and play roles in cell-cell communication. Tumor-associated macrophages (TAMs) are important constituents of the tumor microenvironment; thus, it is critical to study the features and complex biological functions of TAM-derived exosomes. Here, we constructed a TAM cell model from a mouse macrophage cell line, Ana-1, and performed comparative proteomics on exosomes, exosome-free media, and cells between TAMs and Ana-1. Proteomic analysis between exosome and exosome-free fractions indicated that the functions of exosome dominant proteins were mainly enriched in RNA processing and proteolysis. TAM status dramatically affected the abundances of 20S proteasome subunits and ribosomal proteins in their exosomes. The 20S proteasome activity assay strongly indicated that TAM exosomes possessed higher proteolytic activity. In addition, Ana-1- and TAM-derived exosomes have different RNA profiles, which may result from differential RNA processing proteins. Taken together, our comprehensive proteomics study provides novel views for understanding the complicated roles of macrophage-derived exosomes in the tumor microenvironment.

Comprehensive evaluation of leukocyte lineage derived from human hematopoietic cells in humanized mice.

PubMed

Takahashi, Masayuki; Tsujimura, Noriyuki; Otsuka, Kensuke; Yoshino, Tomoko; Mori, Tetsushi; Matsunaga, Tadashi; Nakasono, Satoshi

2012-04-01

Recently, humanized animals whereby a part of the animal is biologically engineered using human genes or cells have been utilized to overcome interspecific differences. Herein, we analyzed the detail of the differentiation states of various human leukocyte subpopulations in humanized mouse and evaluated comprehensively the similarity of the leukocyte lineage between humanized mice and humans. Humanized mice were established by transplanting human CD34(+) cord blood cells into irradiated severely immunodeficient NOD/Shi-scid/IL2Rγ(null) (NOG) mice, and the phenotypes of human cells contained in bone marrow, thymus, spleen and peripheral blood from the mice were analyzed at monthly intervals until 4 months after cell transplantation. The analysis revealed that transplanted human hematopoietic stem cells via the caudal vein homed and engrafted themselves successfully at the mouse bone marrow. Subsequently, the differentiated leukocytes migrated to the various tissues. Almost all of the leukocytes within the thymus were human cells. Furthermore, analysis of the differentiation states of human leukocytes in various tissues and organs indicated that it is highly likely that the human-like leukocyte lineage can be developed in mice. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Annotation and structural elucidation of bovine milk oligosaccharides and determination of novel fucosylated structures

PubMed Central

Aldredge, Danielle L; Geronimo, Maria R; Hua, Serenus; Nwosu, Charles C; Lebrilla, Carlito B; Barile, Daniela

2013-01-01

Bovine milk oligosaccharides (BMOs) are recognized by the dairy and food industries, as well as by infant formula manufacturers, as novel, high-potential bioactive food ingredients. Recent studies revealed that bovine milk contains complex oligosaccharides structurally related to those previously thought to be present in only human milk. These BMOs are microbiotic modulators involved in important biological activities, including preventing pathogen binding to the intestinal epithelium and serving as nutrients for a selected class of beneficial bacteria. Only a small number of BMO structures are fully elucidated. To better understand the potential of BMOs as a class of biotherapeutics, their detailed structure analysis is needed. This study initiated the development of a structure library of BMOs and a comprehensive evaluation of structure-related specificity. The bovine milk glycome was profiled by high-performance mass spectrometry and advanced separation techniques to obtain a comprehensive catalog of BMOs, including several novel, lower abundant neutral and fucosylated oligosaccharides that are often overlooked during analysis. Structures were identified using isomer-specific tandem mass spectroscopy and targeted exoglycosidase digestions to produce a BMO library detailing retention time, accurate mass and structure to allow their rapid identification in future studies. PMID:23436288

Comprehensive Analysis and Characterization of Linear Antigenic Domains on HN Protein from Genotype VII Newcastle Disease Virus Using Yeast Surface Display System

PubMed Central

Li, Tao; Wang, Gaoling; Shi, Bingtian; Liu, Peixin; Si, Wei; Wang, Bin; Jiang, Li; Zhou, Lunjiang; Xiu, Jinsheng; Liu, Henggui

2015-01-01

Circulation of genotype VII Newcastle disease virus (NDV) has posed a great threat for the poultry industry worldwide. Antibodies against Hemagglutinin-neuraminidase (HN), a membrane protein of NDV with critical roles in NDV infection, have been reported to provide chickens protection from NDV infection. In this study, we comprehensively analyzed the in vivo antibody responses against the linear antigenic domains of the HN protein from genotype VII NDV using a yeast surface display system. The results revealed four distinct regions of HN, P1 (1-52aa), P2 (53-192aa), P3 (193-302aa) and P4 (303-571aa), respectively, according to their antigenic potency. Analysis by FACS and ELISA assay indicated P2 to be the dominant linear antigenic domain, with the immunogenic potency to protect the majority of chickens from NDV challenge. In contrast, the P1, P3 and P4 domains showed weak antigenicity in vivo and could not protect chickens from NDV challenge. These results provide important insight into the characteristic of humoral immune responses elicited by HN of NDV in vivo. PMID:26121247

The Comprehension Problems for Second-Language Learners with Poor Reading Comprehension Despite Adequate Decoding: A Meta-Analysis

ERIC Educational Resources Information Center

Spencer, Mercedes; Wagner, Richard K.

2017-01-01

We conducted a meta-analysis of 16 existing studies to examine the nature of the comprehension problems for children who were second-language learners with poor reading comprehension despite adequate decoding. Results indicated that these children had deficits in oral language (d = -0.80), but these deficits were not as severe as their reading…

Factors Affecting the Learning of English as a Second Language in Israel.

ERIC Educational Resources Information Center

Abu-Rabia, Salim

1996-01-01

Explores the effects of the attitudes and culture of Israeli-Jewish English-language students on their reading comprehension. Eighth-grade students read stories in Hebrew and English and answered questions both about the stories and their own attitudes. Reveals that culturally familiar texts boost reading comprehension scores. (MJP)

CH-47D Rotating System Fault Sensing for Condition Based Maintenance

DTIC Science & Technology

2011-03-01

replacement. This research seeks to create an analytical model in the Rotorcraft Comprehensive Analysis System which will enable the identifica- tion of...answer my many questions. Without your assistance and that of Dr. Jon Keller and Mr. Clayton Kachelle at AMRDEC, the Rotorcraft Comprehensive Analysis...20 3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . 20 3.2 Rotorcraft Comprehensive Analysis

Comprehensive machine learning analysis of Hydra behavior reveals a stable basal behavioral repertoire

PubMed Central

Taralova, Ekaterina; Dupre, Christophe; Yuste, Rafael

2018-01-01

Animal behavior has been studied for centuries, but few efficient methods are available to automatically identify and classify it. Quantitative behavioral studies have been hindered by the subjective and imprecise nature of human observation, and the slow speed of annotating behavioral data. Here, we developed an automatic behavior analysis pipeline for the cnidarian Hydra vulgaris using machine learning. We imaged freely behaving Hydra, extracted motion and shape features from the videos, and constructed a dictionary of visual features to classify pre-defined behaviors. We also identified unannotated behaviors with unsupervised methods. Using this analysis pipeline, we quantified 6 basic behaviors and found surprisingly similar behavior statistics across animals within the same species, regardless of experimental conditions. Our analysis indicates that the fundamental behavioral repertoire of Hydra is stable. This robustness could reflect a homeostatic neural control of "housekeeping" behaviors which could have been already present in the earliest nervous systems. PMID:29589829

Structure and Function of Iron-Loaded Synthetic Melanin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yiwen; Xie, Yijun; Wang, Zhao

We describe a synthetic method for increasing and controlling the iron loading of synthetic melanin nanoparticles and use the resulting materials to perform a systematic quantitative investigation on their structure- property relationship. A comprehensive analysis by magnetometry, electron paramagnetic resonance, and nuclear magnetic relaxation dispersion reveals the complexities of their magnetic behavior and how these intraparticle magnetic interactions manifest in useful material properties such as their performance as MRI contrast agents. This analysis allows predictions of the optimal iron loading through a quantitative modeling of antiferromagnetic coupling that arises from proximal iron ions. This study provides a detailed understanding ofmore » this complex class of synthetic biomaterials and gives insight into interactions and structures prevalent in naturally occurring melanins.« less

Processes that Inform Multicultural Supervision: A Qualitative Meta-Analysis.

PubMed

Tohidian, Nilou B; Quek, Karen Mui-Teng

2017-10-01

As the fields of counseling and psychotherapy have become more cognizant that individuals, couples, and families bring with them a myriad of diversity factors into therapy, multicultural competency has also become a crucial component in the development of clinicians during clinical supervision and training. We employed a qualitative meta-analysis to provide a detailed and comprehensive description of similar themes identified in primary qualitative studies that have investigated supervisory practices with an emphasis on diversity. Findings revealed six meta-categories, namely: (a) Supervisor's Multicultural Stances; (b) Supervisee's Multicultural Encounters; (c) Competency-Based Content in Supervision; (d) Processes Surrounding Multicultural Supervision; (e) Culturally Attuned Interventions; and (f) Multicultural Supervisory Alliance. Implications for practice are discussed. © 2017 American Association for Marriage and Family Therapy.

Discovery and characterization of antibody variants using mass spectrometry-based comparative analysis for biosimilar candidates of monoclonal antibody drugs.

PubMed

Li, Wenhua; Yang, Bin; Zhou, Dongmei; Xu, Jun; Ke, Zhi; Suen, Wen-Chen

2016-07-01

Liquid chromatography mass spectrometry (LC-MS) is the most commonly used technique for the characterization of antibody variants. MAb-X and mAb-Y are two approved IgG1 subtype monoclonal antibody drugs recombinantly produced in Chinese hamster ovary (CHO) cells. We report here that two unexpected and rare antibody variants have been discovered during cell culture process development of biosimilars for these two approved drugs through intact mass analysis. We then used comprehensive mass spectrometry-based comparative analysis including reduced light, heavy chains, and domain-specific mass as well as peptide mapping analysis to fully characterize the observed antibody variants. The "middle-up" mass comparative analysis demonstrated that the antibody variant from mAb-X biosimilar candidate was caused by mass variation of antibody crystalline fragment (Fc), whereas a different variant with mass variation in antibody antigen-binding fragment (Fab) from mAb-Y biosimilar candidate was identified. Endoproteinase Lys-C digested peptide mapping and tandem mass spectrometry analysis further revealed that a leucine to glutamine change in N-terminal 402 site of heavy chain was responsible for the generation of mAb-X antibody variant. Lys-C and trypsin coupled non-reduced and reduced peptide mapping comparative analysis showed that the formation of the light-heavy interchain trisulfide bond resulted in the mAb-Y antibody variant. These two cases confirmed that mass spectrometry-based comparative analysis plays a critical role for the characterization of monoclonal antibody variants, and biosimilar developers should start with a comprehensive structural assessment and comparative analysis to decrease the risk of the process development for biosimilars. Copyright © 2016 Elsevier B.V. All rights reserved.

Developmental transcriptional profiling reveals key insights into Triticeae reproductive development.

PubMed

Tran, Frances; Penniket, Carolyn; Patel, Rohan V; Provart, Nicholas J; Laroche, André; Rowland, Owen; Robert, Laurian S

2013-06-01

Despite their importance, there remains a paucity of large-scale gene expression-based studies of reproductive development in species belonging to the Triticeae. As a first step to address this deficiency, a gene expression atlas of triticale reproductive development was generated using the 55K Affymetrix GeneChip(®) wheat genome array. The global transcriptional profiles of the anther/pollen, ovary and stigma were analyzed at concurrent developmental stages, and co-expressed as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae floral development and function. This comprehensive resource rests upon detailed gene annotations, and the expression profiles are readily accessible via a web browser. © 2013 Her Majesty the Queen in Right of Canada as represented by the Minister of Agriculture and Agri-Food Canada.

Assessment of primary health care: health professionals' perspective.

PubMed

Silva, Simone Albino da; Nogueira, Denismar Alves; Paraizo, Camila Maria da Silva; Fracolli, Lislaine Aparecida

2014-08-01

Objective To assess primary health care attributes of access to a first contact, comprehensiveness, coordination, continuity, family guidance and community orientation. Method An evaluative, quantitative and cross-sectional study with 35 professional teams in the Family Health Program of the Alfenas region, Minas Gerais, Brazil. Data collection was done with the Primary Care Assessment Tool - Brazil, professional version. Results Results revealed a low percentage of medical experts among the participants who evaluated the attributes with high scores, with the exception of access to a first contact. Data analysis revealed needs for improvement: hours of service; forms of communication between clients and healthcare services and between clients and professionals; the mechanism of counter-referral. Conclusion It was concluded that there is a mismatch between the provision of services and the needs of the population, which compromises the quality of primary health care.

[Recent advances in research on Malassezia microbiota in humans].

PubMed

Sugita, Takashi; Zhang, Enshi; Tanaka, Takafumi; Nishikawa, Akemi; Tajima, Mami; Tsuboi, Ryoji

2013-01-01

Malassezia species of lipophilic yeasts account for most fungal microbiota. Although they colonize healthy skin, they are also associated with several skin diseases, including pityriasis versicolor, seborrheic dermatitis, Malassezia folliculitis, and atopic dermatitis. To date, 14 members of the Malassezia genus have been identified. Of these, both M. globosa and M. restricta predominate, regardless of skin-disease type. Comprehensive analysis of fungal microbiota in the skin of patients with atopic dermatitis using an rRNA clone library method revealed that fungal microbiota cluster according to disease severity. The external ear canal and sole of the foot are colonized by specific Malassezia microbiota.

Multicultural development in human services agencies: challenges and solutions.

PubMed

Hyde, Cheryl A

2004-01-01

Comprehensive multicultural organizational development (MCOD) is increasingly necessary in human services agencies. This article presents results from an exploratory study that identified challenges and solutions to MCOD, against the backdrop of daily realities of agency life. The author conducted interviews with 20 consultants and 20 practitioners experienced in MCOD. Qualitative analysis revealed four challenges--socioeconomic environment, organizational dynamics, conceptualization of the change effort, and consultant competence; and four solutions--collaborative environmental relations, leadership development, assessment and planning, and consultant selection. Results suggest the complexities of MCOD and ways that human services agencies can sustain such efforts.

Simulation of non-Newtonian oil-water core annular flow through return bends

NASA Astrophysics Data System (ADS)

Jiang, Fan; Wang, Ke; Skote, Martin; Wong, Teck Neng; Duan, Fei

2018-01-01

The volume of fluid (VOF) model is used together with the continuum surface force (CSF) model to numerically simulate the non-Newtonian oil-water core annular flow across return bends. A comprehensive study is conducted to generate the profiles of pressure, velocity, volume fraction and wall shear stress for different oil properties, flow directions, and bend geometries. It is revealed that the oil core may adhere to the bend wall under certain operating conditions. Through the analysis of the total pressure gradient and fouling angle, suitable bend geometric parameters are identified for avoiding the risk of fouling.

Current practice of radioiodine treatment in the management of differentiated thyroid cancer in Germany.

PubMed

Hoelzer, S; Steiner, D; Bauer, R; Reiners, C; Farahati, J; Hundahl, S A; Dudeck, J

2000-10-01

This prospective, observational study of a cohort of thyroid cancer patients in Germany focusses on the "real-world" practice in the management of thyroid cancer patients. This report includes data from 2376 patients with primary differentiated thyroid carcinoma first diagnosed in the year 1996. The study reveals considerable differences in actual practice concerning surgery and radioiodine treatment. The results indicate that consensus is lacking with respect to the multimodality treatment approach for differentiated thyroid carcinoma. Our analysis represents the most current and comprehensive national assessment of presenting patient characteristics, diagnostic tests, treatment and complications for thyroid cancer.

Similar but Different: Differences in Comprehension Diagnosis on the Neale Analysis of Reading Ability and the York Assessment of Reading for Comprehension

ERIC Educational Resources Information Center

Colenbrander, Danielle; Nickels, Lyndsey; Kohnen, Saskia

2017-01-01

Background: Identifying reading comprehension difficulties is challenging. There are many comprehension tests to choose from, and a child's diagnosis can be influenced by various factors such as a test's format and content and the choice of diagnostic criteria. We investigate these issues with reference to the Neale Analysis of Reading Ability…

The behavioural patterns and neural correlates of concrete and abstract verb processing in aphasia: A novel verb semantic battery.

PubMed

Alyahya, Reem S W; Halai, Ajay D; Conroy, Paul; Lambon Ralph, Matthew A

2018-01-01

Typically, processing is more accurate and efficient for concrete than abstract concepts in both healthy adults and individuals with aphasia. While, concreteness effects have been thoroughly documented with respect to noun processing, other words classes have received little attention despite tending to be less concrete than nouns. The aim of the current study was to explore concrete-abstract differences in verbs and identify their neural correlates in post-stroke aphasia. Given the dearth of comprehension tests for verbs, a battery of neuropsychological tests was developed in this study to assess the comprehension of concrete and abstract verbs. Specifically, a sensitive verb synonym judgment test was generated that varied both the items' imageability and frequency, and a picture-to-word matching test with numerous concrete verbs. Normative data were then collected and the tests were administered to a cohort of 48 individuals with chronic post-stroke aphasia to explore the behavioural patterns and neural correlates of verb processing. The results revealed significantly better comprehension of concrete than abstract verbs, aligning with the existing aphasiological literature on noun processing. In addition, the patients performed better during verb comprehension than verb production. Lesion-symptom correlational analyses revealed common areas that support processing of concrete and abstract verbs, including the left anterior temporal lobe, posterior supramarginal gyrus and superior lateral occipital cortex. A direct contrast between them revealed additional regions with graded differences. Specifically, the left frontal regions were associated with processing abstract verbs; whereas, the left posterior temporal and occipital regions were associated with processing concrete verbs. Moreover, overlapping and distinct neural correlates were identified in association with the comprehension and production of concrete verbs. These patient findings align with data from functional neuroimaging and neuro-stimulation, and existing models of language organisation.

Decoding and Reading Comprehension: A Meta-Analysis to Identify Which Reader and Assessment Characteristics Influence the Strength of the Relationship in English

ERIC Educational Resources Information Center

García, J. Ricardo; Cain, Kate

2014-01-01

The twofold purpose of this meta-analysis was to determine the relative importance of decoding skills to reading comprehension in reading development and to identify which reader characteristics and reading assessment characteristics contribute to differences in the decoding and reading comprehension correlation. A meta-analysis of 110 studies…

Analyse Factorielle d'une Batterie de Tests de Comprehension Orale et Ecrite (Factor Analysis of a Battery of Tests of Listening and Reading Comprehension). Melanges Pedagogiques, 1971.

ERIC Educational Resources Information Center

Lonchamp, F.

This is a presentation of the results of a factor analysis of a battery of tests intended to measure listening and reading comprehension in English as a second language. The analysis sought to answer the following questions: (1) whether the factor analysis method yields results when applied to tests which are not specifically designed for this…

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression

PubMed Central

Megger, Dominik A.; Philipp, Jos; Le-Trilling, Vu Thuy Khanh; Sitek, Barbara; Trilling, Mirko

2017-01-01

Interferons (IFNs) are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction). In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive analysis revealed important insights into the human IFN-regulated proteome and its dynamics of protein induction and repression. Interestingly, the new class of IFN-repressed genes comprises known host factors for highly relevant pathogens such as HIV, dengue virus, and hepatitis C virus. PMID:28959263

Increased plasma proline concentrations are associated with sarcopenia in the elderly

PubMed Central

Adachi, Yusuke; Imaizumi, Akira; Hakamada, Tomomi; Abe, Yasuko; Kaneko, Eiji; Takahashi, Soiciro; Shimokado, Kentaro

2017-01-01

Background and purpose Metabolome analyses have shown that plasma amino acid profiles reflect various pathological conditions, such as cancer and diabetes mellitus. It remains unclear, however, whether plasma amino acid profiles change in patients with sarcopenia. This study therefore aimed to investigate whether sarcopenia-specific changes occur in plasma amino acid profiles. Methods A total of 153 community-dwelling and seven institutionalized elderly individuals (56 men, 104 women; mean age, 77.7±7.0 years) were recruited for this cross-sectional analysis. We performed a comprehensive geriatric assessment, which included an evaluation of hand grip strength, gait speed, muscle mass and blood chemistry, including the concentration of 18 amino acids. Results Twenty-eight of the 160 participants met the criteria for sarcopenia established by the Asian Working Group on Sarcopenia in Older People. Univariate analysis revealed associations between the presence of sarcopenia and a higher plasma concentration of proline and glutamine, lower concentrations of histidine and tryptophan. Multivariable analysis revealed that a higher concentration of proline was the only variable independently associated with sarcopenia. Conclusions The plasma concentration of proline may be useful for understanding the underlying pathophysiology of sarcopenia. PMID:28934309

Revealing the Hidden Relationship by Sparse Modules in Complex Networks with a Large-Scale Analysis

PubMed Central

Jiao, Qing-Ju; Huang, Yan; Liu, Wei; Wang, Xiao-Fan; Chen, Xiao-Shuang; Shen, Hong-Bin

2013-01-01

One of the remarkable features of networks is module that can provide useful insights into not only network organizations but also functional behaviors between their components. Comprehensive efforts have been devoted to investigating cohesive modules in the past decade. However, it is still not clear whether there are important structural characteristics of the nodes that do not belong to any cohesive module. In order to answer this question, we performed a large-scale analysis on 25 complex networks with different types and scales using our recently developed BTS (bintree seeking) algorithm, which is able to detect both cohesive and sparse modules in the network. Our results reveal that the sparse modules composed by the cohesively isolated nodes widely co-exist with the cohesive modules. Detailed analysis shows that both types of modules provide better characterization for the division of a network into functional units than merely cohesive modules, because the sparse modules possibly re-organize the nodes in the so-called cohesive modules, which lack obvious modular significance, into meaningful groups. Compared with cohesive modules, the sizes of sparse ones are generally smaller. Sparse modules are also found to have preferences in social and biological networks than others. PMID:23762457

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression.

PubMed

Megger, Dominik A; Philipp, Jos; Le-Trilling, Vu Thuy Khanh; Sitek, Barbara; Trilling, Mirko

2017-01-01

Interferons (IFNs) are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction). In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive analysis revealed important insights into the human IFN-regulated proteome and its dynamics of protein induction and repression. Interestingly, the new class of IFN-repressed genes comprises known host factors for highly relevant pathogens such as HIV, dengue virus, and hepatitis C virus.

Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides.

PubMed

Hia, Fabian; Chionh, Yok Hian; Pang, Yan Ling Joy; DeMott, Michael S; McBee, Megan E; Dedon, Peter C

2015-03-11

A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Comprehension Problems for Second-Language Learners with Poor Reading Comprehension despite Adequate Decoding: A Meta-Analysis

PubMed Central

Spencer, Mercedes; Wagner, Richard K.

2016-01-01

We conducted a meta-analysis of 16 existing studies to examine the nature of the comprehension problems for children who were second-language learners with poor reading comprehension despite adequate decoding. Results indicated that these children had deficits in oral language (d = −0.80), but these deficits were not as severe as their reading comprehension deficit (d = −2.47). Second-language learners also had weaker oral language skills compared to native-speaking children regardless of comprehension status (d = −0.84). We discuss theoretical and practical implications of the finding that second-language learners who are poor at reading comprehension despite adequate decoding have deficits in oral language but the deficit is not sufficient to explain their deficit in reading comprehension. PMID:28461711

The Comprehension Problems for Second-Language Learners with Poor Reading Comprehension despite Adequate Decoding: A Meta-Analysis.

PubMed

Spencer, Mercedes; Wagner, Richard K

2017-05-01

We conducted a meta-analysis of 16 existing studies to examine the nature of the comprehension problems for children who were second-language learners with poor reading comprehension despite adequate decoding. Results indicated that these children had deficits in oral language ( d = -0.80), but these deficits were not as severe as their reading comprehension deficit ( d = -2.47). Second-language learners also had weaker oral language skills compared to native-speaking children regardless of comprehension status ( d = -0.84). We discuss theoretical and practical implications of the finding that second-language learners who are poor at reading comprehension despite adequate decoding have deficits in oral language but the deficit is not sufficient to explain their deficit in reading comprehension.

Bacterial Diversity Analysis during the Fermentation Processing of Traditional Chinese Yellow Rice Wine Revealed by 16S rDNA 454 Pyrosequencing.

PubMed

Fang, Ruo-si; Dong, Ya-chen; Chen, Feng; Chen, Qi-he

2015-10-01

Rice wine is a traditional Chinese fermented alcohol drink. Spontaneous fermentation with the use of the Chinese starter and wheat Qu lead to the growth of various microorganisms during the complete brewing process. It's of great importance to fully understand the composition of bacteria diversity in rice wine in order to improve the quality and solve safety problems. In this study, a more comprehensive bacterial description was shown with the use of bacteria diversity analysis, which enabled us to have a better understanding. Rarefaction, rank abundance, alpha Diversity, beta diversity and principal coordinates analysis simplified their complex bacteria components and provide us theoretical foundation for further investigation. It has been found bacteria diversity is more abundant at mid-term and later stage of brewing process. Bacteria community analysis reveals there is a potential safety hazard existing in the fermentation, since most of the sequence reads are assigned to Enterobacter (7900 at most) and Pantoea (7336 at most), followed by Staphylococcus (2796 at most) and Pseudomonas (1681 at most). Lactic acid bacteria are rare throughout the fermentation process which is not in accordance with other reports. This work may offer us an opportunity to investigate micro ecological fermentation system in food industry. © 2015 Institute of Food Technologists®

Evolutionary and genetic analysis of the VP2 gene of canine parvovirus.

PubMed

Li, Gairu; Ji, Senlin; Zhai, Xiaofeng; Zhang, Yuxiang; Liu, Jie; Zhu, Mengyan; Zhou, Jiyong; Su, Shuo

2017-07-17

Canine parvovirus (CPV) type 2 emerged in 1978 in the USA and quickly spread among dog populations all over the world with high morbidity. Although CPV is a DNA virus, its genomic substitution rate is similar to some RNA viruses. Therefore, it is important to trace the evolution of CPV to monitor the appearance of mutations that might affect vaccine effectiveness. Our analysis shows that the VP2 genes of CPV isolated from 1979 to 2016 are divided into six groups: GI, GII, GIII, GIV, GV, and GVI. Amino acid mutation analysis revealed several undiscovered important mutation sites: F267Y, Y324I, and T440A. Of note, the evolutionary rate of the CPV VP2 gene from Asia and Europe decreased. Codon usage analysis showed that the VP2 gene of CPV exhibits high bias with an ENC ranging from 34.93 to 36.7. Furthermore, we demonstrate that natural selection plays a major role compared to mutation pressure driving CPV evolution. There are few studies on the codon usage of CPV. Here, we comprehensively studied the genetic evolution, codon usage pattern, and evolutionary characterization of the VP2 gene of CPV. The novel findings revealing the evolutionary process of CPV will greatly serve future CPV research.

A, B Seeing: The Role of Constructive Processes in Children's Comprehension Monitoring.

ERIC Educational Resources Information Center

Rubman, Claire N.; Waters, Harriet Salatas

2000-01-01

Using a comprehension-monitoring model, 192 skilled and less skilled readers from 3rd and 6th grade read stories containing inconsistent information. Half of the students constructed a storyboard representation of the stories and half only read the text. Results reveal that storyboard construction enhanced the integration of text propositions and…

Comprehensive MS and Solid-State NMR Metabolomic Profiling Reveals Molecular Variations in Native Periderms from Four Solanum tuberosum Potato Cultivars.

PubMed

Huang, Wenlin; Serra, Olga; Dastmalchi, Keyvan; Jin, Liqing; Yang, Lijia; Stark, Ruth E

2017-03-15

The potato (Solanum tuberosum L.) ranks third in worldwide consumption among food crops. Whereas disposal of potato peels poses significant challenges for the food industry, secondary metabolites in these tissues are also bioactive and essential to crop development. The diverse primary and secondary metabolites reported in whole tubers and wound-healing tissues prompted a comprehensive profiling study of native periderms from four cultivars with distinctive skin morphologies and commercial food uses. Polar and nonpolar soluble metabolites were extracted concurrently, analyzed chromatographically, and characterized with mass spectrometry; the corresponding solid interfacial polymeric residue was examined by solid-state 13 C NMR. In total, 112 secondary metabolites were found in the phellem tissues; multivariate analysis identified 10 polar and 30 nonpolar potential biomarkers that distinguish a single cultivar among Norkotah Russet, Atlantic, Chipeta, and Yukon Gold cultivars which have contrasting russeting features. Compositional trends are interpreted in the context of periderm protective function.

A cellular and regulatory map of the GABAergic nervous system of C. elegans

PubMed Central

Gendrel, Marie; Atlas, Emily G; Hobert, Oliver

2016-01-01

Neurotransmitter maps are important complements to anatomical maps and represent an invaluable resource to understand nervous system function and development. We report here a comprehensive map of neurons in the C. elegans nervous system that contain the neurotransmitter GABA, revealing twice as many GABA-positive neuron classes as previously reported. We define previously unknown glia-like cells that take up GABA, as well as 'GABA uptake neurons' which do not synthesize GABA but take it up from the extracellular environment, and we map the expression of previously uncharacterized ionotropic GABA receptors. We use the map of GABA-positive neurons for a comprehensive analysis of transcriptional regulators that define the GABA phenotype. We synthesize our findings of specification of GABAergic neurons with previous reports on the specification of glutamatergic and cholinergic neurons into a nervous system-wide regulatory map which defines neurotransmitter specification mechanisms for more than half of all neuron classes in C. elegans. DOI: http://dx.doi.org/10.7554/eLife.17686.001 PMID:27740909

Mass spectrometry-based proteomics: basic principles and emerging technologies and directions.

PubMed

Van Riper, Susan K; de Jong, Ebbing P; Carlis, John V; Griffin, Timothy J

2013-01-01

As the main catalytic and structural molecules within living systems, proteins are the most likely biomolecules to be affected by radiation exposure. Proteomics, the comprehensive characterization of proteins within complex biological samples, is therefore a research approach ideally suited to assess the effects of radiation exposure on cells and tissues. For comprehensive characterization of proteomes, an analytical platform capable of quantifying protein abundance, identifying post-translation modifications and revealing members of protein complexes on a system-wide level is necessary. Mass spectrometry (MS), coupled with technologies for sample fractionation and automated data analysis, provides such a versatile and powerful platform. In this chapter we offer a view on the current state of MS-proteomics, and focus on emerging technologies within three areas: (1) New instrumental methods; (2) New computational methods for peptide identification; and (3) Label-free quantification. These emerging technologies should be valuable for researchers seeking to better understand biological effects of radiation on living systems.

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.

PubMed

Ricketts, Christopher J; De Cubas, Aguirre A; Fan, Huihui; Smith, Christof C; Lang, Martin; Reznik, Ed; Bowlby, Reanne; Gibb, Ewan A; Akbani, Rehan; Beroukhim, Rameen; Bottaro, Donald P; Choueiri, Toni K; Gibbs, Richard A; Godwin, Andrew K; Haake, Scott; Hakimi, A Ari; Henske, Elizabeth P; Hsieh, James J; Ho, Thai H; Kanchi, Rupa S; Krishnan, Bhavani; Kwiatkowski, David J; Lui, Wembin; Merino, Maria J; Mills, Gordon B; Myers, Jerome; Nickerson, Michael L; Reuter, Victor E; Schmidt, Laura S; Shelley, C Simon; Shen, Hui; Shuch, Brian; Signoretti, Sabina; Srinivasan, Ramaprasad; Tamboli, Pheroze; Thomas, George; Vincent, Benjamin G; Vocke, Cathy D; Wheeler, David A; Yang, Lixing; Kim, William Y; Robertson, A Gordon; Spellman, Paul T; Rathmell, W Kimryn; Linehan, W Marston

2018-04-03

Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival. Published by Elsevier Inc.

Separating Bulk and Surface Contributions to Electronic Excited-State Processes in Hybrid Mixed Perovskite Thin Films via Multimodal All-Optical Imaging.

PubMed

Simpson, Mary Jane; Doughty, Benjamin; Das, Sanjib; Xiao, Kai; Ma, Ying-Zhong

2017-07-20

A comprehensive understanding of electronic excited-state phenomena underlying the impressive performance of solution-processed hybrid halide perovskite solar cells requires access to both spatially resolved electronic processes and corresponding sample morphological characteristics. Here, we demonstrate an all-optical multimodal imaging approach that enables us to obtain both electronic excited-state and morphological information on a single optical microscope platform with simultaneous high temporal and spatial resolution. Specifically, images were acquired for the same region of interest in thin films of chloride containing mixed lead halide perovskites (CH 3 NH 3 PbI 3-x Cl x ) using femtosecond transient absorption, time-integrated photoluminescence, confocal reflectance, and transmission microscopies. Comprehensive image analysis revealed the presence of surface- and bulk-dominated contributions to the various images, which describe either spatially dependent electronic excited-state properties or morphological variations across the probed region of the thin films. These results show that PL probes effectively the species near or at the film surface.

Separable processes before, during, and after the N400 elicited by previously inferred and new information: evidence from time-frequency decompositions.

PubMed

Steele, Vaughn R; Bernat, Edward M; van den Broek, Paul; Collins, Paul F; Patrick, Christopher J; Marsolek, Chad J

2013-01-25

Successful comprehension during reading often requires inferring information not explicitly presented. This information is readily accessible when subsequently encountered, and a neural correlate of this is an attenuation of the N400 event-related potential (ERP). We used ERPs and time-frequency (TF) analysis to investigate neural correlates of processing inferred information after a causal coherence inference had been generated during text comprehension. Participants read short texts, some of which promoted inference generation. After each text, they performed lexical decisions to target words that were unrelated or inference-related to the preceding text. Consistent with previous findings, inference-related words elicited an attenuated N400 relative to unrelated words. TF analyses revealed unique contributions to the N400 from activity occurring at 1-6 Hz (theta) and 0-2 Hz (delta), supporting the view that multiple, sequential processes underlie the N400. Copyright © 2012 Elsevier B.V. All rights reserved.

A comprehensive wiring diagram of the protocerebral bridge for visual information processing in the Drosophila brain.

PubMed

Lin, Chih-Yung; Chuang, Chao-Chun; Hua, Tzu-En; Chen, Chun-Chao; Dickson, Barry J; Greenspan, Ralph J; Chiang, Ann-Shyn

2013-05-30

How the brain perceives sensory information and generates meaningful behavior depends critically on its underlying circuitry. The protocerebral bridge (PB) is a major part of the insect central complex (CX), a premotor center that may be analogous to the human basal ganglia. Here, by deconstructing hundreds of PB single neurons and reconstructing them into a common three-dimensional framework, we have constructed a comprehensive map of PB circuits with labeled polarity and predicted directions of information flow. Our analysis reveals a highly ordered information processing system that involves directed information flow among CX subunits through 194 distinct PB neuron types. Circuitry properties such as mirroring, convergence, divergence, tiling, reverberation, and parallel signal propagation were observed; their functional and evolutional significance is discussed. This layout of PB neuronal circuitry may provide guidelines for further investigations on transformation of sensory (e.g., visual) input into locomotor commands in fly brains. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Classical test theory and Rasch analysis validation of the Upper Limb Functional Index in subjects with upper limb musculoskeletal disorders.

PubMed

Bravini, Elisabetta; Franchignoni, Franco; Giordano, Andrea; Sartorio, Francesco; Ferriero, Giorgio; Vercelli, Stefano; Foti, Calogero

2015-01-01

To perform a comprehensive analysis of the psychometric properties and dimensionality of the Upper Limb Functional Index (ULFI) using both classical test theory and Rasch analysis (RA). Prospective, single-group observational design. Freestanding rehabilitation center. Convenience sample of Italian-speaking subjects with upper limb musculoskeletal disorders (N=174). Not applicable. The Italian version of the ULFI. Data were analyzed using parallel analysis, exploratory factor analysis, and RA for evaluating dimensionality, functioning of rating scale categories, item fit, hierarchy of item difficulties, and reliability indices. Parallel analysis revealed 2 factors explaining 32.5% and 10.7% of the response variance. RA confirmed the failure of the unidimensionality assumption, and 6 items out of the 25 misfitted the Rasch model. When the analysis was rerun excluding the misfitting items, the scale showed acceptable fit values, loading meaningfully to a single factor. Item separation reliability and person separation reliability were .98 and .89, respectively. Cronbach alpha was .92. RA revealed weakness of the scale concerning dimensionality and internal construct validity. However, a set of 19 ULFI items defined through the statistical process demonstrated a unidimensional structure, good psychometric properties, and clinical meaningfulness. These findings represent a useful starting point for further analyses of the tool (based on modern psychometric approaches and confirmatory factor analysis) in larger samples, including different patient populations and nationalities. Copyright © 2015 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Comprehensive School Reform and Student Achievement: A Meta-Analysis.

ERIC Educational Resources Information Center

Borman, Geoffrey D.; Hewes, Gina M.; Overman, Laura T.; Brown, Shelly

Using 232 studies, this meta analysis reviewed the research on the achievement effects of the nationally disseminated and externally developed school improvement programs known as "whole-school" or "comprehensive" reforms. In addition to reviewing the overall achievement effects of comprehensive school reform (CSR), the meta…

Comprehension of synthetic speech and digitized natural speech by adults with aphasia.

PubMed

Hux, Karen; Knollman-Porter, Kelly; Brown, Jessica; Wallace, Sarah E

2017-09-01

Using text-to-speech technology to provide simultaneous written and auditory content presentation may help compensate for chronic reading challenges if people with aphasia can understand synthetic speech output; however, inherent auditory comprehension challenges experienced by people with aphasia may make understanding synthetic speech difficult. This study's purpose was to compare the preferences and auditory comprehension accuracy of people with aphasia when listening to sentences generated with digitized natural speech, Alex synthetic speech (i.e., Macintosh platform), or David synthetic speech (i.e., Windows platform). The methodology required each of 20 participants with aphasia to select one of four images corresponding in meaning to each of 60 sentences comprising three stimulus sets. Results revealed significantly better accuracy given digitized natural speech than either synthetic speech option; however, individual participant performance analyses revealed three patterns: (a) comparable accuracy regardless of speech condition for 30% of participants, (b) comparable accuracy between digitized natural speech and one, but not both, synthetic speech option for 45% of participants, and (c) greater accuracy with digitized natural speech than with either synthetic speech option for remaining participants. Ranking and Likert-scale rating data revealed a preference for digitized natural speech and David synthetic speech over Alex synthetic speech. Results suggest many individuals with aphasia can comprehend synthetic speech options available on popular operating systems. Further examination of synthetic speech use to support reading comprehension through text-to-speech technology is thus warranted. Copyright © 2017 Elsevier Inc. All rights reserved.

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, T.A.; Holmes, S.; Alekseyenko, A.V.

Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositionalmore » difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.« less

Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation

PubMed Central

Zhang, Yong; Gu, Lianfeng; Hou, Yifeng; Wang, Lulu; Deng, Xian; Hang, Runlai; Chen, Dong; Zhang, Xiansheng; Zhang, Yi; Liu, Chunyan; Cao, Xiaofeng

2015-01-01

Alternative polyadenylation (APA) is a widespread mechanism for gene regulation and has been implicated in flowering, but the molecular basis governing the choice of a specific poly(A) site during the vegetative-to-reproductive growth transition remains unclear. Here we characterize HLP1, an hnRNP A/B protein as a novel regulator for pre-mRNA 3′-end processing in Arabidopsis. Genetic analysis reveals that HLP1 suppresses Flowering Locus C (FLC), a key repressor of flowering in Arabidopsis. Genome-wide mapping of HLP1-RNA interactions indicates that HLP1 binds preferentially to A-rich and U-rich elements around cleavage and polyadenylation sites, implicating its role in 3′-end formation. We show HLP1 is significantly enriched at transcripts involved in RNA metabolism and flowering. Comprehensive profiling of the poly(A) site usage reveals that HLP1 mutations cause thousands of poly(A) site shifts. A distal-to-proximal poly(A) site shift in the flowering regulator FCA, a direct target of HLP1, leads to upregulation of FLC and delayed flowering. Our results elucidate that HLP1 is a novel factor involved in 3′-end processing and controls reproductive timing via targeting APA. PMID:26099751

Matrix factorization reveals aging-specific co-expression gene modules in the fat and muscle tissues in nonhuman primates

NASA Astrophysics Data System (ADS)

Wang, Yongcui; Zhao, Weiling; Zhou, Xiaobo

2016-10-01

Accurate identification of coherent transcriptional modules (subnetworks) in adipose and muscle tissues is important for revealing the related mechanisms and co-regulated pathways involved in the development of aging-related diseases. Here, we proposed a systematically computational approach, called ICEGM, to Identify the Co-Expression Gene Modules through a novel mathematical framework of Higher-Order Generalized Singular Value Decomposition (HO-GSVD). ICEGM was applied on the adipose, and heart and skeletal muscle tissues in old and young female African green vervet monkeys. The genes associated with the development of inflammation, cardiovascular and skeletal disorder diseases, and cancer were revealed by the ICEGM. Meanwhile, genes in the ICEGM modules were also enriched in the adipocytes, smooth muscle cells, cardiac myocytes, and immune cells. Comprehensive disease annotation and canonical pathway analysis indicated that immune cells, adipocytes, cardiomyocytes, and smooth muscle cells played a synergistic role in cardiac and physical functions in the aged monkeys by regulation of the biological processes associated with metabolism, inflammation, and atherosclerosis. In conclusion, the ICEGM provides an efficiently systematic framework for decoding the co-expression gene modules in multiple tissues. Analysis of genes in the ICEGM module yielded important insights on the cooperative role of multiple tissues in the development of diseases.

Valorisation of chicken feathers: Characterisation of chemical properties.

PubMed

Tesfaye, Tamrat; Sithole, Bruce; Ramjugernath, Deresh; Chunilall, Viren

2017-10-01

The characterisation of the chemical properties of the whole chicken feather and its fractions (barb and rachis), was undertaken to identify opportunities for valorizing this waste product. The authors have described the physical, morphological, mechanical, electrical and thermal properties of the chicken feathers and related them to potential valorisation routes of the waste. However, identification of their chemical properties is necessary to complete a comprehensive description of chicken feather fractions. Hence, the chicken feathers were thoroughly characterised by proximate and ultimate analyses, elemental composition, spectroscopic analyses, durability in different solvents, burning test, and hydrophobicity. The proximate analysis of chicken feathers revealed the following compositions: crude lipid (0.83%), crude fibre (2.15%), crude protein (82.36%), ash (1.49%), NFE (1.02%) and moisture content (12.33%) whereas the ultimate analyses showed: carbon (64.47%), nitrogen (10.41%), oxygen (22.34%), and sulphur (2.64%). FTIR analysis revealed that the chicken feather fractions contain amide and carboxylic groups indicative of proteinious functional groups; XRD showed a crystallinity index of 22. Durability and burning tests confirmed that feathers behaved similarly to animal fibre. This reveals that chicken feather can be a valuable raw material in textile, plastic, cosmetics, pharmaceuticals, biomedical and bioenergy industries. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamic metabolome profiling reveals significant metabolic changes during grain development of bread wheat (Triticum aestivum L.).

PubMed

Zhen, Shoumin; Dong, Kun; Deng, Xiong; Zhou, Jiaxing; Xu, Xuexin; Han, Caixia; Zhang, Wenying; Xu, Yanhao; Wang, Zhimin; Yan, Yueming

2016-08-01

Metabolites in wheat grains greatly influence nutritional values. Wheat provides proteins, minerals, B-group vitamins and dietary fiber to humans. These metabolites are important to human health. However, the metabolome of the grain during the development of bread wheat has not been studied so far. In this work the first dynamic metabolome of the developing grain of the elite Chinese bread wheat cultivar Zhongmai 175 was analyzed, using non-targeted gas chromatography/mass spectrometry (GC/MS) for metabolite profiling. In total, 74 metabolites were identified over the grain developmental stages. Metabolite-metabolite correlation analysis revealed that the metabolism of amino acids, carbohydrates, organic acids, amines and lipids was interrelated. An integrated metabolic map revealed a distinct regulatory profile. The results provide information that can be used by metabolic engineers and molecular breeders to improve wheat grain quality. The present metabolome approach identified dynamic changes in metabolite levels, and correlations among such levels, in developing seeds. The comprehensive metabolic map may be useful when breeding programs seek to improve grain quality. The work highlights the utility of GC/MS-based metabolomics, in conjunction with univariate and multivariate data analysis, when it is sought to understand metabolic changes in developing seeds. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

DGCA: A comprehensive R package for Differential Gene Correlation Analysis.

PubMed

McKenzie, Andrew T; Katsyv, Igor; Song, Won-Min; Wang, Minghui; Zhang, Bin

2016-11-15

Dissecting the regulatory relationships between genes is a critical step towards building accurate predictive models of biological systems. A powerful approach towards this end is to systematically study the differences in correlation between gene pairs in more than one distinct condition. In this study we develop an R package, DGCA (for Differential Gene Correlation Analysis), which offers a suite of tools for computing and analyzing differential correlations between gene pairs across multiple conditions. To minimize parametric assumptions, DGCA computes empirical p-values via permutation testing. To understand differential correlations at a systems level, DGCA performs higher-order analyses such as measuring the average difference in correlation and multiscale clustering analysis of differential correlation networks. Through a simulation study, we show that the straightforward z-score based method that DGCA employs significantly outperforms the existing alternative methods for calculating differential correlation. Application of DGCA to the TCGA RNA-seq data in breast cancer not only identifies key changes in the regulatory relationships between TP53 and PTEN and their target genes in the presence of inactivating mutations, but also reveals an immune-related differential correlation module that is specific to triple negative breast cancer (TNBC). DGCA is an R package for systematically assessing the difference in gene-gene regulatory relationships under different conditions. This user-friendly, effective, and comprehensive software tool will greatly facilitate the application of differential correlation analysis in many biological studies and thus will help identification of novel signaling pathways, biomarkers, and targets in complex biological systems and diseases.

Predictors of Reading Comprehension for Struggling Readers: The Case of Spanish-speaking Language Minority Learners.

PubMed

Mancilla-Martinez, Jeannette; Lesaux, Nonie K

2010-08-01

This longitudinal study examined the process of English reading comprehension at age 11 for 173 low achieving Spanish-speaking children. The influence of growth rates, from early childhood (age 4.5) to pre-adolescence (age 11), in vocabulary and word reading skills on this complex process were evaluated using structural equation modeling. Standardized measures of word reading accuracy and productive vocabulary were administered annually, in English and Spanish, and English reading comprehension measures were administered at age 11. Latent growth curve analyses revealed that English skills accounted for all unique variance in English reading comprehension outcomes. Further, expected developmental shifts in the influence of word reading and vocabulary skills over time were not shown, likely on account of students' below grade level reading comprehension achievement. This work underscores the need for theoretical models of comprehension to account for students' skill profiles and abilities.

Predictors of Reading Comprehension for Struggling Readers: The Case of Spanish-speaking Language Minority Learners

PubMed Central

Mancilla-Martinez, Jeannette; Lesaux, Nonie K.

2010-01-01

This longitudinal study examined the process of English reading comprehension at age 11 for 173 low achieving Spanish-speaking children. The influence of growth rates, from early childhood (age 4.5) to pre-adolescence (age 11), in vocabulary and word reading skills on this complex process were evaluated using structural equation modeling. Standardized measures of word reading accuracy and productive vocabulary were administered annually, in English and Spanish, and English reading comprehension measures were administered at age 11. Latent growth curve analyses revealed that English skills accounted for all unique variance in English reading comprehension outcomes. Further, expected developmental shifts in the influence of word reading and vocabulary skills over time were not shown, likely on account of students’ below grade level reading comprehension achievement. This work underscores the need for theoretical models of comprehension to account for students’ skill profiles and abilities. PMID:20856691

Comprehensive analysis of polar and apolar constituents of butter and margarine by nuclear magnetic resonance, reflecting quality and production processes.

PubMed

Schripsema, Jan

2008-04-23

The separation of butter or margarine into polar (soluble in water) and apolar fractions (soluble in chloroform) and subsequent analysis of these fractions by (1)H NMR permits a comprehensive analysis of its constituents. In the polar fraction the preservatives benzoic and sorbic acid, the organic acids citric, lactic, butyric, acetic, and formic acid, and, furthermore, the carbohydrate lactose were quantified. In the apolar fraction the conjugated linoleic acid (CLA) rumenic acid, diglycerides, and linoleic acid were quantified. Rumenic acid is a characteristic component of ruminant fats and was found in all butter samples. The levels varied between 0.50 and 1.08%. Ten brands of Brazilian butter were investigated as was one brand from Norway. Also, two brands of margarine were investigated for comparison. A large variation in especially polar constituents was found between the butter samples, revealing the presence of preservatives in five brands of butter from Brazil, remarkable because these additives are legally not allowed. Furthermore, the levels of organic acids and lactose permitted conclusions about the production process and quality; for example, the presence of higher levels of free butyric acid indicate lipolysis, leading to a lower quality, and low levels of lactose indicate that after churning the residual milk fluids have been removed by an additional washing step in the production process.

The unique role of executive function skills in predicting Hong Kong kindergarteners' reading comprehension.

PubMed

Liu, Yingyi; Sun, Huilin; Lin, Dan; Li, Hong; Yeung, Susanna Siu-Sze; Wong, Terry Tin-Yau

2018-01-15

Word reading and linguistic comprehension skills are two crucial components in reading comprehension, according to the Simple View of Reading (SVR). Some researchers have posited that a third component should be involved in reading and understanding texts, namely executive function (EF) skills. This study was novel in two ways. Not only did we tested EF skills as a predictor of reading comprehension in a non-alphabetic language (i.e., Chinese) to extend the theoretical model of SVR, we also examined reading comprehension further in kindergarten children (age 5) in Hong Kong, in the attempt to reveal possible early precursors of reading comprehension. A group of 170 K3 kindergarteners was recruited in Hong Kong. Children's word reading was assessed. Their linguistic comprehension was assessed with phonological awareness, verbal short-term memory, and vocabulary knowledge. Using a structured observation task, Head-Toes-Knees-Shoulders (HTKS), we measured their composite scores for EF skills. Head-Toes-Knees-Shoulders performance predicted unique variance in children's Chinese reading comprehension concurrently beyond word reading and a set of linguistic comprehension skills. The results highlight the important role of EF skills in beginning readers' reading comprehension. © 2018 The British Psychological Society.

Transcriptional Network Analysis in Muscle Reveals AP-1 as a Partner of PGC-1α in the Regulation of the Hypoxic Gene Program

PubMed Central

Baresic, Mario; Salatino, Silvia; Kupr, Barbara

2014-01-01

Skeletal muscle tissue shows an extraordinary cellular plasticity, but the underlying molecular mechanisms are still poorly understood. Here, we use a combination of experimental and computational approaches to unravel the complex transcriptional network of muscle cell plasticity centered on the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α), a regulatory nexus in endurance training adaptation. By integrating data on genome-wide binding of PGC-1α and gene expression upon PGC-1α overexpression with comprehensive computational prediction of transcription factor binding sites (TFBSs), we uncover a hitherto-underestimated number of transcription factor partners involved in mediating PGC-1α action. In particular, principal component analysis of TFBSs at PGC-1α binding regions predicts that, besides the well-known role of the estrogen-related receptor α (ERRα), the activator protein 1 complex (AP-1) plays a major role in regulating the PGC-1α-controlled gene program of the hypoxia response. Our findings thus reveal the complex transcriptional network of muscle cell plasticity controlled by PGC-1α. PMID:24912679

Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile.

PubMed

Qi, Xiao-Hua; Xu, Xue-Wen; Lin, Xiao-Jian; Zhang, Wen-Jie; Chen, Xue-Hao

2012-03-01

High-throughput tag-sequencing (Tag-seq) analysis based on the Solexa Genome Analyzer platform was applied to analyze the gene expression profiling of cucumber plant at 5 time points over a 24h period of waterlogging treatment. Approximately 5.8 million total clean sequence tags per library were obtained with 143013 distinct clean tag sequences. Approximately 23.69%-29.61% of the distinct clean tags were mapped unambiguously to the unigene database, and 53.78%-60.66% of the distinct clean tags were mapped to the cucumber genome database. Analysis of the differentially expressed genes revealed that most of the genes were down-regulated in the waterlogging stages, and the differentially expressed genes mainly linked to carbon metabolism, photosynthesis, reactive oxygen species generation/scavenging, and hormone synthesis/signaling. Finally, quantitative real-time polymerase chain reaction using nine genes independently verified the tag-mapped results. This present study reveals the comprehensive mechanisms of waterlogging-responsive transcription in cucumber. Copyright © 2011 Elsevier Inc. All rights reserved.

Residual disease at the bronchial stump is positively associated with the risk of bronchoplerual fistula in patients undergoing lung cancer surgery: a meta-analysis

PubMed Central

Li, Shuangjiang; Fan, Jun; Zhou, Jian; Ren, Yutao; Shen, Cheng; Che, Guowei

2016-01-01

OBJECTIVES Residual disease at the bronchial stump (RDBS) is regarded as an important factor possibly resulting in bronchopleural fistula (BPF) after lung cancer surgery, but this has not been confirmed. We conducted this meta-analysis to evaluate the effects of RDBS on BPF formation in patients undergoing lung cancer surgery. METHODS PubMed and EMBASE databases were searched for full-text articles that met our eligibility criteria. Odds ratios (ORs) with 95% confidence interval (95% CI) served as the summarized outcomes. Q-test and I2 statistic were used to evaluate the level of heterogeneity, determining the fixed-effect model or random-effect model for quantitative synthesis. Sensitivity analysis was conducted to identify the possible origins of heterogeneity. The publication bias was assessed by Begg's test. RESULTS A total of eight retrospective observational studies were included in our meta-analysis. In overall analysis, the pooled outcomes indicated that RDBS was significantly associated with BPF formation after lung cancer surgery (OR: 3.12; 95% CI: 1.72–5.64; P < 0.001). In subgroup analysis, the pooled outcomes revealed a significantly increased risk of post-pneumonectomy BPF in patients with RDBS (OR: 2.78; 95% CI: 1.06–7.28; P = 0.037). The subgroup analysis assessing the effects of RDBS on post-lobectomy BPF was given up due to the scarcity of available data. No heterogeneity was revealed within this meta-analysis. No evidence for publication bias was detected by Begg's test. CONCLUSIONS Our meta-analysis indicates that RDBS is positively associated with the increased risk of BPF in patients undergoing lung cancer surgery. The further analysis also reveals an increased risk of post-pneumonectomy BPF in patients with RDBS. More accurate and comprehensive evidence should be collected and summarized in updated meta-analyses. PMID:26614527

Impact of comprehensive two-dimensional gas chromatography with mass spectrometry on food analysis.

PubMed

Tranchida, Peter Q; Purcaro, Giorgia; Maimone, Mariarosa; Mondello, Luigi

2016-01-01

Comprehensive two-dimensional gas chromatography with mass spectrometry has been on the separation-science scene for about 15 years. This three-dimensional method has made a great positive impact on various fields of research, and among these that related to food analysis is certainly at the forefront. The present critical review is based on the use of comprehensive two-dimensional gas chromatography with mass spectrometry in the untargeted (general qualitative profiling and fingerprinting) and targeted analysis of food volatiles; attention is focused not only on its potential in such applications, but also on how recent advances in comprehensive two-dimensional gas chromatography with mass spectrometry will potentially be important for food analysis. Additionally, emphasis is devoted to the many instances in which straightforward gas chromatography with mass spectrometry is a sufficiently-powerful analytical tool. Finally, possible future scenarios in the comprehensive two-dimensional gas chromatography with mass spectrometry food analysis field are discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Personalized comprehensive molecular profiling of high risk osteosarcoma: Implications and limitations for precision medicine.

PubMed

Subbiah, Vivek; Wagner, Michael J; McGuire, Mary F; Sarwari, Nawid M; Devarajan, Eswaran; Lewis, Valerae O; Westin, Shanon; Kato, Shumei; Brown, Robert E; Anderson, Pete

2015-12-01

Despite advances in molecular medicine over recent decades, there has been little advancement in the treatment of osteosarcoma. We performed comprehensive molecular profiling in two cases of metastatic and chemotherapy-refractory osteosarcoma to guide molecularly targeted therapy. Hybridization capture of >300 cancer-related genes plus introns from 28 genes often rearranged or altered in cancer was applied to >50 ng of DNA extracted from tumor samples from two patients with recurrent, metastatic osteosarcoma. The DNA from each sample was sequenced to high, uniform coverage. Immunohistochemical probes and morphoproteomics analysis were performed, in addition to fluorescence in situ hybridization. All analyses were performed in CLIA-certified laboratories. Molecularly targeted therapy based on the resulting profiles was offered to the patients. Biomedical analytics were performed using QIAGEN's Ingenuity® Pathway Analysis. In Patient #1, comprehensive next-generation exome sequencing showed MET amplification, PIK3CA mutation, CCNE1 amplification, and PTPRD mutation. Immunohistochemistry-based morphoproteomic analysis revealed c-Met expression [(p)-c-Met (Tyr1234/1235)] and activation of mTOR/AKT pathway [IGF-1R (Tyr1165/1166), p-mTOR [Ser2448], p-Akt (Ser473)] and expression of SPARC and COX2. Targeted therapy was administered to match the P1K3CA, c-MET, and SPARC and COX2 aberrations with sirolimus+ crizotinib and abraxane+ celecoxib. In Patient #2, aberrations included NF2 loss in exons 2-16, PDGFRα amplification, and TP53 mutation. This patient was enrolled on a clinical trial combining targeted agents temsirolimus, sorafenib and bevacizumab, to match NF2, PDGFRα and TP53 aberrations. Both the patients did not benefit from matched therapy. Relapsed osteosarcoma is characterized by complex signaling and drug resistance pathways. Comprehensive molecular profiling holds great promise for tailoring personalized therapies for cancer. Methods for such profiling are evolving and need to be refined to better assist clinicians in making treatment decisions based on the large amount of data that results from this type of testing. Further research in this area is warranted.

Does mood influence text processing and comprehension? Evidence from an eye-movement study.

PubMed

Scrimin, Sara; Mason, Lucia

2015-09-01

Previous research has indicated that mood influences cognitive processes. However, there is scarce data regarding the link between everyday emotional states and readers' text processing and comprehension. We aim to extend current research on the effects of mood induction on science text processing and comprehension, using eye-tracking methodology. We investigated whether a positive-, negative-, and neutral-induced mood influences online processing, as revealed by indices of visual behaviour during reading, and offline text comprehension, as revealed by post-test questions. We were also interested in the link between text processing and comprehension. Seventy-eight undergraduate students randomly assigned to three mood-induction conditions. Students were mood-induced by watching a video clip. They were then asked to read a scientific text while eye movements were registered. Pre- and post-reading knowledge was assessed through open-ended questions. Experimentally induced moods lead readers to process an expository text differently. Overall, students in a positive mood spent significantly longer on the text processing than students in the negative and neutral moods. Eye-movement patterns indicated more effective processing related to longer proportion of look-back fixation times in positive-induced compared with negative-induced readers. Students in a positive mood also comprehended the text better, learning more factual knowledge, compared with students in the negative group. Only for the positive-induced readers did the more purposeful second-pass reading positively predict text comprehension. New insights are given on the effects of normal mood variations and students' text processing and comprehension by the use of eye-tracking methodology. Important implications for the role of emotional states in educational settings are highlighted. © 2015 The British Psychological Society.

Instruction of Research-Based Comprehension Strategies in Basal Reading Programs

ERIC Educational Resources Information Center

Pilonieta, Paola

2010-01-01

Research supports using research-based comprehension strategies; however, comprehension strategy instruction is not highly visible in basal reading programs or classroom instruction, resulting in many students who struggle with comprehension. A content analysis examined which research-based comprehension strategies were presented in five…

Comprehensive analysis of mutations in the hepatitis delta virus genome based on full-length sequencing in a nationwide cohort study and evolutionary pattern during disease progression.

PubMed

Shirvani-Dastgerdi, E; Amini-Bavil-Olyaee, S; Alavian, S Moayed; Trautwein, C; Tacke, F

2015-05-01

Delta hepatitis, caused by co-infection or super-infection of hepatitis D virus (HDV) in hepatitis B virus (HBV) -infected patients, is the most severe form of chronic hepatitis, often progressing to liver cirrhosis and liver failure. Although 15 million individuals are affected worldwide, molecular data on the HDV genome and its proteins, small and large delta antigen (S-/L-HDAg), are limited. We therefore conducted a nationwide study in HBV-HDV-infected patients from Iran and successfully amplified 38 HDV full genomes and 44 L-HDAg sequences from 34 individuals. Phylogenetic analyses of full-length HDV and L-HDAg isolates revealed that all strains clustered with genotype 1 and showed high genotypic distances to HDV genotypes 2 to 8, with a maximal distance to genotype 3. Longitudinal analyses in individual patients indicated a reverse evolutionary trend, especially in L-HDAg amino acid composition, over time. Besides multiple sequence variations in the hypervariable region of HDV, nucleotide substitutions preferentially occurred in the stabilizing P4 domain of the HDV ribozyme. A high rate of single amino acid changes was detected in structural parts of L-HDAg, whereas its post-translational modification sites were highly conserved. Interestingly, several non-synonymous mutations were positively selected that affected immunogenic epitopes of L-HDAg towards CD8 T-cell- and B-cell-driven immune responses. Hence, our comprehensive molecular analysis comprising a nationwide cohort revealed phylogenetic relationships and provided insight into viral evolution within individual hosts. Moreover, preferential areas of frequent mutations in the HDV ribozyme and antigen protein were determined in this study. Copyright © 2014 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Use of elemental and molecular-mass spectrometry to assess the toxicological effects of inorganic mercury in the mouse Mus musculus.

PubMed

García-Sevillano, Miguel Angel; García-Barrera, Tamara; Navarro, Francisco; Gailer, Jürgen; Gómez-Ariza, José Luiz

2014-09-01

The biochemical response of mice (Mus musculus) to acute subcutaneous inorganic-mercury exposure was assessed over a 14-day period by analyzing cytosolic extracts of the liver, the kidneys, and blood plasma. Integrated metallomic and metabolomic approaches using elemental and molecular-mass spectrometry were used to obtain comprehensive insight into the toxicological effects of mercury regarding its distribution and possible perturbation of metabolic pathways. The metallomic approach involved the use of size-exclusion chromatography (SEC) coupled with multiaffinity chromatography inductively coupled plasma-mass spectrometry (ICP-MS) and isotopic-dilution analysis. The metabolomic approach involved the direct infusion of polar and lipophilic tissue extracts into a mass spectrometer (DIMS) in the positive and negative acquisition mode (ESI+and ESI-). The use of SEC-ICP-MS enabled us to detect changes in the metalloproteome in the liver and the kidneys during the exposure period, and revealed that interactions between Hg and endogenous Cu and Zn adversely affected the homeostasis of these essential metals. The detection of an Hg-Se detoxification product in mouse plasma substantiated the known interaction between Hg and Se in mammals. Use of DIMS in conjunction with partial-least-squares discriminant analysis (PLS-DA) uncovered time-dependent changes of endogenous metabolites over time, corroborated by histopathology investigation of specific mouse tissues. The perturbations of endogenous metabolic profiles were explained in terms of the adverse effect of mercury on energy metabolism (e.g. glycolysis, Krebs cycle), the degradation of membrane phospholipids (apoptosis), and increased levels of specific lipids in plasma. In summary, use of an SEC-ICP-MS-based metallomics approach in conjunction with molecular-mass-spectrometry-based metabolomics is revealed as a promising strategy to more comprehensively investigate the toxicological effects of harmful environmental pollutants and xenobiotics.

Comprehensive rotorcraft analysis methods

NASA Technical Reports Server (NTRS)

Stephens, Wendell B.; Austin, Edward E.

1988-01-01

The development and application of comprehensive rotorcraft analysis methods in the field of rotorcraft technology are described. These large scale analyses and the resulting computer programs are intended to treat the complex aeromechanical phenomena that describe the behavior of rotorcraft. They may be used to predict rotor aerodynamics, acoustic, performance, stability and control, handling qualities, loads and vibrations, structures, dynamics, and aeroelastic stability characteristics for a variety of applications including research, preliminary and detail design, and evaluation and treatment of field problems. The principal comprehensive methods developed or under development in recent years and generally available to the rotorcraft community because of US Army Aviation Research and Technology Activity (ARTA) sponsorship of all or part of the software systems are the Rotorcraft Flight Simulation (C81), Dynamic System Coupler (DYSCO), Coupled Rotor/Airframe Vibration Analysis Program (SIMVIB), Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics (CAMRAD), General Rotorcraft Aeromechanical Stability Program (GRASP), and Second Generation Comprehensive Helicopter Analysis System (2GCHAS).

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

PubMed Central

Reguly, Teresa; Breitkreutz, Ashton; Boucher, Lorrie; Breitkreutz, Bobby-Joe; Hon, Gary C; Myers, Chad L; Parsons, Ainslie; Friesen, Helena; Oughtred, Rose; Tong, Amy; Stark, Chris; Ho, Yuen; Botstein, David; Andrews, Brenda; Boone, Charles; Troyanskya, Olga G; Ideker, Trey; Dolinski, Kara; Batada, Nizar N; Tyers, Mike

2006-01-01

Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. Results We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID () and SGD () databases. Conclusion Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks. PMID:16762047

A Single and Comprehensive Helios Data Archive

NASA Astrophysics Data System (ADS)

Salem, C. S.

2017-12-01

Helios 1 & 2 rank amoung the most important missions in Heliophysics, and the more-than 11 years of data returned by its spacecraft remain of paramount interests to researchers. Their unique trajectories which brought them closer to the Sun than any spaceccraft before or since, enabled their diverse suite of in-situ instruments to return measurements of unprecedented scientific richness. There is however no comprehensive public repository of all Helios in-situ data. Currently, most of the highest resolution data can be obtained from a variety of places, although highly processed and with very little documentation, especially on calibration. Analysis of this data set requires overcoming a number of technical and instrumental issues, knowledge and expertise of which is only possessed by the original PI's of the Helios experiments. We present here a work funded by NASA of aggregating, analyzing, evaluating, documenting and archiving the available Helios 1 and 2 in-situ data. This work at the UC Berkeley Space Sciences Laboratory is being undertaken in close collaboration with colleagues at the University of Koln, at the University of Kiel, at the Imperial College in London and at the Paris Observatory. A careful, detailed, analysis of the Helios fluxgate and search coil magnetic field data as well as plasma data has revealed numerous issues and problems with the available, processed, datasets, that we are still working to solve. We anticipate this comprehensive single archive of all Helios in-situ data, beyond its inherent scientific value, will also be an invaluable asset to the both the Solar Probe Plus and Solar Orbiter missions.

Genetic analysis of Chinese families reveals a novel truncation allele of the retinitis pigmentosa GTPase regulator gene

PubMed Central

Hu, Fang; Zeng, Xiang-Yun; Liu, Lin-Lin; Luo, Yao-Ling; Jiang, Yi-Ping; Wang, Hui; Xie, Jing; Hu, Cheng-Quan; Gan, Lin; Huang, Liang

2014-01-01

AIM To make comprehensive molecular diagnosis for retinitis pigmentosa (RP) patients in a consanguineous Han Chinese family using next generation sequencing based Capture-NGS screen technology. METHODS A five-generation Han Chinese family diagnosed as non-syndromic X-linked recessive RP (XLRP) was recruited, including four affected males, four obligate female carriers and eleven unaffected family members. Capture-NGS was performed using a custom designed capture panel covers 163 known retinal disease genes including 47 RP genes, followed by the validation of detected mutation using Sanger sequencing in all recruited family members. RESULTS Capture-NGS in one affected 47-year-old male reveals a novel mutation, c.2417_2418insG:p.E806fs, in exon ORF15 of RP GTPase regulator (RPGR) gene results in a frameshift change that results in a premature stop codon and a truncated protein product. The mutation was further validated in three of four affected males and two of four female carriers but not in the other unaffected family members. CONCLUSION We have identified a novel mutation, c.2417_2418insG:p.E806fs, in a Han Chinese family with XLRP. Our findings expand the mutation spectrum of RPGR and the phenotypic spectrum of XLRP in Han Chinese families, and confirms Capture-NGS could be an effective and economic approach for the comprehensive molecular diagnosis of RP. PMID:25349787

Expression of uncharacterized male germ cell-specific genes and discovery of novel sperm-tail proteins in mice.

PubMed

Kwon, Jun Tae; Ham, Sera; Jeon, Suyeon; Kim, Youil; Oh, Seungmin; Cho, Chunghee

2017-01-01

The identification and characterization of germ cell-specific genes are essential if we hope to comprehensively understand the mechanisms of spermatogenesis and fertilization. Here, we searched the mouse UniGene databases and identified 13 novel genes as being putatively testis-specific or -predominant. Our in silico and in vitro analyses revealed that the expressions of these genes are testis- and germ cell-specific, and that they are regulated in a stage-specific manner during spermatogenesis. We generated antibodies against the proteins encoded by seven of the genes to facilitate their characterization in male germ cells. Immunoblotting and immunofluorescence analyses revealed that one of these proteins was expressed only in testicular germ cells, three were expressed in both testicular germ cells and testicular sperm, and the remaining three were expressed in sperm of the testicular stages and in mature sperm from the epididymis. Further analysis of the latter three proteins showed that they were all associated with cytoskeletal structures in the sperm flagellum. Among them, MORN5, which is predicted to contain three MORN motifs, is conserved between mouse and human sperm. In conclusion, we herein identify 13 authentic genes with male germ cell-specific expression, and provide comprehensive information about these genes and their encoded products. Our finding will facilitate future investigations into the functional roles of these novel genes in spermatogenesis and sperm functions.

Fixed Route Comprehensive Operational Analysis, 1994 Operating Year. Fourth Installment Route 3: Mill Ridge/Mill Plain Analysis

DOT National Transportation Integrated Search

1995-05-01

In October, of 1992, the Housatonic Area Regional Transit (HART) District published a planning study providing an in-depth analysis of its fixed route bus transit service. This comprehensive operational analysis (COA) was the first detailed analysis ...

Fixed Route Comprehensive Operational Analysis, 1994 Operating Year. First Installment, Route 1: Medical Center/Golden Hill Analysis

DOT National Transportation Integrated Search

1994-07-01

In October, of 1992, the Housatonic Area Regional Transit (HART) District published a planning study providing an in-depth analysis of its fixed route bus transit service. This comprehensive operational analysis (COA) was the first detailed analysis ...

Fixed Route Comprehensive Operational Analysis, 1994 Operating Year. Third Installment, Route 6: Lake Avenue/Danbury Fair Mall Analysis

DOT National Transportation Integrated Search

1995-02-01

In October, of 1992, the Housatonic Area Regional Transit (HART) District published a planning study providing an in-depth analysis of its fixed route bus transit service. This comprehensive operational analysis (COA) was the first detailed analysis ...

Analyzing Remodeling of Cardiac Tissue: A Comprehensive Approach Based on Confocal Microscopy and 3D Reconstructions

PubMed Central

Sachse, F. B.

2015-01-01

Microstructural characterization of cardiac tissue and its remodeling in disease is a crucial step in many basic research projects. We present a comprehensive approach for three-dimensional characterization of cardiac tissue at the submicrometer scale. We developed a compression-free mounting method as well as labeling and imaging protocols that facilitate acquisition of three-dimensional image stacks with scanning confocal microscopy. We evaluated the approach with normal and infarcted ventricular tissue. We used the acquired image stacks for segmentation, quantitative analysis and visualization of important tissue components. In contrast to conventional mounting, compression-free mounting preserved cell shapes, capillary lumens and extracellular laminas. Furthermore, the new approach and imaging protocols resulted in high signal-to-noise ratios at depths up to 60 μm. This allowed extensive analyses revealing major differences in volume fractions and distribution of cardiomyocytes, blood vessels, fibroblasts, myofibroblasts and extracellular space in control versus infarct border zone. Our results show that the developed approach yields comprehensive data on microstructure of cardiac tissue and its remodeling in disease. In contrast to other approaches, it allows quantitative assessment of all major tissue components. Furthermore, we suggest that the approach will provide important data for physiological models of cardiac tissue at the submicrometer scale. PMID:26399990

The neural basis of reversible sentence comprehension: Evidence from voxel-based lesion-symptom mapping in aphasia

PubMed Central

Thothathiri, Malathi; Kimberg, Daniel Y.; Schwartz, Myrna F.

2012-01-01

We explored the neural basis of reversible sentence comprehension in a large group of aphasic patients (N=79). Voxel-based lesion-symptom mapping revealed a significant association between damage in temporoparietal cortex and impaired sentence comprehension. This association remained after we controlled for phonological working memory. We hypothesize that this region plays an important role in the thematic or what-where processing of sentences. In contrast, we detected weak or no association between reversible sentence comprehension and the ventrolateral prefrontal cortex, which includes Broca’s area, even for syntactically complex sentences. This casts doubt on theories that presuppose a critical role for this region in syntactic computations. PMID:21861679

Comprehensive analysis of organic ligands in whole root exudates using nuclear magnetic resonance and gas chromatography-mass spectrometry.

PubMed

Fan, T W; Lane, A N; Pedler, J; Crowley, D; Higashi, R M

1997-08-15

Root exudates in the rhizosphere are vital to the normal life cycle of plants. A key factor is phytometallophores, which function in the nutritional acquisition of iron and zinc and are likely to be important in the uptake of pollutant metals by plants. Unraveling the biochemistry of these compounds is tedious using traditional analyses, which also fall short in providing the overall chemical composition or in detecting unknown or unexpected organic ligands in the exudates. Here, we demonstrate a comprehensive analysis of the exudate composition directly by 1H and 13C multidimensional NMR and silylation GC-MS. The advantages are (a) minimal sample preparation, with no loss of unknown compounds, and reduced net analysis time; (b) structure-based analysis for universal detection and identification; and (c) simultaneous analysis of a large number of constituents in a complex mixture. Using barley root exudates, a large number of common organic and amino acids were identified. Three derivatives of mugineic acid phytosiderophores were also determined, the major one being 3-epihydroxymugineic acid, for which complete 1H and 13C NMR assignments were obtained. Quantification of all major components using these methods revealed a sevenfold increase in total exudation under moderate iron deficiency, with 3-epihydroxymugineic acid comprising approximately 22% of the exudate mixture. As iron deficiency increased, total quantities of exudate per gram of root remained unchanged, but the relative quantity of carbon allocated to phytosiderophore increased to approximately 50% of the total exudate in response to severe iron deficiency.

Exploring the Effects of Digital Note Taking on Student Comprehension of Science Texts

ERIC Educational Resources Information Center

Horney, Mark A.; Anderson-Inman, Lynne; Terra, Fatima

2009-01-01

This study investigated the effects of text notes and voice notes on the comprehension of science texts by fifth grade students. The study was conducted to determine whether digital note taking was an effective reading strategy, and whether one form of digital note taking was more effective than the other. Results revealed that general education…

The Use of Help Options in Multimedia Listening Environments to Aid Language Learning: A Review

ERIC Educational Resources Information Center

Mohsen, Mohammed Ali

2016-01-01

This paper provides a comprehensive review on the use of help options (HOs) in the multimedia listening context to aid listening comprehension (LC) and improve incidental vocabulary learning. The paper also aims to synthesize the research findings obtained from the use of HOs in Computer-Assisted Language Learning (CALL) literature and reveals the…

The Impact of the 2004 Hurricanes on Florida Comprehensive Assessment Test Scores: Implications for School Counselors

ERIC Educational Resources Information Center

Baggerly, Jennifer; Ferretti, Larissa K.

2008-01-01

What is the impact of natural disasters on students' statewide assessment scores? To answer this question, Florida Comprehensive Assessment Test (FCAT) scores of 55,881 students in grades 4 through 10 were analyzed to determine if there were significant decreases after the 2004 hurricanes. Results reveal that there was statistical but no practical…

The Comprehensive Longitudinal Evaluation of the Milwaukee Parental Choice Program: Summary of Final Reports. SCDP Milwaukee Evaluation Report #36

ERIC Educational Resources Information Center

Wolf, Patrick J.

2012-01-01

This report contains a summary of the findings from the various topical reports that comprise the author's comprehensive longitudinal study. As a summary, it does not include extensive details regarding the study samples and scientific methodologies employed in those topical studies. The research revealed a pattern of school choice results that…

A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning

Treesearch

D. Lee Taylor; Teresa N. Hollingsworth; Jack W. McFarland; Niall J. Lennon; Chad Nusbaum; Roger W. Ruess

2014-01-01

Fungi play key roles in ecosystems as mutualists, pathogens, and decomposers. Current estimates of global species richness are highly uncertain, and the importance of stochastic vs. deterministic forces in the assembly of fungal communities is unknown. Molecular studies have so far failed to reach saturated, comprehensive estimates of fungal diversity. To obtain a more...

L1 and L2 Strategy Use in Reading Comprehension of Chinese EFL Readers

ERIC Educational Resources Information Center

Tsai, Yea-Ru; Ernst, Cheryl; Talley, Paul C.

2010-01-01

This study revealed the relationship between L1 (Mandarin Chinese) and L2 (English) strategy use in L2 reading comprehension by focusing on the correlation of L1 reading ability, L2 proficiency and employed reading strategies. The participants, 222 undergraduates learning English as a foreign language (EFL), were classified into skilled and…

The role of sustained attention and display medium in reading comprehension among adolescents with ADHD and without it.

PubMed

Stern, Pnina; Shalev, Lilach

2013-01-01

Difficulties in reading comprehension are common in children and adolescents with Attention Deficit/Hyperactivity Disorder (ADHD). The current study aimed at investigating the relation between sustained attention and reading comprehension among adolescents with and without ADHD. Another goal was to examine the impact of two manipulations of the text on the efficiency of reading comprehension: Spacing (standard- vs. double-spacing) and Type of presentation (computer screen vs. hard copy). Reading comprehension of two groups of adolescents (participants with ADHD and normal controls) was assessed and compared in four different conditions (standard printed, spaced printed, standard on computer screen, spaced on computer screen). In addition, participants completed a visual sustained attention task. Significant differences in reading comprehension and in sustained attention were obtained between the two groups. Also, a significant correlation was obtained between sustained attention and reading comprehension. Moreover, a significant interaction was revealed between presentation-type, spacing and level of sustained attention on reading comprehension. Implications for reading intervention and the importance of early assessment of attention functioning are discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Global resilience analysis of water distribution systems.

PubMed

Diao, Kegong; Sweetapple, Chris; Farmani, Raziyeh; Fu, Guangtao; Ward, Sarah; Butler, David

2016-12-01

Evaluating and enhancing resilience in water infrastructure is a crucial step towards more sustainable urban water management. As a prerequisite to enhancing resilience, a detailed understanding is required of the inherent resilience of the underlying system. Differing from traditional risk analysis, here we propose a global resilience analysis (GRA) approach that shifts the objective from analysing multiple and unknown threats to analysing the more identifiable and measurable system responses to extreme conditions, i.e. potential failure modes. GRA aims to evaluate a system's resilience to a possible failure mode regardless of the causal threat(s) (known or unknown, external or internal). The method is applied to test the resilience of four water distribution systems (WDSs) with various features to three typical failure modes (pipe failure, excess demand, and substance intrusion). The study reveals GRA provides an overview of a water system's resilience to various failure modes. For each failure mode, it identifies the range of corresponding failure impacts and reveals extreme scenarios (e.g. the complete loss of water supply with only 5% pipe failure, or still meeting 80% of demand despite over 70% of pipes failing). GRA also reveals that increased resilience to one failure mode may decrease resilience to another and increasing system capacity may delay the system's recovery in some situations. It is also shown that selecting an appropriate level of detail for hydraulic models is of great importance in resilience analysis. The method can be used as a comprehensive diagnostic framework to evaluate a range of interventions for improving system resilience in future studies. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Mixed messages: An evaluation of NHS Trust Social Media policies in the North West of England.

PubMed

Scragg, B; Shaikh, S; Robinson, L; Mercer, C

2017-08-01

Despite National Health Service (NHS) information strategy promoting the use of Social Media (SoMe) to encourage greater engagement between service users and providers, a team investigating online SoMe interaction between breast screening practitioners and clients found that practitioners alleged discouragement from employers' policies. This study aimed to investigate whether this barrier was genuine, and illuminate whether local policy differed from national strategy. The study used a qualitative grounded theory approach to generate a theory. Nine policies from the North West of England were analysed. A framework was derived from the data, and an analysis of policy tone followed by a detailed coding of policy content was undertaken. Comparative analysis continued by reviewing the literature, and a condensed framework revealed five broad categories that policies addressed. The analysis revealed the policies varied in content, but not in tone, which was mostly discouraging. Coding the content revealed that the most frequently addressed point was that of protecting the employers' reputation, and after further analysis, the resultant condensed framework showed that policies were imbalanced and heavily skewed towards Security, Conduct & Behaviour and Reputation. Practitioners within breast screening services are discouraged by overly prohibitive and prescriptive SoMe policies; with these varying tremendously in comprehensiveness, but with a narrow focus on security and employers reputation; in contrast with national strategy. Recommendations are that policy revision is undertaken with consultation by more than one stakeholder, and SoMe training is offered for all members of NHS staff. Copyright © 2017 The College of Radiographers. Published by Elsevier Ltd. All rights reserved.

Economic analysis of using above ground gas storage devices for compressed air energy storage system

NASA Astrophysics Data System (ADS)

Liu, Jinchao; Zhang, Xinjing; Xu, Yujie; Chen, Zongyan; Chen, Haisheng; Tan, Chunqing

2014-12-01

Above ground gas storage devices for compressed air energy storage (CAES) have three types: air storage tanks, gas cylinders, and gas storage pipelines. A cost model of these gas storage devices is established on the basis of whole life cycle cost (LCC) analysis. The optimum parameters of the three types are determined by calculating the theoretical metallic raw material consumption of these three devices and considering the difficulties in manufacture and the influence of gas storage device number. The LCCs of the three types are comprehensively analyzed and compared. The result reveal that the cost of the gas storage pipeline type is lower than that of the other two types. This study may serve as a reference for designing large-scale CAES systems.

Statistical analysis of trypanosomes' motility

NASA Astrophysics Data System (ADS)

Zaburdaev, Vasily; Uppaluri, Sravanti; Pfohl, Thomas; Engstler, Markus; Stark, Holger; Friedrich, Rudolf

2010-03-01

Trypanosome is a parasite causing the sleeping sickness. The way it moves in the blood stream and penetrates various obstacles is the area of active research. Our goal was to investigate a free trypanosomes' motion in the planar geometry. Our analysis of trypanosomes' trajectories reveals that there are two correlation times - one is associated with a fast motion of its body and the second one with a slower rotational diffusion of the trypanosome as a point object. We propose a system of Langevin equations to model such motion. One of its peculiarities is the presence of multiplicative noise predicting higher level of noise for higher velocity of the trypanosome. Theoretical and numerical results give a comprehensive description of the experimental data such as the mean squared displacement, velocity distribution and auto-correlation function.

Arcing in Leo and Geo Simulated Environments: Comparative Analysis

NASA Technical Reports Server (NTRS)

Vayner, Boris V.; Ferguson, Dale C.; Galofaro, Joel TY.

2006-01-01

Comprehensive tests of two solar array samples in simulated Low Earth Orbit (LEO) and Geosynchronous Orbit (GEO) environments have demonstrated that the arc inception voltage was 2-3 times lower in the LEO plasma than in the GEO vacuum. Arc current pulse wave forms are also essentially different in these environments. Moreover, the wide variations of pulse forms do not allow introducing the definition of a "standard arc wave form" even in GEO conditions. Visual inspection of the samples after testing in a GEO environment revealed considerable damage on coverglass surfaces and interconnects. These harmful consequences can be explained by the discharge energy being one order of magnitude higher in vacuum than in background plasma. The tests also revealed a potential danger of powerful electrostatic discharges that could be initiated on the solar array surface of a satellite in GEO during the ignition of an arcjet thruster.

Spaceflight Alters Bacterial Gene Expression and Virulence and Reveals Role for Global Regulator Hfq

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Ott, C. M.; zuBentrup, K. Honer; Ramamurthy R.; Quick, L.; Porwollik, S.; Cheng, P.; McClellan, M.; Tsaprailis, G.; Radabaugh, T.;

Interdisciplinary geriatric and palliative care team narratives: collaboration practices and barriers.

PubMed

Goldsmith, Joy; Wittenberg-Lyles, Elaine; Rodriguez, Dariela; Sanchez-Reilly, Sandra

2010-01-01

Despite the development and implementation of team training models in geriatrics and palliative care, little attention has been paid to the nature and process of teamwork. Geriatrics and palliative care in the clinical setting offer an interdisciplinary approach structured to meet the comprehensive needs of a patient and his or her family. Fellowship members of an interdisciplinary geriatric and palliative care team participated in semistructured interviews. Team members represented social work, chaplaincy, psychology, nursing, and medicine. A functional narrative analysis revealed four themes: voice of the lifeworld, caregiver teamwork, alone on a team, and storying disciplinary communication. The content-ordering function of narratives revealed a divergence in team members' conceptualization of teamwork and team effectiveness, and group ordering of narratives documented the collaborative nature of teams. The study findings demonstrate the potential for narratives as a pedagogical tool in team training, highlighting the benefits of reflective practice for improving teamwork and sustainability.

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells.

PubMed

Semrau, Stefan; Goldmann, Johanna E; Soumillon, Magali; Mikkelsen, Tarjei S; Jaenisch, Rudolf; van Oudenaarden, Alexander

2017-10-23

Gene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast, exit from pluripotency and lineage commitment have not been studied systematically at the single-cell level. Here we measure the gene expression dynamics of retinoic acid driven mESC differentiation from pluripotency to lineage commitment, using an unbiased single-cell transcriptomics approach. We find that the exit from pluripotency marks the start of a lineage transition as well as a transient phase of increased susceptibility to lineage specifying signals. Our study reveals several transcriptional signatures of this phase, including a sharp increase of gene expression variability and sequential expression of two classes of transcriptional regulators. In summary, we provide a comprehensive analysis of the exit from pluripotency and lineage commitment at the single cell level, a potential stepping stone to improved lineage manipulation through timing of differentiation cues.

Performance evaluation of non-targeted peak-based cross-sample analysis for comprehensive two-dimensional gas chromatography-mass spectrometry data and application to processed hazelnut profiling.

PubMed

Kiefl, Johannes; Cordero, Chiara; Nicolotti, Luca; Schieberle, Peter; Reichenbach, Stephen E; Bicchi, Carlo

2012-06-22

The continuous interest in non-targeted profiling induced the development of tools for automated cross-sample analysis. Such tools were found to be selective or not comprehensive thus delivering a biased view on the qualitative/quantitative peak distribution across 2D sample chromatograms. Therefore, the performance of non-targeted approaches needs to be critically evaluated. This study focused on the development of a validation procedure for non-targeted, peak-based, GC×GC-MS data profiling. The procedure introduced performance parameters such as specificity, precision, accuracy, and uncertainty for a profiling method known as Comprehensive Template Matching. The performance was assessed by applying a three-week validation protocol based on CITAC/EURACHEM guidelines. Optimized ¹D and ²D retention times search windows, MS match factor threshold, detection threshold, and template threshold were evolved from two training sets by a semi-automated learning process. The effectiveness of proposed settings to consistently match 2D peak patterns was established by evaluating the rate of mismatched peaks and was expressed in terms of results accuracy. The study utilized 23 different 2D peak patterns providing the chemical fingerprints of raw and roasted hazelnuts (Corylus avellana L.) from different geographical origins, of diverse varieties and different roasting degrees. The validation results show that non-targeted peak-based profiling can be reliable with error rates lower than 10% independent of the degree of analytical variance. The optimized Comprehensive Template Matching procedure was employed to study hazelnut roasting profiles and in particular to find marker compounds strongly dependent on the thermal treatment, and to establish the correlation of potential marker compounds to geographical origin and variety/cultivar and finally to reveal the characteristic release of aroma active compounds. Copyright © 2012 Elsevier B.V. All rights reserved.

Controlled hydrostatic pressure stress downregulates the expression of ribosomal genes in preimplantation embryos: a possible protection mechanism?

PubMed

Bock, I; Raveh-Amit, H; Losonczi, E; Carstea, A C; Feher, A; Mashayekhi, K; Matyas, S; Dinnyes, A; Pribenszky, C

2016-04-01

The efficiency of various assisted reproductive techniques can be improved by preconditioning the gametes and embryos with sublethal hydrostatic pressure treatment. However, the underlying molecular mechanism responsible for this protective effect remains unknown and requires further investigation. Here, we studied the effect of optimised hydrostatic pressure treatment on the global gene expression of mouse oocytes after embryonic genome activation. Based on a gene expression microarray analysis, a significant effect of treatment was observed in 4-cell embryos derived from treated oocytes, revealing a transcriptional footprint of hydrostatic pressure-affected genes. Functional analysis identified numerous genes involved in protein synthesis that were downregulated in 4-cell embryos in response to hydrostatic pressure treatment, suggesting that regulation of translation has a major role in optimised hydrostatic pressure-induced stress tolerance. We present a comprehensive microarray analysis and further delineate a potential mechanism responsible for the protective effect of hydrostatic pressure treatment.

Untargeted Identification of Wood Type-Specific Markers in Particulate Matter from Wood Combustion.

PubMed

Weggler, Benedikt A; Ly-Verdu, Saray; Jennerwein, Maximilian; Sippula, Olli; Reda, Ahmed A; Orasche, Jürgen; Gröger, Thomas; Jokiniemi, Jorma; Zimmermann, Ralf

2016-09-20

Residential wood combustion emissions are one of the major global sources of particulate and gaseous organic pollutants. However, the detailed chemical compositions of these emissions are poorly characterized due to their highly complex molecular compositions, nonideal combustion conditions, and sample preparation steps. In this study, the particulate organic emissions from a masonry heater using three types of wood logs, namely, beech, birch, and spruce, were chemically characterized using thermal desorption in situ derivatization coupled to a GCxGC-ToF/MS system. Untargeted data analyses were performed using the comprehensive measurements. Univariate and multivariate chemometric tools, such as analysis of variance (ANOVA), principal component analysis (PCA), and ANOVA simultaneous component analysis (ASCA), were used to reduce the data to highly significant and wood type-specific features. This study reveals substances not previously considered in the literature as meaningful markers for differentiation among wood types.

Effective factors in providing holistic care: a qualitative study.

PubMed

Zamanzadeh, Vahid; Jasemi, Madineh; Valizadeh, Leila; Keogh, Brian; Taleghani, Fariba

2015-01-01

Holistic care is a comprehensive model of caring. Previous studies have shown that most nurses do not apply this method. Examining the effective factors in nurses' provision of holistic care can help with enhancing it. Studying these factors from the point of view of nurses will generate real and meaningful concepts and can help to extend this method of caring. A qualitative study was used to identify effective factors in holistic care provision. Data gathered by interviewing 14 nurses from university hospitals in Iran were analyzed with a conventional qualitative content analysis method and by using MAXQDA (professional software for qualitative and mixed methods data analysis) software. Analysis of data revealed three main themes as effective factors in providing holistic care: The structure of educational system, professional environment, and personality traits. Establishing appropriate educational, management systems, and promoting religiousness and encouragement will induce nurses to provide holistic care and ultimately improve the quality of their caring.

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.

PubMed

Shen, Yue; Wang, Yun; Chen, Tai; Gao, Feng; Gong, Jianhui; Abramczyk, Dariusz; Walker, Roy; Zhao, Hongcui; Chen, Shihong; Liu, Wei; Luo, Yisha; Müller, Carolin A; Paul-Dubois-Taine, Adrien; Alver, Bonnie; Stracquadanio, Giovanni; Mitchell, Leslie A; Luo, Zhouqing; Fan, Yanqun; Zhou, Baojin; Wen, Bo; Tan, Fengji; Wang, Yujia; Zi, Jin; Xie, Zexiong; Li, Bingzhi; Yang, Kun; Richardson, Sarah M; Jiang, Hui; French, Christopher E; Nieduszynski, Conrad A; Koszul, Romain; Marston, Adele L; Yuan, Yingjin; Wang, Jian; Bader, Joel S; Dai, Junbiao; Boeke, Jef D; Xu, Xun; Cai, Yizhi; Yang, Huanming

2017-03-10

Here, we report the successful design, construction, and characterization of a 770-kilobase synthetic yeast chromosome II (synII). Our study incorporates characterization at multiple levels-including phenomics, transcriptomics, proteomics, chromosome segregation, and replication analysis-to provide a thorough and comprehensive analysis of a synthetic chromosome. Our Trans-Omics analyses reveal a modest but potentially relevant pervasive up-regulation of translational machinery observed in synII, mainly caused by the deletion of 13 transfer RNAs. By both complementation assays and SCRaMbLE (synthetic chromosome rearrangement and modification by loxP -mediated evolution), we targeted and debugged the origin of a growth defect at 37°C in glycerol medium, which is related to misregulation of the high-osmolarity glycerol response. Despite the subtle differences, the synII strain shows highly consistent biological processes comparable to the native strain. Copyright © 2017, American Association for the Advancement of Science.

Semantic and syntactic reading comprehension strategies used by deaf children with early and late cochlear implantation.

PubMed

Gallego, Carlos; Martín-Aragoneses, M Teresa; López-Higes, Ramón; Pisón, Guzmán

2016-01-01

Deaf students have traditionally exhibited reading comprehension difficulties. In recent years, these comprehension problems have been partially offset through cochlear implantation (CI), and the subsequent improvement in spoken language skills. However, the use of cochlear implants has not managed to fully bridge the gap in language and reading between normally hearing (NH) and deaf children, as its efficacy depends on variables such as the age at implant. This study compared the reading comprehension of sentences in 19 children who received a cochlear implant before 24 months of age (early-CI) and 19 who received it after 24 months (late-CI) with a control group of 19 NH children. The task involved completing sentences in which the last word had been omitted. To complete each sentence children had to choose a word from among several alternatives that included one syntactic and two semantic foils in addition to the target word. The results showed that deaf children with late-CI performed this task significantly worse than NH children, while those with early-CI exhibited no significant differences with NH children, except under more demanding processing conditions (long sentences with infrequent target words). Further, the error analysis revealed a preference of deaf students with early-CI for selecting the syntactic foil over a semantic one, which suggests that they draw upon syntactic cues during sentence processing in the same way as NH children do. In contrast, deaf children with late-CI do not appear to use a syntactic strategy, but neither a semantic strategy based on the use of key words, as the literature suggests. Rather, the numerous errors of both kinds that the late-CI group made seem to indicate an inconsistent and erratic response when faced with a lack of comprehension. These findings are discussed in relation to differences in receptive vocabulary and short-term memory and their implications for sentence reading comprehension. Copyright © 2015 Elsevier Ltd. All rights reserved.

The relationship among pressure ulcer risk factors, incidence and nursing documentation in hospital-acquired pressure ulcer patients in intensive care units.

PubMed

Li, Dan

2016-08-01

To explore the quality/comprehensiveness of nursing documentation of pressure ulcers and to investigate the relationship between the nursing documentation and the incidence of pressure ulcers in four intensive care units. Pressure ulcer prevention requires consistent assessments and documentation to decrease pressure ulcer incidence. Currently, most research is focused on devices to prevent pressure ulcers. Studies have rarely considered the relationship among pressure ulcer risk factors, incidence and nursing documentation. Thus, a study to investigate this relationship is needed to fill this information gap. A retrospective, comparative, descriptive, correlational study. A convenience sample of 196 intensive care units patients at the selected medical centre comprised the study sample. All medical records of patients admitted to intensive care units between the time periods of September 1, 2011 through September 30, 2012 were audited. Data used in the analysis included 98 pressure ulcer patients and 98 non-pressure ulcer patients. The quality and comprehensiveness of pressure ulcer documentation were measured by the modified European Pressure Ulcer Advisory Panel Pressure Ulcers Assessment Instrument and the Comprehensiveness in Nursing Documentation instrument. The correlations between quality/comprehensiveness of pressure ulcer documentation and incidence of pressure ulcers were not statistically significant. Patients with pressure ulcers had longer length of stay than patients without pressure ulcers stay. There were no statistically significant differences in quality/comprehensiveness scores of pressure ulcer documentation between dayshift and nightshift. This study revealed a lack of quality/comprehensiveness in nursing documentation of pressure ulcers. This study demonstrates that staff nurses often perform poorly on documenting pressure ulcer appearance, staging and treatment. Moreover, nursing documentation of pressure ulcers does not provide a complete picture of patients' care needs that require nursing interventions. The implication of this study involves pressure ulcer prevention and litigable risk of nursing documentation. © 2016 John Wiley & Sons Ltd.

Instructional Strategies for Enhancing Learning Disabled Students' Reading Comprehension and Comprehension Test Performance.

ERIC Educational Resources Information Center

Wong, Bernice Y. L.

1986-01-01

Successful instructional strategies for enhancing the reading comprehension and comprehension test performance of learning disabled students are described. Students are taught to self-monitor their comprehension of expository materials and stories through recognition and analysis of recurrent elements and problem passages, content summarization,…

Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus

PubMed Central

Yamamoto, Naoki; Takano, Tomoyuki; Tanaka, Keisuke; Ishige, Taichiro; Terashima, Shin; Endo, Chisato; Kurusu, Takamitsu; Yajima, Shunsuke; Yano, Kentaro; Tada, Yuichi

2015-01-01

The turf grass Sporobolus virginicus is halophyte and has high salinity tolerance. To investigate the molecular basis of its remarkable tolerance, we performed Illumina high-throughput RNA sequencing on roots and shoots of a S. virginicus genotype under normal and saline conditions. The 130 million short reads were assembled into 444,242 unigenes. A comparative analysis of the transcriptome with rice and Arabidopsis transcriptome revealed six turf grass-specific unigenes encoding transcription factors. Interestingly, all of them showed root specific expression and five of them encode bZIP type transcription factors. Another remarkable transcriptional feature of S. virginicus was activation of specific pathways under salinity stress. Pathway enrichment analysis suggested transcriptional activation of amino acid, pyruvate, and phospholipid metabolism. Up-regulation of several unigenes, previously shown to respond to salt stress in other halophytes was also observed. Gene Ontology enrichment analysis revealed that unigenes assigned as proteins in response to water stress, such as dehydrin and aquaporin, and transporters such as cation, amino acid, and citrate transporters, and H+-ATPase, were up-regulated in both shoots and roots under salinity. A correspondence analysis of the enriched pathways in turf grass cells, but not in rice cells, revealed two groups of unigenes similarly up-regulated in the turf grass in response to salt stress; one of the groups, showing excessive up-regulation under salinity, included unigenes homologos to salinity responsive genes in other halophytes. Thus, the present study identified candidate genes involved in salt tolerance of S. virginicus. This genetic resource should be valuable for understanding the mechanisms underlying high salt tolerance in S. virginicus. This information can also provide insight into salt tolerance in other halophytes. PMID:25954282

Australasian disasters of national significance: an epidemiological analysis, 1900-2012.

PubMed

Bradt, David A; Bartley, Bruce; Hibble, Belinda A; Varshney, Kavita

2015-04-01

A regional epidemiological analysis of Australasian disasters in the 20th century to present was undertaken to examine trends in disaster epidemiology; to characterise the impacts on civil society through disaster policy, practice and legislation; and to consider future potential limitations in national disaster resilience. A surveillance definition of disaster was developed conforming to the Centre for Research on the Epidemiology of Disasters (CRED) criteria (≥10 deaths, ≥100 affected, or declaration of state emergency or appeal for international assistance). The authors then applied economic and legislative inclusion criteria to identify additional disasters of national significance. The surveillance definition yielded 165 disasters in the period, from which 65 emerged as disasters of national significance. There were 38 natural disasters, 22 technological disasters, three offshore terrorist attacks and two domestic mass shootings. Geographic analysis revealed that states with major population centres experienced the vast majority of disasters of national significance. Timeline analysis revealed an increasing incidence of disasters since the 1980s, which peaked in the period 2005-2009. Recent seasonal bushfires and floods have incurred the highest death toll and economic losses in Australasian history. Reactive hazard-specific legislation emerged after all terrorist acts and after most disasters of national significance. Timeline analysis reveals an increasing incidence in natural disasters over the past 15 years, with the most lethal and costly disasters occurring in the past 3 years. Vulnerability to disaster in Australasia appears to be increasing. Reactive legislation is a recurrent feature of Australasian disaster response that suggests legislative shortsightedness and a need for comprehensive all-hazards model legislation in the future. © 2015 Australasian College for Emergency Medicine and Australasian Society for Emergency Medicine.

Evaluating comprehensiveness in children's healthcare.

PubMed

Diniz, Suênia Gonçalves de Medeiros; Damasceno, Simone Soares; Coutinho, Simone Elizabeth Duarte; Toso, Beatriz Rosana Gonçalves de Oliveira; Collet, Neusa

2016-12-15

To evaluate the presence and extent of comprehensiveness in children's healthcare in the context of the Family Health Strategy. Evaluative, quantitative, cross-sectional study conducted with 344 family members of children at the Family Health Units of João Pessoa, PB, Brazil. Data were collected using the PCATool Brazil - child version and analysed according to descriptive and exploratory statistics. The attribute of comprehensiveness did not obtain satisfactory scores in the two evaluated dimensions, namely "available services" and "provided services". The low scores reveal that the attribute comprehensiveness is not employed as expected in a primary care unit and points to the issues that must be altered. It was concluded that the services should be restructured to ensure cross-sector performance in the provision of child care. It is also important to improve the relations between professionals and users to promote comprehensive and effective care.

Comprehensive benefit analysis of regional water resources based on multi-objective evaluation

NASA Astrophysics Data System (ADS)

Chi, Yixia; Xue, Lianqing; Zhang, Hui

2018-01-01

The purpose of the water resources comprehensive benefits analysis is to maximize the comprehensive benefits on the aspects of social, economic and ecological environment. Aiming at the defects of the traditional analytic hierarchy process in the evaluation of water resources, it proposed a comprehensive benefit evaluation of social, economic and environmental benefits index from the perspective of water resources comprehensive benefit in the social system, economic system and environmental system; determined the index weight by the improved fuzzy analytic hierarchy process (AHP), calculated the relative index of water resources comprehensive benefit and analyzed the comprehensive benefit of water resources in Xiangshui County by the multi-objective evaluation model. Based on the water resources data in Xiangshui County, 20 main comprehensive benefit assessment factors of 5 districts belonged to Xiangshui County were evaluated. The results showed that the comprehensive benefit of Xiangshui County was 0.7317, meanwhile the social economy has a further development space in the current situation of water resources.

Beyond the word and image: characteristics of a common meaning system for language and vision revealed by functional and structural imaging.

PubMed

Jouen, A L; Ellmore, T M; Madden, C J; Pallier, C; Dominey, P F; Ventre-Dominey, J

2015-02-01

This research tests the hypothesis that comprehension of human events will engage an extended semantic representation system, independent of the input modality (sentence vs. picture). To investigate this, we examined brain activation and connectivity in 19 subjects who read sentences and viewed pictures depicting everyday events, in a combined fMRI and DTI study. Conjunction of activity in understanding sentences and pictures revealed a common fronto-temporo-parietal network that included the middle and inferior frontal gyri, the parahippocampal-retrosplenial complex, the anterior and middle temporal gyri, the inferior parietal lobe in particular the temporo-parietal cortex. DTI tractography seeded from this temporo-parietal cortex hub revealed a multi-component network reaching into the temporal pole, the ventral frontal pole and premotor cortex. A significant correlation was found between the relative pathway density issued from the temporo-parietal cortex and the imageability of sentences for individual subjects, suggesting a potential functional link between comprehension and the temporo-parietal connectivity strength. These data help to define a "meaning" network that includes components of recently characterized systems for semantic memory, embodied simulation, and visuo-spatial scene representation. The network substantially overlaps with the "default mode" network implicated as part of a core network of semantic representation, along with brain systems related to the formation of mental models, and reasoning. These data are consistent with a model of real-world situational understanding that is highly embodied. Crucially, the neural basis of this embodied understanding is not limited to sensorimotor systems, but extends to the highest levels of cognition, including autobiographical memory, scene analysis, mental model formation, reasoning and theory of mind. Copyright © 2014 Elsevier Inc. All rights reserved.

Genome-wide analysis of the Solanum tuberosum (potato) trehalose-6-phosphate synthase (TPS) gene family: evolution and differential expression during development and stress.

PubMed

Xu, Yingchun; Wang, Yanjie; Mattson, Neil; Yang, Liu; Jin, Qijiang

2017-12-01

Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molecular evolution, and expression patterns of this gene family are still lacking in Solanum tuberosum (potato). In this study, a comprehensive analysis of the TPS gene family was conducted in potato. A total of eight putative potato TPS genes (StTPSs) were identified by searching the latest potato genome sequence. The amino acid identity among eight StTPSs varied from 59.91 to 89.54%. Analysis of d N /d S ratios suggested that regions in the TPP (trehalose-6-phosphate phosphatase) domains evolved faster than the TPS domains. Although the sequence of the eight StTPSs showed high similarity (2571-2796 bp), their gene length is highly differentiated (3189-8406 bp). Many of the regulatory elements possibly related to phytohormones, abiotic stress and development were identified in different TPS genes. Based on the phylogenetic tree constructed using TPS genes of potato, and four other Solanaceae plants, TPS genes could be categorized into 6 distinct groups. Analysis revealed that purifying selection most likely played a major role during the evolution of this family. Amino acid changes detected in specific branches of the phylogenetic tree suggests relaxed constraints might have contributed to functional divergence among groups. Moreover, StTPSs were found to exhibit tissue and treatment specific expression patterns upon analysis of transcriptome data, and performing qRT-PCR. This study provides a reference for genome-wide identification of the potato TPS gene family and sets a framework for further functional studies of this important gene family in development and stress response.

Improving Reading Comprehension Using Digital Text: A Meta-Analysis of Interventions

ERIC Educational Resources Information Center

Berkeley, Sheri; Kurz, Leigh Ann; Boykin, Andrea; Evmenova, Anya S.

2015-01-01

Much is known about how to improve students' comprehension when reading printed text; less is known about outcomes when reading digital text. The purpose of this meta-analysis was to analyze research on the impact of digital text interventions. A comprehensive literature search resulted in 27 group intervention studies with 16,513 participants.…

Characterization of GM events by insert knowledge adapted re-sequencing approaches

PubMed Central

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-01-01

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events. PMID:24088728

Characterization of GM events by insert knowledge adapted re-sequencing approaches.

PubMed

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-10-03

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.

Pediatric skin care: what do nurses really know?

PubMed

Drake, Jennifer; Redfern, Wendi S; Sherburne, Eileen; Nugent, Melodee L; Simpson, Pippa

2012-10-01

The purpose of this study was to explore pediatric nurses' knowledge of pressure ulcer prevention, investigate their beliefs and practices, and identify the barriers and facilitators to providing evidence-based pressure ulcer preventive practices. An exploratory, descriptive, and cross-sectional survey was taken of registered nurses in a freestanding children's hospital. Nurses have adequate knowledge of general pressure ulcer prevention; however, they struggle with individualization. Further, analysis revealed that nursing knowledge did not always correlate with nursing practice. Nurses require education on individualized interventions and access to user-friendly, interactive, and comprehensive resources, including unit-based champions and order sets. © 2012, Wiley Periodicals, Inc.

Illustrating an integrated typology of meaning reconstruction in discourse: grief-related disclosures.

PubMed

Kunkel, Adrianne; Dennis, Michael Robert; Garner, Benjamin

2014-01-01

A typology of meaning reconstruction in grief-related discourse is offered as an extension to extant approaches to meaning making as a factor in relieving distress. Sensemaking, acceptance or resignation without understanding, realization of benefits via positive reappraisal, and realignment of roles and relationships are advanced as the 4 types of meaning reconstruction that are formed by the 4 intersections of Park's ( 2010 ) categorical distinctions in meaning making (i.e., searching for comprehensibility/searching for significance and assimilation/accommodation). Interpretive analysis of grief-related texts from an emotional disclosure study reveals 25 themes across the 4 types. Related theoretical insights and practical implications are discussed.

Neural activity associated with metaphor comprehension: spatial analysis.

PubMed

Sotillo, María; Carretié, Luis; Hinojosa, José A; Tapia, Manuel; Mercado, Francisco; López-Martín, Sara; Albert, Jacobo

2005-01-03

Though neuropsychological data indicate that the right hemisphere (RH) plays a major role in metaphor processing, other studies suggest that, at least during some phases of this processing, a RH advantage may not exist. The present study explores, through a temporally agile neural signal--the event-related potentials (ERPs)--, and through source-localization algorithms applied to ERP recordings, whether the crucial phase of metaphor comprehension presents or not a RH advantage. Participants (n=24) were submitted to a S1-S2 experimental paradigm. S1 consisted of visually presented metaphoric sentences (e.g., "Green lung of the city"), followed by S2, which consisted of words that could (i.e., "Park") or could not (i.e., "Semaphore") be defined by S1. ERPs elicited by S2 were analyzed using temporal principal component analysis (tPCA) and source-localization algorithms. These analyses revealed that metaphorically related S2 words showed significantly higher N400 amplitudes than non-related S2 words. Source-localization algorithms showed differential activity between the two S2 conditions in the right middle/superior temporal areas. These results support the existence of an important RH contribution to (at least) one phase of metaphor processing and, furthermore, implicate the temporal cortex with respect to that contribution.

Khat Chewing among Students of Higher Education in Jazan Region, Saudi Arabia: Prevalence, Pattern, and Related Factors

PubMed Central

Alsanosy, Rashad Mohammed; Mahfouz, Mohamed Salih; Gaffar, Abdelrahim Mutwakel

2013-01-01

Objectives. (1) To estimate the prevalence and behavioral patterns of Khat chewing and (2) to investigate factors that influenced the pattern of Khat use among undergraduate students in different higher education institutions in Jazan region, Saudi Arabia. Materials and Methods. A cross-sectional study using a pretested structured self-administered quantitative questionnaire was used to collect data. SPSS version 17 software program was used for data analysis. Results. The overall current Khat chewing prevalence among higher education students was found to be 23.1%, significantly higher among males at 38.5% than among females at 2.1% (P < 0.001). Lifetime Khat chewer students were 24.8% for males at 40.5%, significantly higher compared with females at 3.7% (P < 0.001). Univariate analysis revealed that the gender of student, smoking status of student, a friend's smoking, and Khat chewing were associated with a significant high risk of Khat chewing (P < 0.001   for all). Conclusions. The use of Khat trend is increasing among higher education students in Jazan region. A multilevel, value based, comprehensive, and strategic long-term intervention plan is needed. The comprehensive plan may include social interventions geared by creating recreations alternatives and opportunities for youth and a critical review for current authorities' interventions and services. PMID:23878809

No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis.

PubMed

Loley, Christina; Alver, Maris; Assimes, Themistocles L; Bjonnes, Andrew; Goel, Anuj; Gustafsson, Stefan; Hernesniemi, Jussi; Hopewell, Jemma C; Kanoni, Stavroula; Kleber, Marcus E; Lau, King Wai; Lu, Yingchang; Lyytikäinen, Leo-Pekka; Nelson, Christopher P; Nikpay, Majid; Qu, Liming; Salfati, Elias; Scholz, Markus; Tukiainen, Taru; Willenborg, Christina; Won, Hong-Hee; Zeng, Lingyao; Zhang, Weihua; Anand, Sonia S; Beutner, Frank; Bottinger, Erwin P; Clarke, Robert; Dedoussis, George; Do, Ron; Esko, Tõnu; Eskola, Markku; Farrall, Martin; Gauguier, Dominique; Giedraitis, Vilmantas; Granger, Christopher B; Hall, Alistair S; Hamsten, Anders; Hazen, Stanley L; Huang, Jie; Kähönen, Mika; Kyriakou, Theodosios; Laaksonen, Reijo; Lind, Lars; Lindgren, Cecilia; Magnusson, Patrik K E; Marouli, Eirini; Mihailov, Evelin; Morris, Andrew P; Nikus, Kjell; Pedersen, Nancy; Rallidis, Loukianos; Salomaa, Veikko; Shah, Svati H; Stewart, Alexandre F R; Thompson, John R; Zalloua, Pierre A; Chambers, John C; Collins, Rory; Ingelsson, Erik; Iribarren, Carlos; Karhunen, Pekka J; Kooner, Jaspal S; Lehtimäki, Terho; Loos, Ruth J F; März, Winfried; McPherson, Ruth; Metspalu, Andres; Reilly, Muredach P; Ripatti, Samuli; Sanghera, Dharambir K; Thiery, Joachim; Watkins, Hugh; Deloukas, Panos; Kathiresan, Sekar; Samani, Nilesh J; Schunkert, Heribert; Erdmann, Jeanette; König, Inke R

2016-10-12

In recent years, genome-wide association studies have identified 58 independent risk loci for coronary artery disease (CAD) on the autosome. However, due to the sex-specific data structure of the X chromosome, it has been excluded from most of these analyses. While females have 2 copies of chromosome X, males have only one. Also, one of the female X chromosomes may be inactivated. Therefore, special test statistics and quality control procedures are required. Thus, little is known about the role of X-chromosomal variants in CAD. To fill this gap, we conducted a comprehensive X-chromosome-wide meta-analysis including more than 43,000 CAD cases and 58,000 controls from 35 international study cohorts. For quality control, sex-specific filters were used to adequately take the special structure of X-chromosomal data into account. For single study analyses, several logistic regression models were calculated allowing for inactivation of one female X-chromosome, adjusting for sex and investigating interactions between sex and genetic variants. Then, meta-analyses including all 35 studies were conducted using random effects models. None of the investigated models revealed genome-wide significant associations for any variant. Although we analyzed the largest-to-date sample, currently available methods were not able to detect any associations of X-chromosomal variants with CAD.

Comprehensive analysis of the transcriptional profile of the Mediator complex across human cancer types.

PubMed

Syring, Isabella; Klümper, Niklas; Offermann, Anne; Braun, Martin; Deng, Mario; Boehm, Diana; Queisser, Angela; von Mässenhausen, Anne; Brägelmann, Johannes; Vogel, Wenzel; Schmidt, Doris; Majores, Michael; Schindler, Anne; Kristiansen, Glen; Müller, Stefan C; Ellinger, Jörg; Shaikhibrahim, Zaki; Perner, Sven

2016-04-26

The Mediator complex is a key regulator of gene transcription and several studies demonstrated altered expressions of particular subunits in diverse human diseases, especially cancer. However a systematic study deciphering the transcriptional expression of the Mediator across different cancer entities is still lacking.We therefore performed a comprehensive in silico cancer vs. benign analysis of the Mediator complex subunits (MEDs) for 20 tumor entities using Oncomine datasets. The transcriptional expression profiles across almost all cancer entities showed differentially expressed MEDs as compared to benign tissue. Differential expression of MED8 in renal cell carcinoma (RCC) and MED12 in lung cancer (LCa) were validated and further investigated by immunohistochemical staining on tissue microarrays containing large numbers of specimen. MED8 in clear cell RCC (ccRCC) associated with shorter survival and advanced TNM stage and showed higher expression in metastatic than primary tumors. In vitro, siRNA mediated MED8 knockdown significantly impaired proliferation and motility in ccRCC cell lines, hinting at a role for MED8 to serve as a novel therapeutic target in ccRCC. Taken together, our Mediator complex transcriptome proved to be a valid tool for identifying cancer-related shifts in Mediator complex composition, revealing that MEDs do exhibit cancer specific transcriptional expression profiles.

Hsf and Hsp gene families in Populus: genome-wide identification, organization and correlated expression during development and in stress responses.

PubMed

Zhang, Jin; Liu, Bobin; Li, Jianbo; Zhang, Li; Wang, Yan; Zheng, Huanquan; Lu, Mengzhu; Chen, Jun

2015-03-14

Heat shock proteins (Hsps) are molecular chaperones that are involved in many normal cellular processes and stress responses, and heat shock factors (Hsfs) are the transcriptional activators of Hsps. Hsfs and Hsps are widely coordinated in various biological processes. Although the roles of Hsfs and Hsps in stress responses have been well characterized in Arabidopsis, their roles in perennial woody species undergoing various environmental stresses remain unclear. Here, a comprehensive identification and analysis of Hsf and Hsp families in poplars is presented. In Populus trichocarpa, we identified 42 paralogous pairs, 66.7% resulting from a whole genome duplication. The gene structure and motif composition are relatively conserved in each subfamily. Microarray and quantitative real-time RT-PCR analyses showed that most of the Populus Hsf and Hsp genes are differentially expressed upon exposure to various stresses. A coexpression network between Populus Hsf and Hsp genes was generated based on their expression. Coordinated relationships were validated by transient overexpression and subsequent qPCR analyses. The comprehensive analysis indicates that different sets of PtHsps are downstream of particular PtHsfs and provides a basis for functional studies aimed at revealing the roles of these families in poplar development and stress responses.

Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry.

PubMed

Pesavento, James J; Bullock, Courtney R; LeDuc, Richard D; Mizzen, Craig A; Kelleher, Neil L

2008-05-30

Quantitative proteomics has focused heavily on correlating protein abundances, ratios, and dynamics by developing methods that are protein expression-centric (e.g. isotope coded affinity tag, isobaric tag for relative and absolute quantification, etc.). These methods effectively detect changes in protein abundance but fail to provide a comprehensive perspective of the diversity of proteins such as histones, which are regulated by post-translational modifications. Here, we report the characterization of modified forms of HeLa cell histone H4 with a dynamic range >10(4) using a strictly Top Down mass spectrometric approach coupled with two dimensions of liquid chromatography. This enhanced dynamic range enabled the precise characterization and quantitation of 42 forms uniquely modified by combinations of methylation and acetylation, including those with trimethylated Lys-20, monomethylated Arg-3, and the novel dimethylated Arg-3 (each <1% of all H4 forms). Quantitative analyses revealed distinct trends in acetylation site occupancy depending on Lys-20 methylation state. Because both modifications are dynamically regulated through the cell cycle, we simultaneously investigated acetylation and methylation kinetics through three cell cycle phases and used these data to statistically assess the robustness of our quantitative analysis. This work represents the most comprehensive analysis of histone H4 forms present in human cells reported to date.

The James Supportive Care Screening: integrating science and practice to meet the NCCN guidelines for distress management at a Comprehensive Cancer Center.

PubMed

Wells-Di Gregorio, Sharla; Porensky, Emily K; Minotti, Matthew; Brown, Susan; Snapp, Janet; Taylor, Robert M; Adolph, Michael D; Everett, Sherman; Lowther, Kenneth; Callahan, Kelly; Streva, Devita; Heinke, Vicki; Leno, Debra; Flower, Courtney; McVey, Anne; Andersen, Barbara Lee

2013-09-01

Selecting a measure for oncology distress screening can be challenging. The measure must be brief, but comprehensive, capturing patients' most distressing concerns. The measure must provide meaningful coverage of multiple domains, assess symptom and problem-related distress, and ideally be suited for both clinical and research purposes. From March 2006 to August 2012, the James Supportive Care Screening (SCS) was developed and validated in three phases including content validation, factor analysis, and measure validation. Exploratory factor analyses were completed with 596 oncology patients followed by a confirmatory factor analysis with 477 patients. Six factors were identified and confirmed including (i) emotional concerns; (ii) physical symptoms; (iii) social/practical problems; (iv) spiritual problems; (v) cognitive concerns; and (vi) healthcare decision making/communication issues. Subscale evaluation reveals good to excellent internal consistency, test-retest reliability, and convergent, divergent, and predictive validity. Specificity of individual items was 0.90 and 0.87, respectively, for identifying patients with DSM-IV-TR diagnoses of major depression and generalized anxiety disorder. Results support use of the James SCS to quickly detect the most frequent and distressing symptoms and concerns of cancer patients. The James SCS is an efficient, reliable, and valid clinical and research outcomes measure. Copyright © 2013 John Wiley & Sons, Ltd.

Effect of education on listening comprehension of sentences on healthy elderly: analysis of number of correct responses and task execution time.

PubMed

Silagi, Marcela Lima; Rabelo, Camila Maia; Schochat, Eliane; Mansur, Letícia Lessa

2017-11-13

To analyze the effect of education on sentence listening comprehension on cognitively healthy elderly. A total of 111 healthy elderly, aged 60-80 years of both genders were divided into two groups according to educational level: low education (0-8 years of formal education) and high education (≥9 years of formal education). The participants were assessed using the Revised Token Test, an instrument that supports the evaluation of auditory comprehension of orders with different working memory and syntactic complexity demands. The indicators used for performance analysis were the number of correct responses (accuracy analysis) and task execution time (temporal analysis) in the different blocks. The low educated group had a lower number of correct responses than the high educated group on all blocks of the test. In the temporal analysis, participants with low education had longer execution time for commands on the first four blocks related to working memory. However, the two groups had similar execution time for blocks more related to syntactic comprehension. Education influenced sentence listening comprehension on elderly. Temporal analysis allowed to infer over the relationship between comprehension and other cognitive abilities, and to observe that the low educated elderly did not use effective compensation strategies to improve their performances on the task. Therefore, low educational level, associated with aging, may potentialize the risks for language decline.

Quasi-targeted analysis of hydroxylation-related metabolites of polycyclic aromatic hydrocarbons in human urine by liquid chromatography-mass spectrometry.

PubMed

Tang, Caiming; Tan, Jianhua; Fan, Ruifang; Zhao, Bo; Tang, Caixing; Ou, Weihui; Jin, Jiabin; Peng, Xianzhi

2016-08-26

Metabolite identification is crucial for revealing metabolic pathways and comprehensive potential toxicities of polycyclic aromatic hydrocarbons (PAHs) in human body. In this work, a quasi-targeted analysis strategy was proposed for metabolite identification of monohydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) in human urine using liquid chromatography triple quadruple mass spectrometry (LC-QqQ-MS/MS) combined with liquid chromatography high resolution mass spectrometry (LC-HRMS). Potential metabolites of OH-PAHs were preliminarily screened out by LC-QqQ-MS/MS in association with filtering in a self-constructed information list of possible metabolites, followed by further identification and confirmation with LC-HRMS. The developed method can provide more reliable and systematic results compared with traditional untargeted analysis using LC-HRMS. In addition, data processing for LC-HRMS analysis were greatly simplified. This quasi-targeted analysis method was successfully applied to identifying phase I and phase II metabolites of OH-PAHs in human urine. Five metabolites of hydroxynaphthalene, seven of hydroxyfluorene, four of hydroxyphenanthrene, and three of hydroxypyrene were tentatively identified. Metabolic pathways of PAHs in human body were putatively revealed based on the identified metabolites. The experimental results will be valuable for investigating the metabolic processes of PAHs in human body, and the quasi-targeted analysis strategy can be expanded to the metabolite identification and profiling of other compounds in vivo. Copyright © 2016 Elsevier B.V. All rights reserved.

The Prognostic and Clinicopathological Significance of Tumor-Associated Macrophages in Patients with Gastric Cancer: A Meta-Analysis.

PubMed

Yin, Songcheng; Huang, Jinyu; Li, Zhan; Zhang, Junyan; Luo, Jiazi; Lu, Chunyang; Xu, Hao; Xu, Huimian

2017-01-01

Comprehensive studies have investigated the prognostic and clinicopathological value of tumor-associated macrophages (TAMs) in gastric cancer patients, yet results remain controversial. Therefore, we performed a meta-analysis to clarify this issue. PubMed, Embase, and the Cochrane Library databases were searched to identify eligible studies. We extracted hazard ratios (HRs) and odds ratios (ORs) with their corresponding 95% confidence intervals (95% CIs) to estimate the effect sizes. In addition, subgroup analysis and sensitivity analysis were also conducted. A total of 19 studies involving 2242 patients were included. High generalised TAMs density was significantly associated with poor overall survival (OS) (HR 1.49, 95% CI 1.15-1.95). Subgroup analysis revealed that CD68+ TAMs had no significant effect on OS (HR 1.38, 95% CI 1.00-1.91). High M1 TAMs density was correlated with better OS (HR 0.45, 95% CI 0.32-0.65). By contrast, high density of M2 TAMs was correlated with a poor prognosis for OS (HR 1.48, 95% CI 1.25-1.75). Furthermore, high M2 TAMs density was correlated with larger tumor size, diffuse Lauren type, poor histologic differentiation, deeper tumor invasion, lymph node metastasis, and advanced TNM stage. Overall, this meta-analysis reveal that although CD68+ TAMs infiltration has the neutral prognostic effects on OS, the M1/M2 polarization of TAMs are predicative factor of prognosis in gastric cancer patients.

Effects of an Inverted Instructional Delivery Model on Achievement of Ninth-Grade Physical Science Honors Students

NASA Astrophysics Data System (ADS)

Howell, Donna

This mixed-methods action research study was designed to assess the achievement of ninth-grade Physical Science Honors students by analysis of pre and posttest data. In addition, perceptual data from students, parents, and the researcher were collected to form a complete picture of the flipped lecture format versus the traditional lecture format. The researcher utilized a 4MAT learning cycle in two Physical Science Honors classes. One of these classes was traditionally delivered with lecture-type activities taking place inside the classroom and homework-type activities taking place at home; the other inverted, or flipped, delivered with lecture-type activities taking place outside the classroom and homework-type activities taking place inside the classroom. Existing unit pre and posttests for both classes were analyzed for differences in academic achievement. At the completion of the units, the flipped class students and parents were surveyed, and student focus groups were convened to ascertain their perceptions of the flipped classroom delivery model. Statistical analysis of posttest data revealed that there is no significant difference between the traditional lecture delivery format and the flipped delivery format. Analysis of perceptual data revealed six themes that must be considered when deciding to flip the classroom: how to hold students accountable for viewing the at-home videos, accessibility of students to the required technology, technical considerations relating to the video production, comprehension of the material both during and after viewing the videos, pedagogy of the overall flipped method, and preference for the flipped method overall. Findings revealed that students, parents, and the researcher all had a preference for the flipped class format, provided the above issues are addressed. The flipped class format encourages students to become more responsible for their learning, and, in addition, students reported that the hands-on inquiry activities done in class aided them in learning the subject matter. It is recommended, however, that before instructors decide to flip the classroom, they ensure that all students have access to needed technology, that there is a plan in place for ensuring that the students actually view the assigned videos, that they have a way to create the videos and ensure adequate quality, and that some discussion is held in class after each assigned video to ensure comprehension of the material.

Plasma proteomic analysis reveals altered protein abundances in cardiovascular disease.

PubMed

Lygirou, Vasiliki; Latosinska, Agnieszka; Makridakis, Manousos; Mullen, William; Delles, Christian; Schanstra, Joost P; Zoidakis, Jerome; Pieske, Burkert; Mischak, Harald; Vlahou, Antonia

2018-04-17

Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis. LC-MS/MS was employed to analyze plasma from 32 subjects (19 cases of various CVD phenotypes and 13 controls) in two steps: discovery (13 cases and 8 controls) and test (6 cases and 5 controls) set analysis. Following label-free quantification, the detected proteins were correlated to existing plasma proteomics datasets (plasma proteome database; PPD) and functionally annotated (Cytoscape, Ingenuity Pathway Analysis). Differential expression was defined based on identification confidence (≥ 2 peptides per protein), statistical significance (Mann-Whitney p value ≤ 0.05) and a minimum of twofold change. Peptides detected in at least 50% of samples per group were considered, resulting in a total of 3796 identified proteins (838 proteins based on ≥ 2 peptides). Pathway annotation confirmed the functional relevance of the findings (representation of complement cascade, fibrin clot formation, platelet degranulation, etc.). Correlation of the relative abundance of the proteins identified in the discovery set with their reported concentrations in the PPD was significant, confirming the validity of the quantification method. The discovery set analysis revealed 100 differentially expressed proteins between cases and controls, 39 of which were verified (≥ twofold change) in the test set. These included proteins already studied in the context of CVD (such as apolipoprotein B, alpha-2-macroglobulin), as well as novel findings (such as low density lipoprotein receptor related protein 2 [LRP2], protein SZT2) for which a mechanism of action is suggested. This proteomic study provides a comprehensive dataset to be used for integrative and functional studies in the field. The observed protein changes reflect known CVD-related processes (e.g. lipid uptake, inflammation) but also novel hypotheses for further investigation including a potential pleiotropic role of LPR2 but also links of SZT2 to CVD.

Underage alcohol policies across 50 California cities: an assessment of best practices

PubMed Central

2012-01-01

Background We pursue two primary goals in this article: (1) to test a methodology and develop a dataset on U.S. local-level alcohol policy ordinances, and (2) to evaluate the presence, comprehensiveness, and stringency of eight local alcohol policies in 50 diverse California cities in relationship to recommended best practices in both public health literature and governmental recommendations to reduce underage drinking. Methods Following best practice recommendations from a wide array of authoritative sources, we selected eight local alcohol policy topics (e.g., conditional use permits, responsible beverage service training, social host ordinances, window/billboard advertising ordinances), and determined the presence or absence as well as the stringency (restrictiveness) and comprehensiveness (number of provisions) of each ordinance in each of the 50 cities in 2009. Following the alcohol policy literature, we created scores for each city on each type of ordinance and its associated components. We used these data to evaluate the extent to which recommendations for best practices to reduce underage alcohol use are being followed. Results (1) Compiling datasets of local-level alcohol policy laws and their comprehensiveness and stringency is achievable, even absent comprehensive, on-line, or other legal research tools. (2) We find that, with some exceptions, most of the 50 cities do not have high scores for presence, comprehensiveness, or stringency across the eight key policies. Critical policies such as responsible beverage service and deemed approved ordinances are uncommon, and, when present, they are generally neither comprehensive nor stringent. Even within policies that have higher adoption rates, central elements are missing across many or most cities’ ordinances. Conclusion This study demonstrates the viability of original legal data collection in the U.S. pertaining to local ordinances and of creating quantitative scores for each policy type to reflect comprehensiveness and stringency. Analysis of the resulting dataset reveals that, although the 50 cities have taken important steps to improve public health with regard to underage alcohol use and abuse, there is a great deal more that needs to be done to bring these cities into compliance with best practice recommendations. PMID:22734468

Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

PubMed Central

2013-01-01

Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data. PMID:24059747

Comprehensive machine learning analysis of Hydra behavior reveals a stable basal behavioral repertoire.

PubMed

Han, Shuting; Taralova, Ekaterina; Dupre, Christophe; Yuste, Rafael

2018-03-28

Animal behavior has been studied for centuries, but few efficient methods are available to automatically identify and classify it. Quantitative behavioral studies have been hindered by the subjective and imprecise nature of human observation, and the slow speed of annotating behavioral data. Here, we developed an automatic behavior analysis pipeline for the cnidarian Hydra vulgaris using machine learning. We imaged freely behaving Hydra , extracted motion and shape features from the videos, and constructed a dictionary of visual features to classify pre-defined behaviors. We also identified unannotated behaviors with unsupervised methods. Using this analysis pipeline, we quantified 6 basic behaviors and found surprisingly similar behavior statistics across animals within the same species, regardless of experimental conditions. Our analysis indicates that the fundamental behavioral repertoire of Hydra is stable. This robustness could reflect a homeostatic neural control of "housekeeping" behaviors which could have been already present in the earliest nervous systems. © 2018, Han et al.

Targeted and untargeted-metabolite profiling to track the compositional integrity of ginger during processing using digitally-enhanced HPTLC pattern recognition analysis.

PubMed

Ibrahim, Reham S; Fathy, Hoda

2018-03-30

Tracking the impact of commonly applied post-harvesting and industrial processing practices on the compositional integrity of ginger rhizome was implemented in this work. Untargeted metabolite profiling was performed using digitally-enhanced HPTLC method where the chromatographic fingerprints were extracted using ImageJ software then analysed with multivariate Principal Component Analysis (PCA) for pattern recognition. A targeted approach was applied using a new, validated, simple and fast HPTLC image analysis method for simultaneous quantification of the officially recognized markers 6-, 8-, 10-gingerol and 6-shogaol in conjunction with chemometric Hierarchical Clustering Analysis (HCA). The results of both targeted and untargeted metabolite profiling revealed that peeling, drying in addition to storage employed during processing have a great influence on ginger chemo-profile, the different forms of processed ginger shouldn't be used interchangeably. Moreover, it deemed necessary to consider the holistic metabolic profile for comprehensive evaluation of ginger during processing. Copyright © 2018. Published by Elsevier B.V.

Mathematics is differentially related to reading comprehension and word decoding: Evidence from a genetically-sensitive design

PubMed Central

Harlaar, Nicole; Kovas, Yulia; Dale, Philip S.; Petrill, Stephen A.; Plomin, Robert

2013-01-01

Although evidence suggests that individual differences in reading and mathematics skills are correlated, this relationship has typically only been studied in relation to word decoding or global measures of reading. It is unclear whether mathematics is differentially related to word decoding and reading comprehension. The current study examined these relationships at both a phenotypic and etiological level in a population-based cohort of 5162 twin pairs at age 12. Multivariate genetic analyses of latent phenotypic factors of mathematics, word decoding and reading comprehension revealed substantial genetic and shared environmental correlations among all three domains. However, the phenotypic and genetic correlations between mathematics and reading comprehension were significantly greater than between mathematics and word decoding. Independent of mathematics, there was also evidence for genetic and nonshared environmental links between word decoding and reading comprehension. These findings indicate that word decoding and reading comprehension have partly distinct relationships with mathematics in the middle school years. PMID:24319294

Young readers' use of phonological information: phonological awareness, memory, and comprehension.

PubMed

Gray, Audra; McCutchen, Deborah

2006-01-01

In this study, we explored the relationship between beginning readers' phonological awareness and other aspects of phonological processing, specifically as manifested in short-term memory and comprehension tasks. The theoretical questions underlying the study were (a) what roles phonological processes play in children's beginning reading, from word identification through sentence comprehension, and (b) whether those roles are sufficiently related that potential difficulties at one level directly affect processing at other levels. Phonologically induced effects were observed for word-list memory and for sentence judgments for both novice readers (at the end of kindergarten) and relatively more experienced readers (end of Grades 1 and 2). For both age groups, correlational analyses revealed relationships among phonological awareness, phonological processing in list memory, and word reading. However, phonological processing in sentence comprehension was not related to other types of phonological processing. These results indicate that although phonology plays a role during comprehension, phonological processing may not be as limiting a factor in comprehension as in word reading.

Mathematics is differentially related to reading comprehension and word decoding: Evidence from a genetically-sensitive design.

PubMed

Harlaar, Nicole; Kovas, Yulia; Dale, Philip S; Petrill, Stephen A; Plomin, Robert

2012-08-01

Although evidence suggests that individual differences in reading and mathematics skills are correlated, this relationship has typically only been studied in relation to word decoding or global measures of reading. It is unclear whether mathematics is differentially related to word decoding and reading comprehension. The current study examined these relationships at both a phenotypic and etiological level in a population-based cohort of 5162 twin pairs at age 12. Multivariate genetic analyses of latent phenotypic factors of mathematics, word decoding and reading comprehension revealed substantial genetic and shared environmental correlations among all three domains. However, the phenotypic and genetic correlations between mathematics and reading comprehension were significantly greater than between mathematics and word decoding. Independent of mathematics, there was also evidence for genetic and nonshared environmental links between word decoding and reading comprehension. These findings indicate that word decoding and reading comprehension have partly distinct relationships with mathematics in the middle school years.

Identification of IL11RA and MELK amplification in gastric cancer by comprehensive genomic profiling of gastric cancer cell lines

PubMed Central

Calcagno, Danielle Queiroz; Takeno, Sylvia Santomi; Gigek, Carolina Oliveira; Leal, Mariana Ferreira; Wisnieski, Fernanda; Chen, Elizabeth Suchi; Araújo, Taíssa Maíra Thomaz; Lima, Eleonidas Moura; Melaragno, Maria Isabel; Demachki, Samia; Assumpção, Paulo Pimentel; Burbano, Rommel Rodriguez; Smith, Marília Cardoso

2016-01-01

AIM To identify common copy number alterations on gastric cancer cell lines. METHODS Four gastric cancer cell lines (ACP02, ACP03, AGP01 and PG100) underwent chromosomal comparative genome hybridization and array comparative genome hybridization. We also confirmed the results by fluorescence in situ hybridization analysis using the bacterial artificial chromosome clone and quantitative real time PCR analysis. RESULTS The amplification of 9p13.3 was detected in all cell lines by both methodologies. An increase in the copy number of 9p13.3 was also confirmed by fluorescence in situ hybridization analysis. Moreover, the interleukin 11 receptor alpha (IL11RA) and maternal embryonic leucine zipper kinase (MELK) genes, which are present in the 9p13.3 amplicon, revealed gains of the MELK gene in all the cell lines studied. Additionally, a gain in the copy number of IL11RA and MELK was observed in 19.1% (13/68) and 55.9% (38/68) of primary gastric adenocarcinoma samples, respectively. CONCLUSION The characterization of a small gain region at 9p13.3 in gastric cancer cell lines and primary gastric adenocarcinoma samples has revealed MELK as a candidate target gene that is possibly related to the development of gastric cancer. PMID:27920471

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

PubMed

Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

2015-05-19

Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.

Simultaneous Evaluation of Life Cycle Dynamics between a Host Paramecium and the Endosymbionts of Paramecium bursaria Using Capillary Flow Cytometry.

PubMed

Takahashi, Toshiyuki

2016-08-17

Endosymbioses are driving forces underlying cell evolution. The endosymbiosis exhibited by Paramecium bursaria is an excellent model with which to study symbiosis. A single-cell microscopic analysis of P. bursaria reveals that endosymbiont numbers double when the host is in the division phase. Consequently, endosymbionts must arrange their cell cycle schedule if the culture-condition-dependent change delays the generation time of P. bursaria. However, it remains poorly understood whether endosymbionts keep pace with the culture-condition-dependent behaviors of P. bursaria, or not. Using microscopy and flow cytometry, this study investigated the life cycle behaviors occurring between endosymbionts and the host. To establish a connection between the host cell cycle and endosymbionts comprehensively, multivariate analysis was applied. The multivariate analysis revealed important information related to regulation between the host and endosymbionts. Results show that dividing endosymbionts underwent transition smoothly from the division phase to interphase, when the host was in the logarithmic phase. In contrast, endosymbiont division stagnated when the host was in the stationary phase. This paper explains that endosymbionts fine-tune their cell cycle pace with their host and that a synchronous life cycle between the endosymbionts and the host is guaranteed in the symbiosis of P. bursaria.

Simultaneous Evaluation of Life Cycle Dynamics between a Host Paramecium and the Endosymbionts of Paramecium bursaria Using Capillary Flow Cytometry

PubMed Central

Takahashi, Toshiyuki

2016-01-01

Endosymbioses are driving forces underlying cell evolution. The endosymbiosis exhibited by Paramecium bursaria is an excellent model with which to study symbiosis. A single-cell microscopic analysis of P. bursaria reveals that endosymbiont numbers double when the host is in the division phase. Consequently, endosymbionts must arrange their cell cycle schedule if the culture-condition-dependent change delays the generation time of P. bursaria. However, it remains poorly understood whether endosymbionts keep pace with the culture-condition-dependent behaviors of P. bursaria, or not. Using microscopy and flow cytometry, this study investigated the life cycle behaviors occurring between endosymbionts and the host. To establish a connection between the host cell cycle and endosymbionts comprehensively, multivariate analysis was applied. The multivariate analysis revealed important information related to regulation between the host and endosymbionts. Results show that dividing endosymbionts underwent transition smoothly from the division phase to interphase, when the host was in the logarithmic phase. In contrast, endosymbiont division stagnated when the host was in the stationary phase. This paper explains that endosymbionts fine-tune their cell cycle pace with their host and that a synchronous life cycle between the endosymbionts and the host is guaranteed in the symbiosis of P. bursaria. PMID:27531180

The rubber tree genome shows expansion of gene family associated with rubber biosynthesis.

PubMed

Lau, Nyok-Sean; Makita, Yuko; Kawashima, Mika; Taylor, Todd D; Kondo, Shinji; Othman, Ahmad Sofiman; Shu-Chien, Alexander Chong; Matsui, Minami

2016-06-24

Hevea brasiliensis Muell. Arg, a member of the family Euphorbiaceae, is the sole natural resource exploited for commercial production of high-quality natural rubber. The properties of natural rubber latex are almost irreplaceable by synthetic counterparts for many industrial applications. A paucity of knowledge on the molecular mechanisms of rubber biosynthesis in high yield traits still persists. Here we report the comprehensive genome-wide analysis of the widely planted H. brasiliensis clone, RRIM 600. The genome was assembled based on ~155-fold combined coverage with Illumina and PacBio sequence data and has a total length of 1.55 Gb with 72.5% comprising repetitive DNA sequences. A total of 84,440 high-confidence protein-coding genes were predicted. Comparative genomic analysis revealed strong synteny between H. brasiliensis and other Euphorbiaceae genomes. Our data suggest that H. brasiliensis's capacity to produce high levels of latex can be attributed to the expansion of rubber biosynthesis-related genes in its genome and the high expression of these genes in latex. Using cap analysis gene expression data, we illustrate the tissue-specific transcription profiles of rubber biosynthesis-related genes, revealing alternative means of transcriptional regulation. Our study adds to the understanding of H. brasiliensis biology and provides valuable genomic resources for future agronomic-related improvement of the rubber tree.

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR)

PubMed Central

Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J.; Laclette, Juan P.; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

2015-01-01

Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest. PMID:25989346

Comprehensive Proteomics Analysis of Laticifer Latex Reveals New Insights into Ethylene Stimulation of Natural Rubber Production.

PubMed

Wang, Xuchu; Wang, Dan; Sun, Yong; Yang, Qian; Chang, Lili; Wang, Limin; Meng, Xueru; Huang, Qixing; Jin, Xiang; Tong, Zheng

2015-09-08

Ethylene is a stimulant to increase natural rubber latex. After ethylene application, both fresh yield and dry matter of latex are substantially improved. Moreover, we found that ethylene improves the generation of small rubber particles. However, most genes involved in rubber biosynthesis are inhibited by exogenous ethylene. Therefore, we conducted a proteomics analysis of ethylene-stimulated rubber latex, and identified 287 abundant proteins as well as 143 ethylene responsive latex proteins (ERLPs) with mass spectrometry from the 2-DE and DIGE gels, respectively. In addition, more than 1,600 proteins, including 404 ERLPs, were identified by iTRAQ. Functional classification of ERLPs revealed that enzymes involved in post-translational modification, carbohydrate metabolism, hydrolase activity, and kinase activity were overrepresented. Some enzymes for rubber particle aggregation were inhibited to prolong latex flow, and thus finally improved latex production. Phosphoproteomics analysis identified 59 differential phosphoproteins; notably, specific isoforms of rubber elongation factor and small rubber particle protein that were phosphorylated mainly at serine residues. This post-translational modification and isoform-specific phosphorylation might be important for ethylene-stimulated latex production. These results not only deepen our understanding of the rubber latex proteome but also provide new insights into the use of ethylene to stimulate rubber latex production.

Reading Speed, Comprehension and Eye Movements While Reading Japanese Novels: Evidence from Untrained Readers and Cases of Speed-Reading Trainees

PubMed Central

Miyata, Hiromitsu; Minagawa-Kawai, Yasuyo; Watanabe, Shigeru; Sasaki, Toyofumi; Ueda, Kazuhiro

2012-01-01

Background A growing body of evidence suggests that meditative training enhances perception and cognition. In Japan, the Park-Sasaki method of speed-reading involves organized visual training while forming both a relaxed and concentrated state of mind, as in meditation. The present study examined relationships between reading speed, sentence comprehension, and eye movements while reading short Japanese novels. In addition to normal untrained readers, three middle-level trainees and one high-level expert on this method were included for the two case studies. Methodology/Principal Findings In Study 1, three of 17 participants were middle-level trainees on the speed-reading method. Immediately after reading each story once on a computer monitor, participants answered true or false questions regarding the content of the novel. Eye movements while reading were recorded using an eye-tracking system. Results revealed higher reading speed and lower comprehension scores in the trainees than in the untrained participants. Furthermore, eye-tracking data by untrained participants revealed multiple correlations between reading speed, accuracy and eye-movement measures, with faster readers showing shorter fixation durations and larger saccades in X than slower readers. In Study 2, participants included a high-level expert and 14 untrained students. The expert showed higher reading speed and statistically comparable, although numerically lower, comprehension scores compared with the untrained participants. During test sessions this expert moved her eyes along a nearly straight horizontal line as a first pass, without moving her eyes over the whole sentence display as did the untrained students. Conclusions/Significance In addition to revealing correlations between speed, comprehension and eye movements in reading Japanese contemporary novels by untrained readers, we describe cases of speed-reading trainees regarding relationships between these variables. The trainees overall tended to show poor performance influenced by the speed-accuracy trade-off, although this trade-off may be reduced in the case of at least one high-level expert. PMID:22590519

Oral cancer screening: knowledge is not enough.

PubMed

Tax, C L; Haslam, S Kim; Brillant, Mgs; Doucette, H J; Cameron, J E; Wade, S E

2017-08-01

The purpose of this cross-sectional study was to investigate whether dental hygienists are transferring their knowledge of oral cancer screening into practice. This study also wanted to gain insight into the barriers that might prevent dental hygienists from performing these screenings. A 27-item survey instrument was constructed to study the oral cancer screening practices of licensed dental hygienists in Nova Scotia. A total of 623 practicing dental hygienists received the survey. The response rate was 34% (n = 212) yielding a maximum margin of error of 5.47 at a 95% confidence level. Descriptive statistics were calculated using IBM SPSS Statistics v21 software (Armonk, NY:IBM Corp). Qualitative thematic analysis was performed on any open-ended responses. This study revealed that while dental hygienists perceived themselves as being knowledgeable about oral cancer screening, they were not transferring this knowledge to actual practice. Only a small percentage (13%) of respondents were performing a comprehensive extra-oral examination, and 7% were performing a comprehensive intra-oral examination. The respondents identified several barriers that prevented them from completing a comprehensive oral cancer screening. Early detection of oral cancer reduces mortality rates so there is a professional responsibility to ensure that comprehensive oral cancer screenings are being performed on patients. Dental hygienists may not have the authority in a dental practice to overcome all of the barriers that are preventing them from performing these screenings. Public awareness about oral cancer screenings could increase the demand for screenings and thereby play a role in changing practice norms. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Neural correlates of multimodal metaphor comprehension: Evidence from event-related potentials and time-frequency decompositions.

PubMed

Ma, Qingguo; Hu, Linfeng; Xiao, Can; Bian, Jun; Jin, Jia; Wang, Qiuzhen

2016-11-01

The present study examined the event-related potential (ERP) and time-frequency components correlates with the comprehension process of multimodal metaphors that were represented by the combination of "a vehicle picture+a written word of an animal". Electroencephalogram data were recorded when participants decided whether the metaphor using an animal word for the vehicle rendered by a picture was appropriate or not. There were two conditions: appropriateness (e.g., sport utility vehicles+tiger) vs. inappropriateness (e.g., sport utility vehicles+cat). The ERP results showed that inappropriate metaphor elicited larger N300 (280-360ms) and N400 (380-460ms) amplitude than appropriate one, which were different from previous exclusively verbal metaphor studies that rarely observed the N300 effect. A P600 (550-750ms) was also observed and larger in appropriate metaphor condition. Besides, the time-frequency principal component analysis revealed that two independent theta activities indexed the separable processes (retrieval of semantic features and semantic integration) underlying the N300 and N400. Delta band was also induced within a later time window and best characterized the integration process underlying P600. These results indicate the specific cognitive mechanism of multimodal metaphor comprehension that is different from verbal metaphor processing, mirrored by several separable processes indexed by ERP components and time-frequency components. The present study extends the metaphor research by uncovering the functional roles of delta and theta as well as their unique contributions to the ERP components during multimodal metaphor comprehension. Copyright © 2016 Elsevier B.V. All rights reserved.

Complementary and Alternative Medicine Use in Individuals Presenting for Care at a Comprehensive Cancer Center.

PubMed

Judson, Patricia L; Abdallah, Reem; Xiong, Yin; Ebbert, Judith; Lancaster, Johnathan M

2017-03-01

To define the use of complementary and alternative medicine (CAM) in individuals presenting for care at a comprehensive cancer center. A total of 17 639 individuals presenting to an NCI-designated Comprehensive Cancer Center (and consortium sites) completed a questionnaire regarding CAM use. Data were analyzed using the univariate χ 2 test to assess CAM use associated with a number of variables, including cancer status, age, gender, marital status, ethnicity, race, employment, and education level. Eighty-seven percent of individuals who completed the CAM survey acknowledged CAM therapy use within the previous 12 months. Of the 5 broad categories of CAM, the most commonly used were biologically based approaches (14 759/17 639 [83.67%]), mind-body interventions (4624/17 485 [26.45%]), manipulative and body-based therapies (3957/17 537 [22.56%]), alternative medical systems (429/15 952 [2.69%]), and energy therapies (270/15 872 [1.7%]). CAM use was more prevalent among women, non-Hispanics, Caucasians, patients 60 to 69 years of age, and those who are married, have a higher level of education, and are employed ( P < .005). This is the largest report of CAM use in individuals presenting for care at a comprehensive cancer center. Our analysis revealed that a very high percentage of patients utilize CAM. Because many of these CAM interventions are not studied in oncology patients, additional research on safety, efficacy, and mechanisms of action are essential. Furthermore, it is important that oncologists understand CAM modalities and counsel their patients about their use.

Comprehensive CT Evaluation in Acute Ischemic Stroke: Impact on Diagnosis and Treatment Decisions

PubMed Central

Löve, Askell; Siemund, Roger; Andsberg, Gunnar; Cronqvist, Mats; Holtås, Stig; Björkman-Burtscher, Isabella

2011-01-01

Background. With modern CT imaging a comprehensive overview of cerebral macro- and microcirculation can be obtained within minutes in acute ischemic stroke. This opens for patient stratification and individualized treatment. Methods. Four patients with acute ischemic stroke of different aetiologies and/or treatments were chosen for illustration of the comprehensive CT protocol and its value in subsequent treatment decisions. The patients were clinically evaluated according to the NIHSS-scale, examined with the comprehensive CT protocol including both CT angiography and CT perfusion, and followed up by MRI. Results. The comprehensive CT examination protocol increased the examination time but did not delay treatment initiation. In some cases CT angiography revealed the cause of stroke while CT perfusion located and graded the perfusion defect with reasonable accuracy, confirmed by follow-up MR-diffusion. In the presented cases findings of the comprehensive CT examination influenced the treatment strategy. Conclusions. The comprehensive CT examination is a fast and safe method allowing accurate diagnosis and making way for individualized treatment in acute ischemic stroke. PMID:21603175

Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds.

PubMed

Edea, Z; Bhuiyan, M S A; Dessie, T; Rothschild, M F; Dadi, H; Kim, K S

2015-02-01

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69,903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.

Horizontal gene transfer in silkworm, Bombyx mori.

PubMed

Zhu, Bo; Lou, Miao-Miao; Xie, Guan-Lin; Zhang, Guo-Qing; Zhou, Xue-Ping; Li, Bin; Jin, Gu-Lei

2011-05-19

The domesticated silkworm, Bombyx mori, is the model insect for the order Lepidoptera, has economically important values, and has gained some representative behavioral characteristics compared to its wild ancestor. The genome of B. mori has been fully sequenced while function analysis of BmChi-h and BmSuc1 genes revealed that horizontal gene transfer (HGT) maybe bestow a clear selective advantage to B. mori. However, the role of HGT in the evolutionary history of B. mori is largely unexplored. In this study, we compare the whole genome of B. mori with those of 382 prokaryotic and eukaryotic species to investigate the potential HGTs. Ten candidate HGT events were defined in B. mori by comprehensive sequence analysis using Maximum Likelihood and Bayesian method combining with EST checking. Phylogenetic analysis of the candidate HGT genes suggested that one HGT was plant-to- B. mori transfer while nine were bacteria-to- B. mori transfer. Furthermore, functional analysis based on expression, coexpression and related literature searching revealed that several HGT candidate genes have added important characters, such as resistance to pathogen, to B. mori. Results from this study clearly demonstrated that HGTs play an important role in the evolution of B. mori although the number of HGT events in B. mori is in general smaller than those of microbes and other insects. In particular, interdomain HGTs in B. mori may give rise to functional, persistent, and possibly evolutionarily significant new genes.

Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis

NASA Astrophysics Data System (ADS)

Li, Yue; Zhang, Zhaolei

2014-11-01

Carcinogenesis consists of oncogenesis and metastasis, and intriguingly microRNAs (miRNAs) are involved in both processes. Although aberrant miRNA activities are prevalent in diverse tumor types, the exact mechanisms for how they regulate cancerous processes are not always clear. To this end, we performed a large-scale pan-cancer analysis via a novel probabilistic approach to infer recurrent miRNA-target interactions implicated in 12 cancer types using data from The Cancer Genome Atlas. We discovered ~20,000 recurrent miRNA regulations, which are enriched for cancer-related miRNAs/genes. Notably, miRNA 200 family (miR-200/141/429) is among the most prominent miRNA regulators, which is known to be involved in metastasis. Importantly, the recurrent miRNA regulatory network is not only enriched for cancer pathways but also for extracellular matrix (ECM) organization and ECM-receptor interactions. The results suggest an intriguing cancer mechanism involving miRNA-mediated cell-to-cell communication, which possibly involves delivery of tumorigenic miRNA messengers to adjacent cells via exosomes. Finally, survival analysis revealed 414 recurrent-prognostic associations, where both gene and miRNA involved in each interaction conferred significant prognostic power in one or more cancer types. Together, our comprehensive pan-cancer analysis provided not only biological insights into metastasis but also brought to bear the clinical relevance of the proposed recurrent miRNA-gene associations.

Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs.

PubMed

Campion, S R; Ameen, A S; Lai, L; King, J M; Munzenmaier, T N

2001-08-15

This report describes the application of a simple computational tool, AAPAIR.TAB, for the systematic analysis of the cysteine-rich EGF, Sushi, and Laminin motif/sequence families at the two-amino acid level. Automated dipeptide frequency/bias analysis detects preferences in the distribution of amino acids in established protein families, by determining which "ordered dipeptides" occur most frequently in comprehensive motif-specific sequence data sets. Graphic display of the dipeptide frequency/bias data revealed family-specific preferences for certain dipeptides, but more importantly detected a shared preference for employment of the ordered dipeptides Gly-Tyr (GY) and Gly-Phe (GF) in all three protein families. The dipeptide Asn-Gly (NG) also exhibited high-frequency and bias in the EGF and Sushi motif families, whereas Asn-Thr (NT) was distinguished in the Laminin family. Evaluation of the distribution of dipeptides identified by frequency/bias analysis subsequently revealed the highly restricted localization of the G(F/Y) and N(G/T) sequence elements at two separate sites of extreme conservation in the consensus sequence of all three sequence families. The similar employment of the high-frequency/bias dipeptides in three distinct protein sequence families was further correlated with the concurrence of these shared molecular determinants at similar positions within the distinctive scaffolds of three structurally divergent, but similarly employed, motif modules.

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids.

PubMed

Schmitz, Alexander; Fischer, Sabine C; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H K

2017-03-03

Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid's size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 10 5 to 1 × 10 6  cells/mm 3 . Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.

Comprehension of Co-Speech Gestures in Aphasic Patients: An Eye Movement Study.

PubMed

Eggenberger, Noëmi; Preisig, Basil C; Schumacher, Rahel; Hopfner, Simone; Vanbellingen, Tim; Nyffeler, Thomas; Gutbrod, Klemens; Annoni, Jean-Marie; Bohlhalter, Stephan; Cazzoli, Dario; Müri, René M

2016-01-01

Co-speech gestures are omnipresent and a crucial element of human interaction by facilitating language comprehension. However, it is unclear whether gestures also support language comprehension in aphasic patients. Using visual exploration behavior analysis, the present study aimed to investigate the influence of congruence between speech and co-speech gestures on comprehension in terms of accuracy in a decision task. Twenty aphasic patients and 30 healthy controls watched videos in which speech was either combined with meaningless (baseline condition), congruent, or incongruent gestures. Comprehension was assessed with a decision task, while remote eye-tracking allowed analysis of visual exploration. In aphasic patients, the incongruent condition resulted in a significant decrease of accuracy, while the congruent condition led to a significant increase in accuracy compared to baseline accuracy. In the control group, the incongruent condition resulted in a decrease in accuracy, while the congruent condition did not significantly increase the accuracy. Visual exploration analysis showed that patients fixated significantly less on the face and tended to fixate more on the gesturing hands compared to controls. Co-speech gestures play an important role for aphasic patients as they modulate comprehension. Incongruent gestures evoke significant interference and deteriorate patients' comprehension. In contrast, congruent gestures enhance comprehension in aphasic patients, which might be valuable for clinical and therapeutic purposes.

Improved word comprehension in Global aphasia using a modified semantic feature analysis treatment.

PubMed

Munro, Philippa; Siyambalapitiya, Samantha

2017-01-01

Limited research has investigated treatment of single word comprehension in people with aphasia, despite numerous studies examining treatment of naming deficits. This study employed a single case experimental design to examine efficacy of a modified semantic feature analysis (SFA) therapy in improving word comprehension in an individual with Global aphasia, who presented with a semantically based comprehension impairment. Ten treatment sessions were conducted over a period of two weeks. Following therapy, the participant demonstrated improved comprehension of treatment items and generalisation to control items, measured by performance on a spoken word picture matching task. Improvements were also observed on other language assessments (e.g. subtests of WAB-R; PALPA subtest 47) and were largely maintained over a period of 12 weeks without further therapy. This study provides support for the efficacy of a modified SFA therapy in remediating single word comprehension in individuals with aphasia with a semantically based comprehension deficit.

Predicting Employment Outcomes of Consumers of State-Operated Comprehensive Rehabilitation Centers

ERIC Educational Resources Information Center

Beach, David Thomas

2009-01-01

This study used records from a state-operated comprehensive rehabilitation center to investigate possible predictive factors related to completing comprehensive rehabilitation center programs and successful vocational rehabilitation (VR) case closure. An analysis of demographic data of randomly selected comprehensive rehabilitation center…

On the Parity of Structural Persistence in Language Production and Comprehension

PubMed Central

Tooley, Kristen M.; Bock, Kathryn

2014-01-01

Structural priming creates structural persistence. That is, differences in experience with syntax can change subsequent language performance, and the changes can be observed in both language production and comprehension. However, the effects in comprehension and production appear to differ. In comprehension, persistence is typically found when the verbs are the same in primes and targets; in production, persistence occurs without verb overlap. The contrast suggests a theoretically important hypothesis: parsing in comprehension is lexically driven while formulation in production is structurally driven. A major weakness in this hypothesis about comprehension-production differences is that its empirical motivation rests on the outcomes of experiments in which the priming manipulations differ, the primed sentence structures differ, and the measures of priming differ. To sharpen the comparison, we examined structural persistence with and without verb overlap in both reading comprehension and spoken production, using the same prime presentation procedure, the same syntactic structures, the same sentences, and the same participants. These methods yielded abstract sructural persistence in comprehension as well as production. A measure of the strength of persistence revealed significant effects of priming and verb overlap without significant comprehension—production differences. This argues for uniformity in the structural mechanisms of language processing. PMID:24803423

Comprehensive Analysis of the Soybean (Glycine max) GmLAX Auxin Transporter Gene Family

PubMed Central

Chai, Chenglin; Wang, Yongqin; Valliyodan, Babu; Nguyen, Henry T.

2016-01-01

The phytohormone auxin plays a critical role in regulation of plant growth and development as well as plant responses to abiotic stresses. This is mainly achieved through its uneven distribution in plant via a polar auxin transport process. Auxin transporters are major players in polar auxin transport. The AUXIN RESISTENT 1/LIKE AUX1 (AUX/LAX) auxin influx carriers belong to the amino acid permease family of proton-driven transporters and function in the uptake of indole-3-acetic acid (IAA). In this study, genome-wide comprehensive analysis of the soybean AUX/LAX (GmLAX) gene family, including phylogenic relationships, chromosome localization, and gene structure, was carried out. A total of 15 GmLAX genes, including seven duplicated gene pairs, were identified in the soybean genome. They were distributed on 10 chromosomes. Despite their higher percentage identities at the protein level, GmLAXs exhibited versatile tissue-specific expression patterns, indicating coordinated functioning during plant growth and development. Most GmLAXs were responsive to drought and dehydration stresses and auxin and abscisic acid (ABA) stimuli, in a tissue- and/or time point- sensitive mode. Several GmLAX members were involved in responding to salt stress. Sequence analysis revealed that promoters of GmLAXs contained different combinations of stress-related cis-regulatory elements. These studies suggest that the soybean GmLAXs were under control of a very complex regulatory network, responding to various internal and external signals. This study helps to identity candidate GmLAXs for further analysis of their roles in soybean development and adaption to adverse environments. PMID:27014306

Assessing Footwear Effects from Principal Features of Plantar Loading during Running.

PubMed

Trudeau, Matthieu B; von Tscharner, Vinzenz; Vienneau, Jordyn; Hoerzer, Stefan; Nigg, Benno M

2015-09-01

The effects of footwear on the musculoskeletal system are commonly assessed by interpreting the resultant force at the foot during the stance phase of running. However, this approach overlooks loading patterns across the entire foot. An alternative technique for assessing foot loading across different footwear conditions is possible using comprehensive analysis tools that extract different foot loading features, thus enhancing the functional interpretation of the differences across different interventions. The purpose of this article was to use pattern recognition techniques to develop and use a novel comprehensive method for assessing the effects of different footwear interventions on plantar loading. A principal component analysis was used to extract different loading features from the stance phase of running, and a support vector machine (SVM) was used to determine whether and how these loading features were different across three shoe conditions. The results revealed distinct loading features at the foot during the stance phase of running. The loading features determined from the principal component analysis allowed successful classification of all three shoe conditions using the SVM. Several differences were found in the location and timing of the loading across each pairwise shoe comparison using the output from the SVM. The analysis approach proposed can successfully be used to compare different loading patterns with a much greater resolution than has been reported previously. This study has several important applications. One such application is that it would not be relevant for a user to select a shoe or for a manufacturer to alter a shoe's construction if the classification across shoe conditions would not have been significant.

A lead discovery strategy driven by a comprehensive analysis of proteases in the peptide substrate space

PubMed Central

Sukuru, Sai Chetan K; Nigsch, Florian; Quancard, Jean; Renatus, Martin; Chopra, Rajiv; Brooijmans, Natasja; Mikhailov, Dmitri; Deng, Zhan; Cornett, Allen; Jenkins, Jeremy L; Hommel, Ulrich; Davies, John W; Glick, Meir

2010-01-01

We present here a comprehensive analysis of proteases in the peptide substrate space and demonstrate its applicability for lead discovery. Aligned octapeptide substrates of 498 proteases taken from the MEROPS peptidase database were used for the in silico analysis. A multiple-category naïve Bayes model, trained on the two-dimensional chemical features of the substrates, was able to classify the substrates of 365 (73%) proteases and elucidate statistically significant chemical features for each of their specific substrate positions. The positional awareness of the method allows us to identify the most similar substrate positions between proteases. Our analysis reveals that proteases from different families, based on the traditional classification (aspartic, cysteine, serine, and metallo), could have substrates that differ at the cleavage site (P1–P1′) but are similar away from it. Caspase-3 (cysteine protease) and granzyme B (serine protease) are previously known examples of cross-family neighbors identified by this method. To assess whether peptide substrate similarity between unrelated proteases could reliably translate into the discovery of low molecular weight synthetic inhibitors, a lead discovery strategy was tested on two other cross-family neighbors—namely cathepsin L2 and matrix metallo proteinase 9, and calpain 1 and pepsin A. For both these pairs, a naïve Bayes classifier model trained on inhibitors of one protease could successfully enrich those of its neighbor from a different family and vice versa, indicating that this approach could be prospectively applied to lead discovery for a novel protease target with no known synthetic inhibitors. PMID:20799349

Can Arabic Proverbs Enhance Arabic-Speaking Students' Comprehension of Financial Concepts?: An Empirical Study in Randomly Selected Business Schools in Dubai

ERIC Educational Resources Information Center

Warsame, Mohammed H.; Ireri, Edward M.

2017-01-01

In this study, we investigated the use of Arabic proverbs and quotes for teaching finance courses to Arabic-speaking students who are nonnative speakers of English. The study found that the use of Arabic proverbs and quotes greatly enhances the students' comprehension of the finance topics covered. Similarly, the study revealed that the use of…

Flying under the radar: figurative language impairments in focal lesion patients

PubMed Central

Ianni, Geena R.; Cardillo, Eileen R.; McQuire, Marguerite; Chatterjee, Anjan

2014-01-01

Despite the prevalent and natural use of metaphor in everyday language, the neural basis of this powerful communication device remains poorly understood. Early studies of brain-injured patients suggested the right hemisphere plays a critical role in metaphor comprehension, but more recent patient and neuroimaging studies do not consistently support this hypothesis. One explanation for this discrepancy is the challenge in designing optimal tasks for brain-injured populations. As traditional aphasia assessments do not assess figurative language comprehension, we designed a new metaphor comprehension task to consider whether impaired metaphor processing is missed by standard clinical assessments. Stimuli consisted of 60 pairs of moderately familiar metaphors and closely matched literal sentences. Sentences were presented visually in a randomized order, followed by four adjective-noun answer choices (target + three foil types). Participants were instructed to select the phrase that best matched the meaning of the sentence. We report the performance of three focal lesion patients and a group of 12 healthy, older controls. Controls performed near ceiling in both conditions, with slightly more accurate performance on literal than metaphoric sentences. While the Western Aphasia Battery (Kertesz, 1982) and the objects and actions naming battery (Druks and Masterson, 2000) indicated minimal to no language difficulty, our metaphor comprehension task indicated three different profiles of metaphor comprehension impairment in the patients’ performance. Single case statistics revealed comparable impairment on metaphoric and literal sentences, disproportionately greater impairment on metaphors than literal sentences, and selective impairment on metaphors. We conclude our task reveals that patients can have selective metaphor comprehension deficits. These deficits are not captured by traditional neuropsychological language assessments, suggesting overlooked communication difficulties. PMID:25404906

Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits.

PubMed

Wu, Hong-xia; Jia, Hui-min; Ma, Xiao-wei; Wang, Song-biao; Yao, Quan-sheng; Xu, Wen-tian; Zhou, Yi-gang; Gao, Zhong-shan; Zhan, Ru-lin

2014-06-13

Here we used Illumina RNA-seq technology for transcriptome sequencing of a mixed fruit sample from 'Zill' mango (Mangifera indica Linn) fruit pericarp and pulp during the development and ripening stages. RNA-seq generated 68,419,722 sequence reads that were assembled into 54,207 transcripts with a mean length of 858bp, including 26,413 clusters and 27,794 singletons. A total of 42,515(78.43%) transcripts were annotated using public protein databases, with a cut-off E-value above 10(-5), of which 35,198 and 14,619 transcripts were assigned to gene ontology terms and clusters of orthologous groups respectively. Functional annotation against the Kyoto Encyclopedia of Genes and Genomes database identified 23,741(43.79%) transcripts which were mapped to 128 pathways. These pathways revealed many previously unknown transcripts. We also applied mass spectrometry-based transcriptome data to characterize the proteome of ripe fruit. LC-MS/MS analysis of the mango fruit proteome was using tandem mass spectrometry (MS/MS) in an LTQ Orbitrap Velos (Thermo) coupled online to the HPLC. This approach enabled the identification of 7536 peptides that matched 2754 proteins. Our study provides a comprehensive sequence for a systemic view of transcriptome during mango fruit development and the most comprehensive fruit proteome to date, which are useful for further genomics research and proteomic studies. Our study provides a comprehensive sequence for a systemic view of both the transcriptome and proteome of mango fruit, and a valuable reference for further research on gene expression and protein identification. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Implementation of a gerontology nurse specialist role in primary health care: Health professional and older adult perspectives.

PubMed

King, Anna I I; Boyd, Michal L; Dagley, Lynelle; Raphael, Deborah L

2018-02-01

To explore an innovative primary healthcare gerontology nurse specialist role from the perspectives of older people and health professionals. Primary care is struggling to meet the needs and demands of complex older people. New models which incorporate holistic assessment and care coordination are necessary. A qualitative descriptive general inductive design was used. Older people at risk of health and functional decline were identified and received a comprehensive gerontology assessment and care coordination. Older adults (75 years+) enrolled within one of three primary healthcare practices in Auckland, New Zealand were eligible. Healthcare professionals directly involved with the primary healthcare gerontology nurse specialist model were invited for study participation. Face-to-face interviews were held with five older people and six health professionals were interviewed by telephone. A semistructured interview guide was used for all interviews. A general inductive approach was undertaken for analysis to systematically identify codes and themes. Data analysis revealed two central themes from the older people perspective: "holistic expertise" and "communication." Two main themes were identified from the health professional perspective: "competency" and "service delivery." Results showed the gerontology nurse specialist role was highly regarded by both older people and the health professionals. The in-home comprehensive geriatric assessment was identified as greatly beneficial. The competence and care coordination of the gerontology nurse specialist reduced fragmentation and were deemed immensely valuable. Care coordination should be recognised as a key component to meeting the complex needs of at-risk older people in the community. The expert knowledge of the gerontology nurse specialist and in-home comprehensive geriatric assessment were crucial aspects of the new model. Equally important was the assimilation of primary and secondary care infrastructure to upskill and deliver mentorship to the gerontology nurse specialist. © 2017 John Wiley & Sons Ltd.

Comprehensively Measuring Health-Related Subjective Well-Being: Dimensionality Analysis for Improved Outcome Assessment in Health Economics.

PubMed

de Vries, Marieke; Emons, Wilco H M; Plantinga, Arnoud; Pietersma, Suzanne; van den Hout, Wilbert B; Stiggelbout, Anne M; van den Akker-van Marle, M Elske

2016-01-01

Allocation of inevitably limited financial resources for health care requires assessment of an intervention's effectiveness. Interventions likely affect quality of life (QOL) more broadly than is measurable with commonly used health-related QOL utility scales. In line with the World Health Organization's definition of health, a recent Delphi procedure showed that assessment needs to put more emphasis on mental and social dimensions. To identify the core dimensions of health-related subjective well-being (HR-SWB) for a new, more comprehensive outcome measure. We formulated items for each domain of an initial Delphi-based set of 21 domains of HR-SWB. We tested these items in a large sample (N = 1143) and used dimensionality analyses to find a smaller number of latent factors. Exploratory factor analysis suggested a five-factor model, which explained 65% of the total variance. Factors related to physical independence, positive affect, negative affect, autonomy, and personal growth. Correlations between the factors ranged from 0.19 to 0.59. A closer inspection of the factors revealed an overlap between the newly identified core dimensions of HR-SWB and the validation scales, but the dimensions of HR-SWB also seemed to reflect additional aspects. This shows that the dimensions of HR-SWB we identified go beyond the existing health-related QOL instruments. We identified a set of five key dimensions to be included in a new, comprehensive measure of HR-SWB that reliably captures these dimensions and fills in the gaps of the existent measures used in economic evaluations. Copyright © 2016 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Comprehensive analysis of the mutation spectrum in 301 German ALS families.

PubMed

Müller, Kathrin; Brenner, David; Weydt, Patrick; Meyer, Thomas; Grehl, Torsten; Petri, Susanne; Grosskreutz, Julian; Schuster, Joachim; Volk, Alexander E; Borck, Guntram; Kubisch, Christian; Klopstock, Thomas; Zeller, Daniel; Jablonka, Sibylle; Sendtner, Michael; Klebe, Stephan; Knehr, Antje; Günther, Kornelia; Weis, Joachim; Claeys, Kristl G; Schrank, Berthold; Sperfeld, Anne-Dorte; Hübers, Annemarie; Otto, Markus; Dorst, Johannes; Meitinger, Thomas; Strom, Tim M; Andersen, Peter M; Ludolph, Albert C; Weishaupt, Jochen H

2018-04-12

Recent advances in amyotrophic lateral sclerosis (ALS) genetics have revealed that mutations in any of more than 25 genes can cause ALS, mostly as an autosomal-dominant Mendelian trait. Detailed knowledge about the genetic architecture of ALS in a specific population will be important for genetic counselling but also for genotype-specific therapeutic interventions. Here we combined fragment length analysis, repeat-primed PCR, Southern blotting, Sanger sequencing and whole exome sequencing to obtain a comprehensive profile of genetic variants in ALS disease genes in 301 German pedigrees with familial ALS. We report C9orf72 mutations as well as variants in consensus splice sites and non-synonymous variants in protein-coding regions of ALS genes. We furthermore estimate their pathogenicity by taking into account type and frequency of the respective variant as well as segregation within the families. 49% of our German ALS families carried a likely pathogenic variant in at least one of the earlier identified ALS genes. In 45% of the ALS families, likely pathogenic variants were detected in C9orf72, SOD1, FUS, TARDBP or TBK1 , whereas the relative contribution of the other ALS genes in this familial ALS cohort was 4%. We identified several previously unreported rare variants and demonstrated the absence of likely pathogenic variants in some of the recently described ALS disease genes. We here present a comprehensive genetic characterisation of German familial ALS. The present findings are of importance for genetic counselling in clinical practice, for molecular research and for the design of diagnostic gene panels or genotype-specific therapeutic interventions in Europe. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Community-Dwelling People Screened Positive for Dementia in Primary Care: A Comprehensive, Multivariate Descriptive Analysis Using Data from the DelpHi-Study.

PubMed

Thyrian, Jochen René; Eichler, Tilly; Michalowsky, Bernhard; Wucherer, Diana; Reimann, Melanie; Hertel, Johannes; Richter, Steffen; Dreier, Adina; Hoffmann, Wolfgang

2016-03-30

Efficient help and care for people with dementia (PWD) is dependent on knowledge about PWD in primary care. This analysis comprehensively describes community-dwelling PWD in primary care with respect to various dementia care specific variables. The analyses are based on baseline data of the ongoing general practitioner-based, randomized, controlled intervention trial DelpHi-MV (Dementia: life- and person-centered help). 6,838 patients were screened for dementia in 136 GP practices; 17.1% were screened positive, 54.4% of those agreed to participate and data could be assessed in n = 516 subjects. We assessed age, sex, living situation, cognitive status, functional status, level of impairment, comorbidities, formal diagnosis of dementia, depression, neuropsychiatric symptoms, quality of life, utilization of medical support, and pharmacological therapy. Concerning clinical-, dementia-, and health-related variables, the sample under examination was on average mildly cognitively and functionally impaired (MMSE, m = 22.2; BADL, m = 3.7). A level of care was assigned in 38.0%. Depression was identified in 15.4% and other frequent comorbidities were high blood pressure (83.3%), coronary heart diseases (37.1%), cerebrovascular diseases (22.3%), among others. In 48.6%, neuropsychiatric symptoms were present in a clinically relevant severity. Pharmacological treatment with antidementia medication was received by 25.8% and antidepressant medication by 14.0%. Utilization of services was generally low. The comprehensive description of people screened positive for dementia in primary care reveals a complex and unique population of patients. They are considerably underdiagnosed and in their majority mildly to moderately affected. More in-depth analyses are needed to study relations, associations and interactions between different variables.

'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

PubMed

Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

2018-01-01

A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

The L441P mutation of cystic fibrosis transmembrane conductance regulator and its molecular pathogenic mechanisms in a Korean patient with cystic fibrosis.

PubMed

Gee, Heon Yung; Kim, Chang Keun; Kim, So Won; Lee, Ji Hyun; Kim, Jeong-Ho; Kim, Kyung Hwan; Lee, Min Goo

2010-01-01

Cystic fibrosis (CF) is an autosomal recessive disorder usually found in populations of white Caucasian descent. CF is caused by mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. A 5-yr-old Korean girl was admitted complaining of coughing and greenish sputum. Chest radiographs and computed tomographic (CT) scan revealed diffuse bronchiectasis in both lungs. The patient had chronic diarrhea and poor weight gain, and the abdominal pancreaticobiliary CT scan revealed atrophy of the pancreas. Finally, CF was confirmed by the repeated analysis of the quantitative pilocarpine iontophoresis test. The chloride concentration of sweat samples taken from both forearms of the pateint was an average of 88.7 mM/L (normal value <40 mM/L). After a comprehensive search for mutations in the CFTR gene, the patient was found to carry the non-synonymous L441P mutation in one allele. Molecular physiologic analysis of the L441P mutation of CFTR revealed that the L441P mutation completely abolished the CFTR Cl(-) channel activity by disrupting proper protein folding and membrane trafficking of CFTR protein. These results confirmed the pathogenicity of the L441P mutation of CFTR circulating in the Korean population. The possibility of CF should be suspected in patients with chronic bronchiectasis, although the frequency of CF is relatively rare in East Asia.

Factors associated with syphilis infection: a comprehensive analysis based on a case-control study.

PubMed

Xiao, Y; Li, S-L; Lin, H-L; Lin, Z-F; Zhu, X-Z; Fan, J-Y; Gao, K; Zhang, H-L; Lin, L-R; Liu, L-L; Tong, M-L; Niu, J-J; Yang, T-C

2016-04-01

This study aimed to comprehensively evaluate factors that influence the likelihood of syphilis infection from risk-taking behaviours and medical conditions. A retrospective case-control study was conducted by enrolling 664 syphilis inpatients (excluding 11 congenital syphilis patients) and 800 sex- and age-matched controls. Medical histories, clinical data and patient interview data were collected and subjected to logistic regression analyses. The prevalence of syphilis in the study population was 3·9% (675/17,304). By univariate analysis, syphilis infection was associated with migration between cities, marital status, smoking, reproductive history, hypertension, elevated blood urea nitrogen (BUN) and infection with hepatitis B virus (HBV) (P < 0·05). A high rate of syphilis-HBV co-infection was observed in HIV-negative patients and further research revealed an association between syphilis and specific HBV serological reactivity. Syphilis was also associated with the frequency, duration and status of tobacco use. Multivariate analysis indicated that syphilis infection was independently associated with migration between cities [adjusted odds ratio (aOR) 1·368, 95% confidence interval (CI) 1·048-1·785], current smoking (aOR 1·607, 95% CI 1·177-2·195), elevated BUN (aOR 1·782, 95% CI 1·188-2·673) and some serological patterns of HBV infection. To prevent the spread of infectious diseases, inpatients and blood donors should be tested for HIV, syphilis, HBV and HCV simultaneously.

The Effects of Music on Pain: A Meta-Analysis.

PubMed

Lee, Jin Hyung

2016-01-01

Numerous meta-analyses have been conducted on the topic of music and pain, with the latest comprehensive study published in 2006. Since that time, more than 70 randomized controlled trials (RCTs) have been published, necessitating a new and comprehensive review. The aim of this meta-analysis was to examine published RCT studies investigating the effect of music on pain. The present study included RCTs published between 1995 and 2014. Studies were obtained by searching 12 databases and hand-searching related journals and reference lists. Main outcomes were pain intensity, emotional distress from pain, vital signs, and amount of analgesic intake. Study quality was evaluated according to the Cochrane Collaboration guidelines. Analysis of the 97 included studies revealed that music interventions had statistically significant effects in decreasing pain on 0-10 pain scales (MD = -1.13), other pain scales (SMD = -0.39), emotional distress from pain (MD = -10.83), anesthetic use (SMD = -0.56), opioid intake (SMD = -0.24), non-opioid intake (SMD = -0.54), heart rate (MD = -4.25), systolic blood pressure (MD = -3.34), diastolic blood pressure (MD = -1.18), and respiration rate (MD = -1.46). Subgroup and moderator analyses yielded additional clinically informative outcomes. Considering all the possible benefits, music interventions may provide an effective complementary approach for the relief of acute, procedural, and cancer/chronic pain in the medical setting. © the American Music Therapy Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Commentary on: "Comprehensive transcriptional analysis of early-stage urothelial carcinoma." Hedegaard J, Lamy P, Nordentoft I, Algaba F, Høyer S, Ulhøi BP, Vang S, Reinert T, Hermann GG, Mogensen K, Thomsen MB, Nielsen MM, Marquez M, Segersten U, Aine M, Höglund M, Birkenkamp-Demtröder K, Fristrup N, Borre M, Hartmann A, Stöhr R, Wach S, Keck B, Seitz AK, Nawroth R, Maurer T, Tulic C, Simic T, Junker K, Horstmann M, Harving N, Petersen AC, Calle ML, Steyerberg EW, Beukers W, van Kessel KE, Jensen JB, Pedersen JS, Malmström PU, Malats N, Real FX, Zwarthoff EC, Ørntoft TF, Dyrskjøt L. Cancer Cell. 2016 Jul 11;30(1):27-42.

PubMed

Lee, Byron H

2017-09-01

Non-muscle-invasive bladder cancer (NMIBC) is a heterogeneous disease with widely different outcomes. We performed a comprehensive transcriptional analysis of 460 early-stage urothelial carcinomas and showed that NMIBC can be subgrouped into 3 major classes with basal- and luminal-like characteristics and different clinical outcomes. Large differences in biological processes such as the cell cycle, epithelial-mesenchymal transition, and differentiation were observed. Analysis of transcript variants revealed frequent mutations in genes encoding proteins involved in chromatin organization and cytoskeletal functions. Furthermore, mutations in well-known cancer driver genes (e.g., TP53 and ERBB2) were primarily found in high-risk tumors, together with APOBEC-related mutational signatures. The identification of subclasses in NMIBC may offer better prognostication and treatment selection based on subclass assignment. Copyright © 2017 Elsevier Inc. All rights reserved.

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models.

PubMed

Erguler, Kamil; Stumpf, Michael P H

2011-05-01

The size and complexity of cellular systems make building predictive models an extremely difficult task. In principle dynamical time-course data can be used to elucidate the structure of the underlying molecular mechanisms, but a central and recurring problem is that many and very different models can be fitted to experimental data, especially when the latter are limited and subject to noise. Even given a model, estimating its parameters remains challenging in real-world systems. Here we present a comprehensive analysis of 180 systems biology models, which allows us to classify the parameters with respect to their contribution to the overall dynamical behaviour of the different systems. Our results reveal candidate elements of control in biochemical pathways that differentially contribute to dynamics. We introduce sensitivity profiles that concisely characterize parameter sensitivity and demonstrate how this can be connected to variability in data. Systematically linking data and model sloppiness allows us to extract features of dynamical systems that determine how well parameters can be estimated from time-course measurements, and associates the extent of data required for parameter inference with the model structure, and also with the global dynamical state of the system. The comprehensive analysis of so many systems biology models reaffirms the inability to estimate precisely most model or kinetic parameters as a generic feature of dynamical systems, and provides safe guidelines for performing better inferences and model predictions in the context of reverse engineering of mathematical models for biological systems.

Functional Analysis of the Polyketide Synthase Genes in the Filamentous Fungus Gibberella zeae (Anamorph Fusarium graminearum)

PubMed Central

Gaffoor, Iffa; Brown, Daren W.; Plattner, Ron; Proctor, Robert H.; Qi, Weihong; Trail, Frances

2005-01-01

Polyketides are a class of secondary metabolites that exhibit a vast diversity of form and function. In fungi, these compounds are produced by large, multidomain enzymes classified as type I polyketide synthases (PKSs). In this study we identified and functionally disrupted 15 PKS genes from the genome of the filamentous fungus Gibberella zeae. Five of these genes are responsible for producing the mycotoxins zearalenone, aurofusarin, and fusarin C and the black perithecial pigment. A comprehensive expression analysis of the 15 genes revealed diverse expression patterns during grain colonization, plant colonization, sexual development, and mycelial growth. Expression of one of the PKS genes was not detected under any of 18 conditions tested. This is the first study to genetically characterize a complete set of PKS genes from a single organism. PMID:16278459

Chromosome 2 short arm translocations revealed by M-FISH analysis of neuroblastoma cell lines.

PubMed

Van Roy, N; Van Limbergen, H; Vandesompele, J; Van Gele, M; Poppe, B; Laureys, G; De Paepe, A; Speleman, F

2000-12-01

M-FISH analysis was performed on 18 neuroblastoma cell lines, which were previously studied with cytogenetic, standard FISH and CGH data. One of the most striking findings of this study was the detection of chromosome 2 short arm rearrangements in 61% of the investigated cell lines. These rearrangements resulted from translocations with various partner chromosomes. All translocations, except one were unbalanced, leading to the consistent gain of chromosome segment 2pter-p22. A cryptic balanced translocation t(2;4) was observed with a breakpoint located in the vicinity of MYCN in cell line NBL-S. Combination of M-FISH results together with cytogenetic, standard FISH and CGH data yielded the most comprehensive description of chromosome 2 short arm rearrangements, leading to a consistent gain of chromosome 2 short arm material. Copyright 2000 Wiley-Liss, Inc.

Chemical Effect on Wellbore Instability of Nahr Umr Shale

PubMed Central

Nie, Zhen

2013-01-01

Wellbore instability is one of the major problems that hamper the drilling speed in Halfaya Oilfield. Comprehensive analysis of geological and engineering data indicates that Halfaya Oilfield features fractured shale in the Nahr Umr Formation. Complex accidents such as wellbore collapse and sticking emerged frequently in this formation. Tests and theoretical analysis revealed that wellbore instability in the Halfaya Oilfield was influenced by chemical effect of fractured shale and the formation water with high ionic concentration. The influence of three types of drilling fluids on the rock mechanical properties of Nahr Umr Shale is tested, and time-dependent collapse pressure is calculated. Finally, we put forward engineering countermeasures for safety drilling in Halfaya Oilfield and point out that increasing the ionic concentration and improving the sealing capacity of the drilling fluid are the way to keep the wellbore stable. PMID:24282391

Chemical effect on wellbore instability of Nahr Umr Shale.

PubMed

Yu, Baohua; Yan, Chuanliang; Nie, Zhen

2013-01-01

Wellbore instability is one of the major problems that hamper the drilling speed in Halfaya Oilfield. Comprehensive analysis of geological and engineering data indicates that Halfaya Oilfield features fractured shale in the Nahr Umr Formation. Complex accidents such as wellbore collapse and sticking emerged frequently in this formation. Tests and theoretical analysis revealed that wellbore instability in the Halfaya Oilfield was influenced by chemical effect of fractured shale and the formation water with high ionic concentration. The influence of three types of drilling fluids on the rock mechanical properties of Nahr Umr Shale is tested, and time-dependent collapse pressure is calculated. Finally, we put forward engineering countermeasures for safety drilling in Halfaya Oilfield and point out that increasing the ionic concentration and improving the sealing capacity of the drilling fluid are the way to keep the wellbore stable.

Dehospitalisation at a general hospital in Minas Gerais: challenges and prospects.

PubMed

Silva, Kênia Lara; Sena, Roseni Rosângela de; Castro, Wesley Souza

2018-06-07

To analyse the dehospitalisation process at a general public hospital in Minas Gerais, Brazil, from the perspective of managers, health workers, users and their families. This is a qualitative, exploratory, descriptive study based on the principles of methodological and theoretical dialectics. The participants were 24 hospital health workers and 15 companions of users going through the process of dehospitalisation. Data were collected from April to June 2015 using semi-structured interviews and a field journal records and subsequently subjected to content analysis. Analysis of the empirical material led to the construction of the following categories: Dehospitalisation: viewpoint of the institution and Family organisation for the dehospitalisation process. The study reveals a deficiency in the implementation, systematisation, internal reorganisation and continuity of care after dehospitalisation. Current dehospitalisation strategies do not favour comprehensiveness and continuity of home care.

Cross-Linguistic Transfer of Oral Language, Decoding, Phonological Awareness and Reading Comprehension: A Meta-Analysis of the Correlational Evidence

ERIC Educational Resources Information Center

Melby-Lervag, Monica; Lervag, Arne

2011-01-01

We present a meta-analysis of cross-linguistic transfer of oral language (vocabulary and listening comprehension), phonology (decoding and phonological awareness) and reading comprehension. Our findings show a small meta-correlation between first (L1) and second (L2) oral language and a moderate to large correlation between L1 and L2 phonological…

Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High Performance Liquid Chromatography-Mass Spectrometry-based Experimental and Computational Pipeline*

PubMed Central

Ranninger, Christina; Rurik, Marc; Limonciel, Alice; Ruzek, Silke; Reischl, Roland; Wilmes, Anja; Jennings, Paul; Hewitt, Philip; Dekant, Wolfgang; Kohlbacher, Oliver; Huber, Christian G.

2015-01-01

Untargeted metabolomics has the potential to improve the predictivity of in vitro toxicity models and therefore may aid the replacement of expensive and laborious animal models. Here we describe a long term repeat dose nephrotoxicity study conducted on the human renal proximal tubular epithelial cell line, RPTEC/TERT1, treated with 10 and 35 μmol·liter−1 of chloroacetaldehyde, a metabolite of the anti-cancer drug ifosfamide. Our study outlines the establishment of an automated and easy to use untargeted metabolomics workflow for HPLC-high resolution mass spectrometry data. Automated data analysis workflows based on open source software (OpenMS, KNIME) enabled a comprehensive and reproducible analysis of the complex and voluminous metabolomics data produced by the profiling approach. Time- and concentration-dependent responses were clearly evident in the metabolomic profiles. To obtain a more comprehensive picture of the mode of action, transcriptomics and proteomics data were also integrated. For toxicity profiling of chloroacetaldehyde, 428 and 317 metabolite features were detectable in positive and negative modes, respectively, after stringent removal of chemical noise and unstable signals. Changes upon treatment were explored using principal component analysis, and statistically significant differences were identified using linear models for microarray assays. The analysis revealed toxic effects only for the treatment with 35 μmol·liter−1 for 3 and 14 days. The most regulated metabolites were glutathione and metabolites related to the oxidative stress response of the cells. These findings are corroborated by proteomics and transcriptomics data, which show, among other things, an activation of the Nrf2 and ATF4 pathways. PMID:26055719

Research on dissociative seizures: A bibliometric analysis and visualization of the scientific landscape.

PubMed

Popkirov, Stoyan; Jungilligens, Johannes; Schlegel, Uwe; Wellmer, Jörg

2018-06-01

Dissociative seizures are a common and often elusive differential diagnosis in epilepsy centers. Considering their high prevalence, long diagnostic delays, and disappointing rates of treatment response, scientific research dedicated to dissociative seizures is surprisingly scarce. In order to chart the scientific landscape of dissociative seizures and to visualize thematic clusters and trends in research, a comprehensive bibliometric analysis was performed. The Web of Science database was examined to identify relevant English language documents from the last half-century. A total of 1751 documents with titles referring to dissociative seizures were identified. Automated textual analysis of all titles and abstracts revealed that research clusters around three major topics: differential diagnosis in epilepsy centers, management and treatment, and psychopathology. Time analysis of term networks revealed that the focus of clinical research has moved from diagnostic procedures to treatment approaches. Furthermore, interest within etiological research is shifting from an emphasis on early life trauma and personality traits to the role of anxiety and emotion regulation. With respect to individual contributing authors, a relatively small network of prolific scientists with a remarkable degree of collaboration emerges. By mapping relevant publications, it becomes evident that dissociative seizures still represent a subject mostly within the realm of neurology and epileptology, with a tendency to settle in the latter domain. This analysis sheds light on an important niche subject and highlights trends in research focus and output. Copyright © 2018 Elsevier Inc. All rights reserved.

The top skin-associated genes: a comparative analysis of human and mouse skin transcriptomes.

PubMed

Gerber, Peter Arne; Buhren, Bettina Alexandra; Schrumpf, Holger; Homey, Bernhard; Zlotnik, Albert; Hevezi, Peter

2014-06-01

The mouse represents a key model system for the study of the physiology and biochemistry of skin. Comparison of skin between mouse and human is critical for interpretation and application of data from mouse experiments to human disease. Here, we review the current knowledge on structure and immunology of mouse and human skin. Moreover, we present a systematic comparison of human and mouse skin transcriptomes. To this end, we have recently used a genome-wide database of human gene expression to identify genes highly expressed in skin, with no, or limited expression elsewhere - human skin-associated genes (hSAGs). Analysis of our set of hSAGs allowed us to generate a comprehensive molecular characterization of healthy human skin. Here, we used a similar database to generate a list of mouse skin-associated genes (mSAGs). A comparative analysis between the top human (n=666) and mouse (n=873) skin-associated genes (SAGs) revealed a total of only 30.2% identity between the two lists. The majority of shared genes encode proteins that participate in structural and barrier functions. Analysis of the top functional annotation terms revealed an overlap for morphogenesis, cell adhesion, structure, and signal transduction. The results of this analysis, discussed in the context of published data, illustrate the diversity between the molecular make up of skin of both species and grants a probable explanation, why results generated in murine in vivo models often fail to translate into the human.

Profiling and bioinformatics analyses reveal differential circular RNA expression in radioresistant esophageal cancer cells.

PubMed

Su, Huafang; Lin, Fuqiang; Deng, Xia; Shen, Lanxiao; Fang, Ya; Fei, Zhenghua; Zhao, Lihao; Zhang, Xuebang; Pan, Huanle; Xie, Deyao; Jin, Xiance; Xie, Congying

2016-07-28

Acquired radioresistance during radiotherapy is considered as the most important reason for local tumor recurrence or treatment failure. Circular RNAs (circRNAs) have recently been identified as microRNA sponges and involve in various biological processes. The purpose of this study is to investigate the role of circRNAs in the radioresistance of esophageal cancer. Total RNA was isolated from human parental cell line KYSE-150 and self-established radioresistant esophageal cancer cell line KYSE-150R, and hybridized to Arraystar Human circRNA Array. Quantitative real-time PCR was used to confirm the circRNA expression profiles obtained from the microarray data. Bioinformatic tools including gene ontology (GO) analysis, KEGG pathway analysis and network analysis were done for further assessment. Among the detected candidate 3752 circRNA genes, significant upregulation of 57 circRNAs and downregulation of 17 circRNAs in human radioresistant esophageal cancer cell line KYSE-150R were observed compared with the parental cell line KYSE-150 (fold change ≥2.0 and P < 0.05). There were 9 out of these candidate circRNAs were validated by real-time PCR. GO analysis revealed that numerous target genes, including most microRNAs were involved in the biological processes. There were more than 400 target genes enrichment on Wnt signaling pathway. CircRNA_001059 and circRNA_000167 were the two largest nodes in circRNA/microRNA co-expression network. Our study revealed a comprehensive expression and functional profile of differentially expressed circRNAs in radioresistant esophageal cancer cells, indicating possible involvement of these dysregulated circRNAs in the development of radiation resistance.

Genetic diversity and features analysis of type VI secretion systems loci in avian pathogenic Escherichia coli by wide genomic scanning.

PubMed

Ma, Jiale; Sun, Min; Bao, Yinli; Pan, Zihao; Zhang, Wei; Lu, Chengping; Yao, Huochun

2013-12-01

Avian pathogenic Escherichia coli (APEC) strains frequently cause extra-intestinal infections and significant economic losses. Recent studies revealed that the type VI secretion system (T6SS) is involved in APEC pathogenesis. Here we provide the first evidence of three distinguishable and conserved T6SS loci in APEC genomes. In addition, we present the prevalence and comparative genomic analysis of these three T6SS loci in 472 APEC isolates. The prevalence of T6SS1, T6SS2 and T6SS3 loci were 14.62% (69/472), 2.33% (11/472) and 0.85% (4/472) positive in the APEC collections, respectively, and revealed that >85% of the strains contained T6SS loci which consisted of the virulent phylogenetic groups D and B2. Comprehensive analysis showed prominent characteristics of T6SS1 locus, including wildly prevalence, rich sequence diversity, versatile VgrG islands and excellent expression competence in various E. coli pathotypes. Whereas the T6SS2 locus infatuated with ECOR groups B2 and sequence conservation, of which are only expressed in meningitis E. coli. Regrettably, the T6SS3 locus was encoded in negligible APEC isolates and lacked several key genes. An in-depth analysis about VgrG proteins indicated that their COG4253 and gp27 domain were involved in the transport of putative effector islands and recognition of host cells respectively, which revealed that VgrG proteins played an important role in functions formation of T6SS. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming

PubMed Central

Kroeker, Kristy J; Kordas, Rebecca L; Crim, Ryan; Hendriks, Iris E; Ramajo, Laura; Singh, Gerald S; Duarte, Carlos M; Gattuso, Jean-Pierre

2013-01-01

Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, and policy. As research on the topic expands at an exponential rate, a comprehensive understanding of the variability in organisms' responses and corresponding levels of certainty is necessary to forecast the ecological effects. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining biological responses to ocean acidification. The results reveal decreased survival, calcification, growth, development and abundance in response to acidification when the broad range of marine organisms is pooled together. However, the magnitude of these responses varies among taxonomic groups, suggesting there is some predictable trait-based variation in sensitivity, despite the investigation of approximately 100 new species in recent research. The results also reveal an enhanced sensitivity of mollusk larvae, but suggest that an enhanced sensitivity of early life history stages is not universal across all taxonomic groups. In addition, the variability in species' responses is enhanced when they are exposed to acidification in multi-species assemblages, suggesting that it is important to consider indirect effects and exercise caution when forecasting abundance patterns from single-species laboratory experiments. Furthermore, the results suggest that other factors, such as nutritional status or source population, could cause substantial variation in organisms' responses. Last, the results highlight a trend towards enhanced sensitivity to acidification when taxa are concurrently exposed to elevated seawater temperature. PMID:23505245

An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species

PubMed Central

Hung, Li-Yuan; Chen, Yen-Ju; Mai, Te-Lun; Chen, Chia-Ying; Yang, Min-Yu; Chiang, Tai-Wei; Wang, Yi-Da

2018-01-01

Abstract Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence editing sites using clustering and conservation strategies based on RNA sequencing data alone, without using single-nucleotide polymorphism information or genome sequencing data from the same sample. We thereby unveil the first evolutionary landscape of A-to-I editing maps across 20 metazoan species (from worm to human), providing unprecedented evidence on how the editing mechanism gradually expands its territory and increases its influence along the history of evolution. Our result revealed that highly clustered and conserved editing sites tended to have a higher editing level and a higher magnitude of the ADAR motif. The ratio of the frequencies of nonsynonymous editing to that of synonymous editing remarkably increased with increasing the conservation level of A-to-I editing. These results thus suggest potentially functional benefit of highly clustered and conserved editing sites. In addition, spatiotemporal dynamics analyses reveal a conserved enrichment of editing and ADAR expression in the central nervous system throughout more than 300 Myr of divergent evolution in complex animals and the comparability of editing patterns between invertebrates and between vertebrates during development. This study provides evolutionary and dynamic aspects of A-to-I editome across metazoan species, expanding this important but understudied class of nongenomically encoded events for comprehensive characterization. PMID:29294013

Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming.

PubMed

Kroeker, Kristy J; Kordas, Rebecca L; Crim, Ryan; Hendriks, Iris E; Ramajo, Laura; Singh, Gerald S; Duarte, Carlos M; Gattuso, Jean-Pierre

2013-06-01

Ocean acidification represents a threat to marine species worldwide, and forecasting the ecological impacts of acidification is a high priority for science, management, and policy. As research on the topic expands at an exponential rate, a comprehensive understanding of the variability in organisms' responses and corresponding levels of certainty is necessary to forecast the ecological effects. Here, we perform the most comprehensive meta-analysis to date by synthesizing the results of 228 studies examining biological responses to ocean acidification. The results reveal decreased survival, calcification, growth, development and abundance in response to acidification when the broad range of marine organisms is pooled together. However, the magnitude of these responses varies among taxonomic groups, suggesting there is some predictable trait-based variation in sensitivity, despite the investigation of approximately 100 new species in recent research. The results also reveal an enhanced sensitivity of mollusk larvae, but suggest that an enhanced sensitivity of early life history stages is not universal across all taxonomic groups. In addition, the variability in species' responses is enhanced when they are exposed to acidification in multi-species assemblages, suggesting that it is important to consider indirect effects and exercise caution when forecasting abundance patterns from single-species laboratory experiments. Furthermore, the results suggest that other factors, such as nutritional status or source population, could cause substantial variation in organisms' responses. Last, the results highlight a trend towards enhanced sensitivity to acidification when taxa are concurrently exposed to elevated seawater temperature. © 2013 Blackwell Publishing Ltd.

Comprehensive investigation of the electronic excitation of W(CO)6 by photoabsorption and theoretical analysis in the energy region from 3.9 to 10.8 eV.

PubMed

Mendes, Mónica; Regeta, Khrystyna; Ferreira da Silva, Filipe; Jones, Nykola C; Hoffmann, Søren Vrønning; García, Gustavo; Daniel, Chantal; Limão-Vieira, Paulo

2017-01-01

High-resolution vacuum ultraviolet photoabsorption measurements in the wavelength range of 115-320 nm (10.8-3.9 eV) have been performed together with comprehensive relativistic time-dependent density functional calculations (TDDFT) on the low-lying excited sates of tungsten hexacarbonyl, W(CO) 6 . The higher resolution obtained reveals previously unresolved spectral features of W(CO) 6 . The spectrum shows two higher-energy bands (in the energy ranges of 7.22-8.12 eV and 8.15-9.05 eV), one of them with clear vibrational structure, and a few lower-energy shoulders in addition to a couple of lower-energy metal-to-ligand charge-transfer (MLCT) bands reported in the literature before. Absolute photoabsorption cross sections are reported and, where possible, compared to previously published results. On the basis of this combined experimental/theoretical study the absorption spectrum of the complex has been totally re-assigned between 3.9 and 10.8 eV under the light of spin-orbit coupling (SOC) effects. The present comprehensive knowledge of the nature of the electronically excited states may be of relevance to estimate neutral dissociation cross sections of W(CO) 6 , a precursor molecule in focused electron beam induced deposition (FEBID) processes, from electron scattering measurements.

Comprehensive investigation of the electronic excitation of W(CO)6 by photoabsorption and theoretical analysis in the energy region from 3.9 to 10.8 eV

PubMed Central

Mendes, Mónica; Regeta, Khrystyna; Ferreira da Silva, Filipe; Jones, Nykola C; Hoffmann, Søren Vrønning; García, Gustavo

2017-01-01

High-resolution vacuum ultraviolet photoabsorption measurements in the wavelength range of 115–320 nm (10.8–3.9 eV) have been performed together with comprehensive relativistic time-dependent density functional calculations (TDDFT) on the low-lying excited sates of tungsten hexacarbonyl, W(CO)6. The higher resolution obtained reveals previously unresolved spectral features of W(CO)6. The spectrum shows two higher-energy bands (in the energy ranges of 7.22–8.12 eV and 8.15–9.05 eV), one of them with clear vibrational structure, and a few lower-energy shoulders in addition to a couple of lower-energy metal-to-ligand charge-transfer (MLCT) bands reported in the literature before. Absolute photoabsorption cross sections are reported and, where possible, compared to previously published results. On the basis of this combined experimental/theoretical study the absorption spectrum of the complex has been totally re-assigned between 3.9 and 10.8 eV under the light of spin–orbit coupling (SOC) effects. The present comprehensive knowledge of the nature of the electronically excited states may be of relevance to estimate neutral dissociation cross sections of W(CO)6, a precursor molecule in focused electron beam induced deposition (FEBID) processes, from electron scattering measurements. PMID:29114447

From genetics to genomics: ethics, policy, and parental decision-making.

PubMed

Wilfond, Benjamin; Ross, Lainie Friedman

2009-07-01

Ethical evaluation of genetic testing in children is traditionally based on balancing clinical benefits and risks. However, this focus can be inconsistent with the general practice of respecting parental decision-making about their children's health care. We argue that respect for parental decision-making should play a larger role in shaping pediatric genetic testing practices, and play a similar role regarding decisions to use emerging genomic technologies. Genomic testing involves the examination of thousands of DNA markers spanning genes throughout the genome and their interrelationships, yielding virtually limitless interpretations. We presume that parents and providers should proceed cautiously in applying genomic testing in children, as we explore how genomic testing will stress the fault lines of the traditional ethical analysis. Empirical data about the psychosocial risks and benefits of genetic testing of children do not reveal serious harms, yet virtually no such data exist yet about genomic testing. Unless empirical social and behavioral data indicate that genomic testing is highly likely to cause serious harms to the children, parental decisions to obtain comprehensive genomic testing in their children should be respected. Once comprehensive genomic testing of children becomes routine, resultant information may be more easily integrated by families than anticipated. Research on the social and behavioral impact of comprehensive genomic testing on children and their families is needed to further inform parents, clinicians, and policy makers.

What is your neural function, visual narrative conjunction? Grammar, meaning, and fluency in sequential image processing.

PubMed

Cohn, Neil; Kutas, Marta

2017-01-01

Visual narratives sometimes depict successive images with different characters in the same physical space; corpus analysis has revealed that this occurs more often in Japanese manga than American comics. We used event-related brain potentials to determine whether comprehension of "visual narrative conjunctions" invokes not only incremental mental updating as traditionally assumed, but also, as we propose, "grammatical" combinatoric processing. We thus crossed (non)/conjunction sequences with character (in)/congruity. Conjunctions elicited a larger anterior negativity (300-500 ms) than nonconjunctions, regardless of congruity, implicating "grammatical" processes. Conjunction and incongruity both elicited larger P600s (500-700 ms), indexing updating. Both conjunction effects were modulated by participants' frequency of reading manga while growing up. Greater anterior negativity in frequent manga readers suggests more reliance on combinatoric processing; larger P600 effects in infrequent manga readers suggest more resources devoted to mental updating. As in language comprehension, it seems that processing conjunctions in visual narratives is not just mental updating but also partly grammatical, conditioned by comic readers' experience with specific visual narrative structures.

Are your students ready for anatomy and physiology? Developing tools to identify students at risk for failure.

PubMed

Gultice, Amy; Witham, Ann; Kallmeyer, Robert

2015-06-01

High failure rates in introductory college science courses, including anatomy and physiology, are common at institutions across the country, and determining the specific factors that contribute to this problem is challenging. To identify students at risk for failure in introductory physiology courses at our open-enrollment institution, an online pilot survey was administered to 200 biology students. The survey results revealed several predictive factors related to academic preparation and prompted a comprehensive analysis of college records of >2,000 biology students over a 5-yr period. Using these historical data, a model that was 91% successful in predicting student success in these courses was developed. The results of the present study support the use of surveys and similar models to identify at-risk students and to provide guidance in the development of evidence-based advising programs and pedagogies. This comprehensive approach may be a tangible step in improving student success for students from a wide variety of backgrounds in anatomy and physiology courses. Copyright © 2015 The American Physiological Society.

Integrating the iPad into an intensive, comprehensive aphasia program.

PubMed

Hoover, Elizabeth L; Carney, Anne

2014-02-01

The proliferation of tablet technology and the development of apps to support aphasia rehabilitation offer increasing opportunities for speech-language pathologists in a clinical setting. This article describes the components of an Intensive Comprehensive Aphasia Program at Boston University and details how usage of the iPad (Apple Inc., Cupertino, CA) was incorporated. We describe how the iPad was customized for use in individual, dyadic, and group treatment formats and how its use was encouraged through home practice tasks. In addition to providing the participants with step-by-step instructions for the usage of each new app, participants had multiple opportunities for practice across various treatment formats. Examples of how the participants continued using their iPad beyond the program suggest how the usage of this device has generalized into their day-to-day life. An overall summary of performance on targeted linguistic measures as well as an analysis of functional and quality-of-life measures reveal statistically significant improvements pre- to posttreatment. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Proteomic Analysis of Excretory-Secretory Products of Mesocestoides corti Metacestodes Reveals Potential Suppressors of Dendritic Cell Functions

PubMed Central

Vendelova, Emilia; Camargo de Lima, Jeferson; Lorenzatto, Karina Rodrigues; Monteiro, Karina Mariante; Mueller, Thomas; Veepaschit, Jyotishman; Grimm, Clemens; Brehm, Klaus; Hrčková, Gabriela; Lutz, Manfred B.; Ferreira, Henrique B.

2016-01-01

Accumulating evidences have assigned a central role to parasite-derived proteins in immunomodulation. Here, we report on the proteomic identification and characterization of immunomodulatory excretory-secretory (ES) products from the metacestode larva (tetrathyridium) of the tapeworm Mesocestoides corti (syn. M. vogae). We demonstrate that ES products but not larval homogenates inhibit the stimuli-driven release of the pro-inflammatory, Th1-inducing cytokine IL-12p70 by murine bone marrow-derived dendritic cells (BMDCs). Within the ES fraction, we biochemically narrowed down the immunosuppressive activity to glycoproteins since active components were lipid-free, but sensitive to heat- and carbohydrate-treatment. Finally, using bioassay-guided chromatographic analyses assisted by comparative proteomics of active and inactive fractions of the ES products, we defined a comprehensive list of candidate proteins released by M. corti tetrathyridia as potential suppressors of DC functions. Our study provides a comprehensive library of somatic and ES products and highlight some candidate parasite factors that might drive the subversion of DC functions to facilitate the persistence of M. corti tetrathyridia in their hosts. PMID:27736880

Individual differences in children's memory and reading comprehension: an investigation of semantic and inhibitory deficits.

PubMed

Cain, Kate

2006-07-01

Three experiments compared the verbal memory skills of children with poor reading comprehension with that of same-age good comprehenders. The aims were to determine if semantic and/or inhibitory deficits explained comprehenders' problems on measures of verbal short-term memory and verbal working memory. In Experiment 1 there were no group differences on word- and number-based measures of short-term storage and no evidence that semantic knowledge mediated word recall. In Experiment 2 poor comprehenders were impaired on word- and number-based assessments of working memory, the greatest deficit found on the word-based task. Error analysis of both word-based tasks revealed that poor comprehenders were more likely to recall items that should have been inhibited than were good comprehenders. Experiment 3 extended this finding: Poor comprehenders were less able to inhibit information that was no longer relevant. Together, these findings suggest that individual differences in inhibitory processing influence the ability to regulate the contents of working memory, which may contribute to the differential memory performance of good and poor comprehenders.

Increased Diversity of Libraries from Libraries: Chemoinformatic Analysis of Bis-Diazacyclic Libraries

PubMed Central

López-Vallejo, Fabian; Nefzi, Adel; Bender, Andreas; Owen, John R.; Nabney, Ian T.; Houghten, Richard A.; Medina-Franco, Jose L.

2011-01-01

Combinatorial libraries continue to play a key role in drug discovery. To increase structural diversity, several experimental methods have been developed. However, limited efforts have been performed so far to quantify the diversity of the broadly used diversity-oriented synthetic (DOS) libraries. Herein we report a comprehensive characterization of 15 bis-diazacyclic combinatorial libraries obtained through libraries from libraries, which is a DOS approach. Using MACCS keys, radial and different pharmacophoric fingerprints as well as six molecular properties, it was demonstrated the increased structural and property diversity of the libraries from libraries over the individual libraries. Comparison of the libraries to existing drugs, NCI Diversity and the Molecular Libraries Small Molecule Repository revealed the structural uniqueness of the combinatorial libraries (mean similarity < 0.5 for any fingerprint representation). In particular, bis-cyclic thiourea libraries were the most structurally dissimilar to drugs retaining drug-like character in property space. This study represents the first comprehensive quantification of the diversity of libraries from libraries providing a solid quantitative approach to compare and contrast the diversity of DOS libraries with existing drugs or any other compound collection. PMID:21294850

Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance

PubMed Central

Plantegenet, Stephanie; Weber, Johann; Goldstein, Darlene R; Zeller, Georg; Nussbaumer, Cindy; Thomas, Jérôme; Weigel, Detlef; Harshman, Keith; Hardtke, Christian S

2009-01-01

In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regulatory element polymorphisms. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here, we analyzed ELPs observed between the Eil-0 and Lc-0 accessions. Compared with non-variable controls, 5′ regulatory sequence variation in the corresponding genes is indeed increased. However, ∼42% of all the ELP genes also carry major transcription unit deletions in one parent as revealed by genome tiling arrays, representing a >4-fold enrichment over controls. Within the subset of ELPs with simple inheritance, this proportion is even higher and deletions are generally more severe. Similar results were obtained from analyses of the Bay-0 and Sha accessions, using alternative technical approaches. Collectively, our results suggest that drastic structural changes are a major cause for ELPs with simple inheritance, corroborating experimentally observed indel preponderance in cloned Arabidopsis QTL. PMID:19225455

Separating Bulk and Surface Contributions to Electronic Excited-State Processes in Hybrid Mixed Perovskite Thin Films via Multimodal All-Optical Imaging

DOE PAGES

Simpson, Mary Jane; Doughty, Benjamin; Das, Sanjib; ...

2017-07-04

A comprehensive understanding of electronic excited-state phenomena underlying the impressive performance of solution-processed hybrid halide perovskite solar cells requires access to both spatially resolved electronic processes and corresponding sample morphological characteristics. In this paper, we demonstrate an all-optical multimodal imaging approach that enables us to obtain both electronic excited-state and morphological information on a single optical microscope platform with simultaneous high temporal and spatial resolution. Specifically, images were acquired for the same region of interest in thin films of chloride containing mixed lead halide perovskites (CH 3NH 3PbI 3–xCl x) using femtosecond transient absorption, time-integrated photoluminescence, confocal reflectance, and transmissionmore » microscopies. Comprehensive image analysis revealed the presence of surface- and bulk-dominated contributions to the various images, which describe either spatially dependent electronic excited-state properties or morphological variations across the probed region of the thin films. Finally, these results show that PL probes effectively the species near or at the film surface.« less

Comprehensive School Reform and Achievement: A Meta-Analysis. Educator's Summary

ERIC Educational Resources Information Center

Center for Data-Driven Reform in Education (NJ3), 2008

2008-01-01

Which comprehensive school reform programs have been proven to help elementary and secondary students achieve? To find out, this review summarizes evidence on comprehensive school reform (CSR) models in elementary and secondary schools. Comprehensive school reform models are programs used schoolwide to improve student achievement. They typically…

Maternal Bias and Escape from X Chromosome Imprinting in the Midgestation Mouse Placenta

PubMed Central

Finn, Elizabeth H; Smith, Cheryl L; Rodriguez, Jesse; Sidow, Arend; Baker, Julie C

2014-01-01

To investigate the epigenetic landscape at the interface between mother and fetus, we provide a comprehensive analysis of parent-of-origin bias in the mouse placenta. Using F1 interspecies hybrids between mus musculus (C57BL/6J) and mus musculus castaneus, we sequenced RNA from 23 individual midgestation placentas, five late stage placentas, and two yolk sac samples and then used SNPs to determine whether transcripts were preferentially generated from the maternal or paternal allele. In the placenta, we find 103 genes that show significant and reproducible parent-of-origin bias, of which 78 are novel candidates. Most (96%) show a strong maternal bias which we demonstrate, via multiple mathematical models, pyrosequencing, and FISH, is not due to maternal decidual contamination. Analysis of the X chromosome also reveals paternal expression of Xist and several genes that escape inactivation, most significantly Alas2, Fhl1, and Slc38a5. Finally, sequencing individual placentas allowed us to reveal notable expression similarity between littermates. In all, we observe a striking preference for maternal transcription in the midgestation mouse placenta and a dynamic imprinting landscape in extraembryonic tissues, reflecting the complex nature of epigenetic pathways in the placenta. PMID:24594094

Oceanic protists with different forms of acquired phototrophy display contrasting biogeographies and abundance.

PubMed

Leles, S G; Mitra, A; Flynn, K J; Stoecker, D K; Hansen, P J; Calbet, A; McManus, G B; Sanders, R W; Caron, D A; Not, F; Hallegraeff, G M; Pitta, P; Raven, J A; Johnson, M D; Glibert, P M; Våge, S

2017-08-16

This first comprehensive analysis of the global biogeography of marine protistan plankton with acquired phototrophy shows these mixotrophic organisms to be ubiquitous and abundant; however, their biogeography differs markedly between different functional groups. These mixotrophs, lacking a constitutive capacity for photosynthesis (i.e. non-constitutive mixotrophs, NCMs), acquire their phototrophic potential through either integration of prey-plastids or through endosymbiotic associations with photosynthetic microbes. Analysis of field data reveals that 40-60% of plankton traditionally labelled as (non-phototrophic) microzooplankton are actually NCMs, employing acquired phototrophy in addition to phagotrophy. Specialist NCMs acquire chloroplasts or endosymbionts from specific prey, while generalist NCMs obtain chloroplasts from a variety of prey. These contrasting functional types of NCMs exhibit distinct seasonal and spatial global distribution patterns. Mixotrophs reliant on 'stolen' chloroplasts, controlled by prey diversity and abundance, dominate in high-biomass areas. Mixotrophs harbouring intact symbionts are present in all waters and dominate particularly in oligotrophic open ocean systems. The contrasting temporal and spatial patterns of distribution of different mixotroph functional types across the oceanic provinces, as revealed in this study, challenges traditional interpretations of marine food web structures. Mixotrophs with acquired phototrophy (NCMs) warrant greater recognition in marine research. © 2017 The Author(s).

Social Anxiety among Chinese People

PubMed Central

Fan, Qianqian; Chang, Weining C.

2015-01-01

The experience of social anxiety has largely been investigated among Western populations; much less is known about social anxiety in other cultures. Unlike the Western culture, the Chinese emphasize interdependence and harmony with social others. In addition, it is unclear if Western constructed instruments adequately capture culturally conditioned conceptualizations and manifestations of social anxiety that might be specific to the Chinese. The present study employed a sequence of qualitative and quantitative approaches to examine the assessment of social anxiety among the Chinese people. Interviews and focus group discussions with Chinese participants revealed that some items containing the experience of social anxiety among the Chinese are not present in existing Western measures. Factor analysis was employed to examine the factor structure of the more comprehensive scale. This approach revealed an “other concerned anxiety” factor that appears to be specific to the Chinese. Subsequent analysis found that the new factor—other concerned anxiety—functioned the same as other social anxiety factors in their association with risk factors of social anxiety, such as attachment, parenting, behavioral inhibition/activation, and attitude toward group. The implications of these findings for a more culturally sensitive assessment tool of social anxiety among the Chinese were discussed. PMID:26380367

Microstructural analysis of mass transport phenomena in gas diffusion media for high current density operation in PEM fuel cells

NASA Astrophysics Data System (ADS)

Kotaka, Toshikazu; Tabuchi, Yuichiro; Mukherjee, Partha P.

2015-04-01

Cost reduction is a key issue for commercialization of fuel cell electric vehicles (FCEV). High current density operation is a solution pathway. In order to realize high current density operation, it is necessary to reduce mass transport resistance in the gas diffusion media commonly consisted of gas diffusion layer (GDL) and micro porous layer (MPL). However, fundamental understanding of the underlying mass transport phenomena in the porous components is not only critical but also not fully understood yet due to the inherent microstructural complexity. In this study, a comprehensive analysis of electron and oxygen transport in the GDL and MPL is conducted experimentally and numerically with three-dimensional (3D) microstructural data to reveal the structure-transport relationship. The results reveal that the mass transport in the GDL is strongly dependent on the local microstructural variations, such as local pore/solid volume fractions and connectivity. However, especially in the case of the electrical conductivity of MPL, the contact resistance between carbon particles is the dominant factor. This suggests that reducing the contact resistance between carbon particles and/or the number of contact points along the transport pathway can improve the electrical conductivity of MPL.

What changes in neural oscillations can reveal about developmental cognitive neuroscience: language development as a case in point.

PubMed

Maguire, Mandy J; Abel, Alyson D

2013-10-01

EEG is a primary method for studying temporally precise neuronal processes across the lifespan. Most of this work focuses on event related potentials (ERPs); however, using time-locked time frequency analysis to decompose the EEG signal can identify and distinguish multiple changes in brain oscillations underlying cognition (Bastiaansen et al., 2010). Further this measure is thought to reflect changes in inter-neuronal communication more directly than ERPs (Nunez and Srinivasan, 2006). Although time frequency has elucidated cognitive processes in adults, applying it to cognitive development is still rare. Here, we review the basics of neuronal oscillations, some of what they reveal about adult cognitive function, and what little is known relating to children. We focus on language because it develops early and engages complex cortical networks. Additionally, because time frequency analysis of the EEG related to adult language comprehension has been incredibly informative, using similar methods with children will shed new light on current theories of language development and increase our understanding of how neural processes change over the lifespan. Our goal is to emphasize the power of this methodology and encourage its use throughout developmental cognitive neuroscience. Copyright © 2013 Elsevier Ltd. All rights reserved.

Effect of annealing on the sub-bandgap, defects and trapping states of ZnO nanostructures

NASA Astrophysics Data System (ADS)

Wahyuono, Ruri Agung; Hermann-Westendorf, Felix; Dellith, Andrea; Schmidt, Christa; Dellith, Jan; Plentz, Jonathan; Schulz, Martin; Presselt, Martin; Seyring, Martin; Rettenmeyer, Markus; Dietzek, Benjamin

2017-02-01

Annealing treatment was applied to different mesoporous ZnO nanostructures prepared by wet chemical synthesis, i.e. nanoflowers (NFs), spherical aggregates (SPs), and nanorods (NRs). The sub-bandgap, defect properties as well as the trapping state characteristics after annealing were characterized spectroscopically, including ultrasensitive photothermal deflection spectroscopy (PDS), photoluminescence and photo-electrochemical methods. The comprehensive experimental analysis reveals that annealing alters both the bandgap and the sub-bandgap. The defect concentration and the density of surface traps in the ZnO nanostructures are suppressed upon annealing as deduced from photoluminescence and open-circuit voltage decay analysis. The photo-electrochemical investigations reveal that the surface traps dominate the near conduction band edge of ZnO and, hence, lead to high recombination rates when used in DSSCs. The density of bulk traps in ZnO SPs is higher than that in ZnO NFs and ZnO NRs and promote lower recombination loss between photoinjected electrons with the electrolyte-oxidized species on the surface. The highest power conversion efficiency of ZnO NFs-, ZnO SPs-, and ZnO NRs-based DSSC obtained in our system is 2.0, 4.5, and 1.8%, respectively.

High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism.

PubMed

Bao, Yun-Juan; Xu, Zixiang; Li, Yang; Yao, Zhi; Sun, Jibin; Song, Hui

2017-06-01

The soil with petroleum contamination is one of the most studied soil ecosystems due to its rich microorganisms for hydrocarbon degradation and broad applications in bioremediation. However, our understanding of the genomic properties and functional traits of the soil microbiome is limited. In this study, we used high-throughput metagenomic sequencing to comprehensively study the microbial community from petroleum-contaminated soils near Tianjin Dagang oilfield in eastern China. The analysis reveals that the soil metagenome is characterized by high level of community diversity and metabolic versatility. The metageome community is predominated by γ-Proteobacteria and α-Proteobacteria, which are key players for petroleum hydrocarbon degradation. The functional study demonstrates over-represented enzyme groups and pathways involved in degradation of a broad set of xenobiotic aromatic compounds, including toluene, xylene, chlorobenzoate, aminobenzoate, DDT, methylnaphthalene, and bisphenol. A composite metabolic network is proposed for the identified pathways, thus consolidating our identification of the pathways. The overall data demonstrated the great potential of the studied soil microbiome in the xenobiotic aromatics degradation. The results not only establish a rich reservoir for novel enzyme discovery but also provide putative applications in bioremediation. Copyright © 2016. Published by Elsevier B.V.

Genome-wide analyses of the bZIP family reveal their involvement in the development, ripening and abiotic stress response in banana

PubMed Central

Hu, Wei; Wang, Lianzhe; Tie, Weiwei; Yan, Yan; Ding, Zehong; Liu, Juhua; Li, Meiying; Peng, Ming; Xu, Biyu; Jin, Zhiqiang

2016-01-01

The leucine zipper (bZIP) transcription factors play important roles in multiple biological processes. However, less information is available regarding the bZIP family in the important fruit crop banana. In this study, 121 bZIP transcription factor genes were identified in the banana genome. Phylogenetic analysis showed that MabZIPs were classified into 11 subfamilies. The majority of MabZIP genes in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis of two banana genotypes revealed the differential expression patterns of MabZIP genes in different organs, in various stages of fruit development and ripening, and in responses to abiotic stresses, including drought, cold, and salt. Interaction networks and co-expression assays showed that group A MabZIP-mediated networks participated in various stress signaling, which was strongly activated in Musa ABB Pisang Awak. This study provided new insights into the complicated transcriptional control of MabZIP genes and provided robust tissue-specific, development-dependent, and abiotic stress-responsive candidate MabZIP genes for potential applications in the genetic improvement of banana cultivars. PMID:27445085

Changes in coral reef communities across a natural gradient in seawater pH.

PubMed

Barkley, Hannah C; Cohen, Anne L; Golbuu, Yimnang; Starczak, Victoria R; DeCarlo, Thomas M; Shamberger, Kathryn E F

2015-06-01

Ocean acidification threatens the survival of coral reef ecosystems worldwide. The negative effects of ocean acidification observed in many laboratory experiments have been seen in studies of naturally low-pH reefs, with little evidence to date for adaptation. Recently, we reported initial data suggesting that low-pH coral communities of the Palau Rock Islands appear healthy despite the extreme conditions in which they live. Here, we build on that observation with a comprehensive statistical analysis of benthic communities across Palau's natural acidification gradient. Our analysis revealed a shift in coral community composition but no impact of acidification on coral richness, coralline algae abundance, macroalgae cover, coral calcification, or skeletal density. However, coral bioerosion increased 11-fold as pH decreased from the barrier reefs to the Rock Island bays. Indeed, a comparison of the naturally low-pH coral reef systems studied so far revealed increased bioerosion to be the only consistent feature among them, as responses varied across other indices of ecosystem health. Our results imply that whereas community responses may vary, escalation of coral reef bioerosion and acceleration of a shift from net accreting to net eroding reef structures will likely be a global signature of ocean acidification.

Global analysis of lysine acetylation in strawberry leaves.

PubMed

Fang, Xianping; Chen, Wenyue; Zhao, Yun; Ruan, Songlin; Zhang, Hengmu; Yan, Chengqi; Jin, Liang; Cao, Lingling; Zhu, Jun; Ma, Huasheng; Cheng, Zhongyi

2015-01-01

Protein lysine acetylation is a reversible and dynamic post-translational modification. It plays an important role in regulating diverse cellular processes including chromatin dynamic, metabolic pathways, and transcription in both prokaryotes and eukaryotes. Although studies of lysine acetylome in plants have been reported, the throughput was not high enough, hindering the deep understanding of lysine acetylation in plant physiology and pathology. In this study, taking advantages of anti-acetyllysine-based enrichment and high-sensitive-mass spectrometer, we applied an integrated proteomic approach to comprehensively investigate lysine acetylome in strawberry. In total, we identified 1392 acetylation sites in 684 proteins, representing the largest dataset of acetylome in plants to date. To reveal the functional impacts of lysine acetylation in strawberry, intensive bioinformatic analysis was performed. The results significantly expanded our current understanding of plant acetylome and demonstrated that lysine acetylation is involved in multiple cellular metabolism and cellular processes. More interestingly, nearly 50% of all acetylated proteins identified in this work were localized in chloroplast and the vital role of lysine acetylation in photosynthesis was also revealed. Taken together, this study not only established the most extensive lysine acetylome in plants to date, but also systematically suggests the significant and unique roles of lysine acetylation in plants.

Adaptation of avian influenza A (H6N1) virus from avian to human receptor-binding preference

PubMed Central

Wang, Fei; Qi, Jianxun; Bi, Yuhai; Zhang, Wei; Wang, Min; Zhang, Baorong; Wang, Ming; Liu, Jinhua; Yan, Jinghua; Shi, Yi; Gao, George F

2015-01-01

The receptor-binding specificity of influenza A viruses is a major determinant for the host tropism of the virus, which enables interspecies transmission. In 2013, the first human case of infection with avian influenza A (H6N1) virus was reported in Taiwan. To gather evidence concerning the epidemic potential of H6 subtype viruses, we performed comprehensive analysis of receptor-binding properties of Taiwan-isolated H6 HAs from 1972 to 2013. We propose that the receptor-binding properties of Taiwan-isolated H6 HAs have undergone three major stages: initially avian receptor-binding preference, secondarily obtaining human receptor-binding capacity, and recently human receptor-binding preference, which has been confirmed by receptor-binding assessment of three representative virus isolates. Mutagenesis work revealed that E190V and G228S substitutions are important to acquire the human receptor-binding capacity, and the P186L substitution could reduce the binding to avian receptor. Further structural analysis revealed how the P186L substitution in the receptor-binding site of HA determines the receptor-binding preference change. We conclude that the human-infecting H6N1 evolved into a human receptor preference. PMID:25940072

Differential detection of genetic Loci underlying stem and root lignin content in Populus.

PubMed

Yin, Tongming; Zhang, Xinye; Gunter, Lee; Priya, Ranjan; Sykes, Robert; Davis, Mark; Wullschleger, Stan D; Tuskan, Gerald A

2010-11-22

In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G) ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS) varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.

Re-orienting discussions of scientific explanation: A functional perspective.

PubMed

Woody, Andrea I

2015-08-01

Philosophy of science offers a rich lineage of analysis concerning the nature of scientific explanation, but the vast majority of this work, aiming to provide an analysis of the relation that binds a given explanans to its corresponding explanandum, presumes the proper analytic focus rests at the level of individual explanations. There are, however, other questions we could ask about explanation in science, such as: What role(s) does explanatory practice play in science? Shifting focus away from explanations, as achievements, toward explaining, as a coordinated activity of communities, the functional perspective aims to reveal how the practice of explanatory discourse functions within scientific communities given their more comprehensive aims and practices. In this paper, I outline the functional perspective, argue that taking the functional perspective can reveal important methodological roles for explanation in science, and consequently, that beginning here provides resources for developing more adequate responses to traditional concerns. In particular, through an examination of the ideal gas law, I emphasize the normative status of explanations within scientific communities and discuss how such status underwrites a compelling rationale for explanatory power as a theoretical virtue. Copyright © 2015 Elsevier Ltd. All rights reserved.

Significance of 5,10-methylenetetrahydrofolate reductase gene variants in acute lymphoblastic leukemia in Indian population: an experimental, computational and meta-analysis.

PubMed

Bellampalli, Ravishankara; Phani, Nagaraja M; Bhat, Kamalakshi G; Prasad, Krishna; Bhaskaranand, Nalini; Guruprasad, Kanive P; Rai, Padmalatha S; Satyamoorthy, Kapaettu

2015-05-01

Acute lymphoblastic leukemia (ALL) arises due to several genetic alterations in progenitor cells, and methotrexate is frequently used as part of the treatment regimen. Although there is evidence for an effect of 5,10-methylenetetrahydrofolate reductase gene (MTHFR) C677T and A1298C variations on drug response in ALL, its risk association for ALL is still unresolved. In a case-control study of 203 patients with ALL and 246 controls and meta-analysis in the Indian population, we showed an insignificant association of MTHFR C677T and A1298C genotypes with childhood and adult ALL. Comprehensive in silico characterization of non-synonymous single nucleotide polymorphisms (nsSNPs) and SNPs of the 3' untranslated region (UTR) revealed nine nsSNPs as deleterious, and three SNPs in the 3'UTR could possibly alter the binding of miRNAs. The study revealed that several overlooked SNPs may contribute to the risk of ALL susceptibility and further studies of these SNPs with functional characterization in a large sample size are required to understand the significant role of MTHFR in ALL development.

Social Anxiety among Chinese People.

PubMed

Fan, Qianqian; Chang, Weining C

2015-01-01

The experience of social anxiety has largely been investigated among Western populations; much less is known about social anxiety in other cultures. Unlike the Western culture, the Chinese emphasize interdependence and harmony with social others. In addition, it is unclear if Western constructed instruments adequately capture culturally conditioned conceptualizations and manifestations of social anxiety that might be specific to the Chinese. The present study employed a sequence of qualitative and quantitative approaches to examine the assessment of social anxiety among the Chinese people. Interviews and focus group discussions with Chinese participants revealed that some items containing the experience of social anxiety among the Chinese are not present in existing Western measures. Factor analysis was employed to examine the factor structure of the more comprehensive scale. This approach revealed an "other concerned anxiety" factor that appears to be specific to the Chinese. Subsequent analysis found that the new factor-other concerned anxiety-functioned the same as other social anxiety factors in their association with risk factors of social anxiety, such as attachment, parenting, behavioral inhibition/activation, and attitude toward group. The implications of these findings for a more culturally sensitive assessment tool of social anxiety among the Chinese were discussed.

Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.

PubMed

Han, Xiaoping; Chen, Haide; Huang, Daosheng; Chen, Huidong; Fei, Lijiang; Cheng, Chen; Huang, He; Yuan, Guo-Cheng; Guo, Guoji

2018-04-05

Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. We use high throughput single-cell RNA-sequencing (scRNA-seq), based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body system. We present a cellular-state landscape for hPSC early differentiation that covers multiple cellular lineages, including neural, muscle, endothelial, stromal, liver, and epithelial cells. Through pseudotime analysis, we construct the developmental trajectories of these progenitor cells and reveal the gene expression dynamics in the process of cell differentiation. We further reprogram primed H9 cells into naïve-like H9 cells to study the cellular-state transition process. We find that genes related to hemogenic endothelium development are enriched in naïve-like H9. Functionally, naïve-like H9 show higher potency for differentiation into hematopoietic lineages than primed cells. Our single-cell analysis reveals the cellular-state landscape of hPSC early differentiation, offering new insights that can be harnessed for optimization of differentiation protocols.

Proteomic Analysis of the Human Skin Proteome after In Vivo Treatment with Sodium Dodecyl Sulphate

PubMed Central

Parkinson, Erika; Skipp, Paul; Aleksic, Maja; Garrow, Andrew; Dadd, Tony; Hughes, Michael; Clough, Geraldine; O′Connor, C. David

2014-01-01

Background Skin has a variety of functions that are incompletely understood at the molecular level. As the most accessible tissue in the body it often reveals the first signs of inflammation or infection and also represents a potentially valuable source of biomarkers for several diseases. In this study we surveyed the skin proteome qualitatively using gel electrophoresis, liquid chromatography tandem mass spectrometry (GeLC-MS/MS) and quantitatively using an isobaric tagging strategy (iTRAQ) to characterise the response of human skin following exposure to sodium dodecyl sulphate (SDS). Results A total of 653 skin proteins were assigned, 159 of which were identified using GeLC-MS/MS and 616 using iTRAQ, representing the most comprehensive proteomic study in human skin tissue. Statistical analysis of the available iTRAQ data did not reveal any significant differences in the measured skin proteome after 4 hours exposure to the model irritant SDS. Conclusions This study represents the first step in defining the critical response to an irritant at the level of the proteome and provides a valuable resource for further studies at the later stages of irritant exposure. PMID:24849295

Developmental, Component-Based Model of Reading Fluency: An Investigation of Predictors of Word-Reading Fluency, Text-Reading Fluency, and Reading Comprehension.

PubMed

Kim, Young-Suk Grace

2015-01-01

The primary goal was to expand our understanding of text reading fluency (efficiency or automaticity)-how its relation to other constructs (e.g., word reading fluency and reading comprehension) changes over time and how it is different from word reading fluency and reading comprehension. We examined (1) developmentally changing relations among word reading fluency, listening comprehension, text reading fluency, and reading comprehension; (2) the relation of reading comprehension to text reading fluency; (3) unique emergent literacy predictors (i.e., phonological awareness, orthographic awareness, morphological awareness, letter name knowledge, vocabulary) of text reading fluency vs. word reading fluency; and (4) unique language and cognitive predictors (e.g., vocabulary, grammatical knowledge, theory of mind) of text reading fluency vs. reading comprehension. These questions were addressed using longitudinal data (two timepoints; Mean age = 5;24 & 6;08) from Korean-speaking children ( N = 143). Results showed that listening comprehension was related to text reading fluency at time 2, but not at time 1. At both times text reading fluency was related to reading comprehension, and reading comprehension was related to text reading fluency over and above word reading fluency and listening comprehension. Orthographic awareness was related to text reading fluency over and above other emergent literacy skills and word reading fluency. Vocabulary and grammatical knowledge were independently related to text reading fluency and reading comprehension whereas theory of mind was related to reading comprehension, but not text reading fluency. These results reveal developmental nature of relations and mechanism of text reading fluency in reading development.

Developmental, Component-Based Model of Reading Fluency: An Investigation of Predictors of Word-Reading Fluency, Text-Reading Fluency, and Reading Comprehension

PubMed Central

Kim, Young-Suk Grace

2015-01-01

The primary goal was to expand our understanding of text reading fluency (efficiency or automaticity)—how its relation to other constructs (e.g., word reading fluency and reading comprehension) changes over time and how it is different from word reading fluency and reading comprehension. We examined (1) developmentally changing relations among word reading fluency, listening comprehension, text reading fluency, and reading comprehension; (2) the relation of reading comprehension to text reading fluency; (3) unique emergent literacy predictors (i.e., phonological awareness, orthographic awareness, morphological awareness, letter name knowledge, vocabulary) of text reading fluency vs. word reading fluency; and (4) unique language and cognitive predictors (e.g., vocabulary, grammatical knowledge, theory of mind) of text reading fluency vs. reading comprehension. These questions were addressed using longitudinal data (two timepoints; Mean age = 5;24 & 6;08) from Korean-speaking children (N = 143). Results showed that listening comprehension was related to text reading fluency at time 2, but not at time 1. At both times text reading fluency was related to reading comprehension, and reading comprehension was related to text reading fluency over and above word reading fluency and listening comprehension. Orthographic awareness was related to text reading fluency over and above other emergent literacy skills and word reading fluency. Vocabulary and grammatical knowledge were independently related to text reading fluency and reading comprehension whereas theory of mind was related to reading comprehension, but not text reading fluency. These results reveal developmental nature of relations and mechanism of text reading fluency in reading development. PMID:26435550

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zentgraf, Florian; Baum, Elias; Dreizler, Andreas

Planar particle image velocimetry (PIV) and tomographic PIV (TPIV) measurements are utilized to analyze turbulent statistical theory quantities and the instantaneous turbulence within a single-cylinder optical engine. Measurements are performed during the intake and mid-compression stroke at 800 and 1500 RPM. TPIV facilitates the evaluation of spatially resolved Reynolds stress tensor (RST) distributions, anisotropic Reynolds stress invariants, and instantaneous turbulent vortical structures. The RST analysis describes distributions of individual velocity fluctuation components that arise from unsteady turbulent flow behavior as well as cycle-to-cycle variability (CCV). A conditional analysis, for which instantaneous PIV images are sampled by their tumble center location,more » reveals that CCV and turbulence have similar contributions to RST distributions at the mean tumble center, but turbulence is dominant in regions peripheral to the tumble center. Analysis of the anisotropic Reynolds stress invariants reveals the spatial distribution of axisymmetric expansion, axisymmetric contraction, and 3D isotropy within the cylinder. Findings indicate that the mid-compression flow exhibits a higher tendency toward 3D isotropy than the intake flow. A novel post-processing algorithm is utilized to classify the geometry of instantaneous turbulent vortical structures and evaluate their frequency of occurrence within the cylinder. Findings are coupled with statistical theory quantities to provide a comprehensive understanding of the distribution of turbulent velocity components, the distribution of anisotropic states of turbulence, and compare the turbulent vortical flow distribution that is theoretically expected to what is experimentally observed. The analyses reveal requisites of important turbulent flow quantities and discern their sensitivity to the local flow topography and engine operation.« less

An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

PubMed Central

Habermann, Bianca; Bebin, Anne-Gaelle; Herklotz, Stephan; Volkmer, Michael; Eckelt, Kay; Pehlke, Kerstin; Epperlein, Hans Henning; Schackert, Hans Konrad; Wiebe, Glenis; Tanaka, Elly M

2004-01-01

Background The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum. Results Two cDNA libraries, one made from stage 18-22 embryos and the other from day-6 regenerating tail blastemas, generated 17,352 sequences. From the sequenced ESTs, 6,377 contigs were assembled that probably represent 25% of the expressed genes in this organism. Sequence comparison revealed significant homology to entries in the NCBI non-redundant database. Further examination of this gene set revealed the presence of genes involved in important cell and developmental processes, including cell proliferation, cell differentiation and cell-cell communication. On the basis of these data, we have performed phylogenetic analysis of key cell-cycle regulators. Interestingly, while cell-cycle proteins such as the cyclin B family display expected evolutionary relationships, the cyclin-dependent kinase inhibitor 1 gene family shows an unusual evolutionary behavior among the amphibians. Conclusions Our analysis reveals the importance of a comprehensive sequence set from a representative of the Caudata and illustrates that the EST sequence database is a rich source of molecular, developmental and regeneration studies. To aid in data mining, the ESTs have been organized into an easily searchable database that is freely available online. PMID:15345051

Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles.

PubMed

Aiese Cigliano, Riccardo; Sanseverino, Walter; Cremona, Gaetana; Ercolano, Maria R; Conicella, Clara; Consiglio, Federica M

2013-01-28

Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (HMs) in tomato are sketchy. Based on recently released tomato whole-genome sequences, we identified in silico 32 histone acetyltransferases (HATs), 15 histone deacetylases (HDACs), 52 histone methytransferases (HMTs) and 26 histone demethylases (HDMs), and compared them with those detected in Arabidopsis (Arabidopsis thaliana), maize (Zea mays) and rice (Oryza sativa) orthologs. Comprehensive analysis of the protein domain architecture and phylogeny revealed the presence of non-canonical motifs and new domain combinations, thereby suggesting for HATs the existence of a new family in plants. Due to species-specific diversification during evolutionary history tomato has fewer HMs than Arabidopsis. The transcription profiles of HMs within tomato organs revealed a broad functional role for some HMs and a more specific activity for others, suggesting key HM regulators in tomato development. Finally, we explored S. pennellii introgression lines (ILs) and integrated the map position of HMs, their expression profiles and the phenotype of ILs. We thereby proved that the strategy was useful to identify HM candidates involved in carotenoid biosynthesis in tomato fruits. In this study, we reveal the structure, phylogeny and spatial expression of members belonging to the classical families of HMs in tomato. We provide a framework for gene discovery and functional investigation of HMs in other Solanaceae species.

Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ansong, Charles; Wu, Si; Meng, Da

Characterization of the mature protein complement in cells is crucial for a better understanding of cellular processes on a systems-wide scale. Bottom-up proteomic approaches often lead to loss of critical information about an endogenous protein’s actual state due to post translational modifications (PTMs) and other processes. Top-down approaches that involve analysis of the intact protein can address this concern but present significant analytical challenges related to the separation quality needed, measurement sensitivity, and speed that result in low throughput and limited coverage. Here we used single-dimension ultra high pressure liquid chromatography mass spectrometry to investigate the comprehensive ‘intact’ proteome ofmore » the Gram negative bacterial pathogen Salmonella Typhimurium. Top-down proteomics analysis revealed 563 unique proteins including 1665 proteoforms generated by PTMs, representing the largest microbial top-down dataset reported to date. Our analysis not only confirmed several previously recognized aspects of Salmonella biology and bacterial PTMs in general, but also revealed several novel biological insights. Of particular interest was differential utilization of the protein S-thiolation forms S-glutathionylation and S-cysteinylation in response to infection-like conditions versus basal conditions, which was corroborated by changes in corresponding biosynthetic pathways. This differential utilization highlights underlying metabolic mechanisms that modulate changes in cellular signaling, and represents to our knowledge the first report of S-cysteinylation in Gram negative bacteria. The demonstrated utility of our simple proteome-wide intact protein level measurement strategy for gaining biological insight should promote broader adoption and applications of top-down proteomics approaches.« less