Many-body Tunneling and Nonequilibrium Dynamics of Doublons in Strongly Correlated Quantum Dots.

PubMed

Hou, WenJie; Wang, YuanDong; Wei, JianHua; Zhu, ZhenGang; Yan, YiJing

2017-05-30

Quantum tunneling dominates coherent transport at low temperatures in many systems of great interest. In this work we report a many-body tunneling (MBT), by nonperturbatively solving the Anderson multi-impurity model, and identify it a fundamental tunneling process on top of the well-acknowledged sequential tunneling and cotunneling. We show that the MBT involves the dynamics of doublons in strongly correlated systems. Proportional to the numbers of dynamical doublons, the MBT can dominate the off-resonant transport in the strongly correlated regime. A T 3/2 -dependence of the MBT current on temperature is uncovered and can be identified as a fingerprint of the MBT in experiments. We also prove that the MBT can support the coherent long-range tunneling of doublons, which is well consistent with recent experiments on ultracold atoms. As a fundamental physical process, the MBT is expected to play important roles in general quantum systems.

On testing models for the pressure-strain correlation of turbulence using direct simulations

NASA Technical Reports Server (NTRS)

Speziale, Charles G.; Gatski, Thomas B.; Sarkar, Sutanu

1992-01-01

Direct simulations of homogeneous turbulence have, in recent years, come into widespread use for the evaluation of models for the pressure-strain correlation of turbulence. While work in this area has been beneficial, the increasingly common practice of testing the slow and rapid parts of these models separately in uniformly strained turbulent flows is shown in this paper to be unsound. For such flows, the decomposition of models for the total pressure-strain correlation into slow and rapid parts is ambiguous. Consequently, when tested in this manner, misleading conclusions can be drawn about the performance of pressure-strain models. This point is amplified by illustrative calculations of homogeneous shear flow where other pitfalls in the evaluation of models are also uncovered. More meaningful measures for testing the performance of pressure-strain models in uniformly strained turbulent flows are proposed and the implications for turbulence modeling are discussed.

Intermittent fasting promotes adipose thermogenesis and metabolic homeostasis via VEGF-mediated alternative activation of macrophage.

PubMed

Kim, Kyoung-Han; Kim, Yun Hye; Son, Joe Eun; Lee, Ju Hee; Kim, Sarah; Choe, Min Seon; Moon, Joon Ho; Zhong, Jian; Fu, Kiya; Lenglin, Florine; Yoo, Jeong-Ah; Bilan, Philip J; Klip, Amira; Nagy, Andras; Kim, Jae-Ryong; Park, Jin Gyoon; Hussein, Samer Mi; Doh, Kyung-Oh; Hui, Chi-Chung; Sung, Hoon-Ki

2017-11-01

Intermittent fasting (IF), a periodic energy restriction, has been shown to provide health benefits equivalent to prolonged fasting or caloric restriction. However, our understanding of the underlying mechanisms of IF-mediated metabolic benefits is limited. Here we show that isocaloric IF improves metabolic homeostasis against diet-induced obesity and metabolic dysfunction primarily through adipose thermogenesis in mice. IF-induced metabolic benefits require fasting-mediated increases of vascular endothelial growth factor (VEGF) expression in white adipose tissue (WAT). Furthermore, periodic adipose-VEGF overexpression could recapitulate the metabolic improvement of IF in non-fasted animals. Importantly, fasting and adipose-VEGF induce alternative activation of adipose macrophage, which is critical for thermogenesis. Human adipose gene analysis further revealed a positive correlation of adipose VEGF-M2 macrophage-WAT browning axis. The present study uncovers the molecular mechanism of IF-mediated metabolic benefit and suggests that isocaloric IF can be a preventive and therapeutic approach against obesity and metabolic disorders.

Intermittent fasting promotes adipose thermogenesis and metabolic homeostasis via VEGF-mediated alternative activation of macrophage

PubMed Central

Kim, Kyoung-Han; Kim, Yun Hye; Son, Joe Eun; Lee, Ju Hee; Kim, Sarah; Choe, Min Seon; Moon, Joon Ho; Zhong, Jian; Fu, Kiya; Lenglin, Florine; Yoo, Jeong-Ah; Bilan, Philip J; Klip, Amira; Nagy, Andras; Kim, Jae-Ryong; Park, Jin Gyoon; Hussein, Samer MI; Doh, Kyung-Oh; Hui, Chi-chung; Sung, Hoon-Ki

2017-01-01

Intermittent fasting (IF), a periodic energy restriction, has been shown to provide health benefits equivalent to prolonged fasting or caloric restriction. However, our understanding of the underlying mechanisms of IF-mediated metabolic benefits is limited. Here we show that isocaloric IF improves metabolic homeostasis against diet-induced obesity and metabolic dysfunction primarily through adipose thermogenesis in mice. IF-induced metabolic benefits require fasting-mediated increases of vascular endothelial growth factor (VEGF) expression in white adipose tissue (WAT). Furthermore, periodic adipose-VEGF overexpression could recapitulate the metabolic improvement of IF in non-fasted animals. Importantly, fasting and adipose-VEGF induce alternative activation of adipose macrophage, which is critical for thermogenesis. Human adipose gene analysis further revealed a positive correlation of adipose VEGF-M2 macrophage-WAT browning axis. The present study uncovers the molecular mechanism of IF-mediated metabolic benefit and suggests that isocaloric IF can be a preventive and therapeutic approach against obesity and metabolic disorders. PMID:29039412

Peer Influence, Genetic Propensity, and Binge Drinking: A Natural Experiment and a Replication.

PubMed

Guo, Guang; Li, Yi; Wang, Hongyu; Cai, Tianji; Duncan, Greg J

2015-11-01

The authors draw data from the College Roommate Study (ROOM) and the National Longitudinal Study of Adolescent Health to investigate gene-environment interaction effects on youth binge drinking. In ROOM, the environmental influence was measured by the precollege drinking behavior of randomly assigned roommates. Random assignment safeguards against friend selection and removes the threat of gene-environment correlation that makes gene-environment interaction effects difficult to interpret. On average, being randomly assigned a drinking peer as opposed to a nondrinking peer increased college binge drinking by 0.5-1.0 episodes per month, or 20%-40% the average amount of binge drinking. However, this peer influence was found only among youths with a medium level of genetic propensity for alcohol use; those with either a low or high genetic propensity were not influenced by peer drinking. A replication of the findings is provided in data drawn from Add Health. The study shows that gene-environment interaction analysis can uncover social-contextual effects likely to be missed by traditional sociological approaches.

Uncovering factors affecting use of the emergency department for less urgent health problems in urban and rural areas.

PubMed

Hodgins, Marilyn J; Wuest, Judith

2007-09-01

People who access the emergency department for less urgent health problems have been described as inappropriate users of the health-care system.Yet little is known about the factors precipitating such use and how these differ based on location of the emergency department. In this descriptive-correlational study guided by Andersen's Model of Health Services Use, 1612 people who presented to an emergency department with a less urgent health problem were interviewed. Analysis revealed rural/urban differences in the characteristics of patients, nature of the problems, actions taken, and factors precipitating the visit. Despite its popularity, the predictive capabilities of Andersen's model were limited in explaining use of self-treatment or willingness to wait for treatment. The findings show that an emergency department's roles and functions vary according to its location. Such insights provide direction for developing services that respond to the needs of people with less urgent health problems that are cognizant of geographic location.

Using RIXS to uncover elementary charge and spin excitations

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

Jia, Chunjing; Wohlfeld, Krzysztof; Wang, Yao

2016-05-13

Despite significant progress in resonant inelastic x-ray scattering (RIXS) experiments on cuprates at the Cu L-edge, a theoretical understanding of the cross section remains incomplete in terms of elementary excitations and the connection to both charge and spin structure factors. Here, we use state-of-the-art, unbiased numerical calculations to study the low-energy excitations probed by RIXS in the Hubbard model, relevant to the cuprates. The results highlight the importance of scattering geometry, in particular, both the incident and scattered x-ray photon polarization, and they demonstrate that on a qualitative level the RIXS spectral shape in the cross-polarized channel approximates that ofmore » the spin dynamical structure factor. Furthermore, in the parallel-polarized channel, the complexity of the RIXS process beyond a simple two-particle response complicates the analysis and demonstrates that approximations and expansions that attempt to relate RIXS to less complex correlation functions cannot reproduce the full diversity of RIXS spectral features.« less

Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage

PubMed Central

Radhakrishnan, Ravi

2007-01-01

By employing classical molecular dynamics, correlation analysis of coupling between slow and fast dynamical modes, and free energy (umbrella) sampling using classical as well as mixed quantum mechanics molecular mechanics force fields, we uncover a possible pathway for phosphoryl transfer in the self-cleaving reaction of the minimal hammerhead ribozyme. The significance of this pathway is that it initiates from the minimal hammerhead crystal structure and describes the reaction landscape as a conformational rearrangement followed by a covalent transformation. The delineated mechanism is catalyzed by two metal (Mg2+) ions, proceeds via an in-line-attack by CYT 17 O2′ on the scissile phosphorous (ADE 1.1 P), and is therefore consistent with the experimentally observed inversion configuration. According to the delineated mechanism, the coupling between slow modes involving the hammerhead backbone with fast modes in the cleavage site appears to be crucial for setting up the in-line nucleophilic attack. PMID:17545240

Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2011-01-01

The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg4 and Glu53 during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution. PMID:22098751

Comparing lagged linear correlation, lagged regression, Granger causality, and vector autoregression for uncovering associations in EHR data.

PubMed

Levine, Matthew E; Albers, David J; Hripcsak, George

2016-01-01

Time series analysis methods have been shown to reveal clinical and biological associations in data collected in the electronic health record. We wish to develop reliable high-throughput methods for identifying adverse drug effects that are easy to implement and produce readily interpretable results. To move toward this goal, we used univariate and multivariate lagged regression models to investigate associations between twenty pairs of drug orders and laboratory measurements. Multivariate lagged regression models exhibited higher sensitivity and specificity than univariate lagged regression in the 20 examples, and incorporating autoregressive terms for labs and drugs produced more robust signals in cases of known associations among the 20 example pairings. Moreover, including inpatient admission terms in the model attenuated the signals for some cases of unlikely associations, demonstrating how multivariate lagged regression models' explicit handling of context-based variables can provide a simple way to probe for health-care processes that confound analyses of EHR data.

Spontaneous eyelid closures link vigilance fluctuation with fMRI dynamic connectivity states

PubMed Central

Wang, Chenhao; Ong, Ju Lynn; Patanaik, Amiya; Chee, Michael W. L.

2016-01-01

Fluctuations in resting-state functional connectivity occur but their behavioral significance remains unclear, largely because correlating behavioral state with dynamic functional connectivity states (DCS) engages probes that disrupt the very behavioral state we seek to observe. Observing spontaneous eyelid closures following sleep deprivation permits nonintrusive arousal monitoring. During periods of low arousal dominated by eyelid closures, sliding-window correlation analysis uncovered a DCS associated with reduced within-network functional connectivity of default mode and dorsal/ventral attention networks, as well as reduced anticorrelation between these networks. Conversely, during periods when participants’ eyelids were wide open, a second DCS was associated with less decoupling between the visual network and higher-order cognitive networks that included dorsal/ventral attention and default mode networks. In subcortical structures, eyelid closures were associated with increased connectivity between the striatum and thalamus with the ventral attention network, and greater anticorrelation with the dorsal attention network. When applied to task-based fMRI data, these two DCS predicted interindividual differences in frequency of behavioral lapsing and intraindividual temporal fluctuations in response speed. These findings with participants who underwent a night of total sleep deprivation were replicated in an independent dataset involving partially sleep-deprived participants. Fluctuations in functional connectivity thus appear to be clearly associated with changes in arousal. PMID:27512040

Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes

PubMed Central

VanderKraats, Nathan D.; Hiken, Jeffrey F.; Decker, Keith F.; Edwards, John R.

2013-01-01

Methylation of the CpG-rich region (CpG island) overlapping a gene’s promoter is a generally accepted mechanism for silencing expression. While recent technological advances have enabled measurement of DNA methylation and expression changes genome-wide, only modest correlations between differential methylation at gene promoters and expression have been found. We hypothesize that stronger associations are not observed because existing analysis methods oversimplify their representation of the data and do not capture the diversity of existing methylation patterns. Recently, other patterns such as CpG island shore methylation and long partially hypomethylated domains have also been linked with gene silencing. Here, we detail a new approach for discovering differential methylation patterns associated with expression change using genome-wide high-resolution methylation data: we represent differential methylation as an interpolated curve, or signature, and then identify groups of genes with similarly shaped signatures and corresponding expression changes. Our technique uncovers a diverse set of patterns that are conserved across embryonic stem cell and cancer data sets. Overall, we find strong associations between these methylation patterns and expression. We further show that an extension of our method also outperforms other approaches by generating a longer list of genes with higher quality associations between differential methylation and expression. PMID:23748561

Differential expression of folate receptor 1 in medulloblastoma and the correlation with clinicopathological characters and target therapeutic potential.

PubMed

Liu, Hailong; Sun, Qianwen; Zhang, Mingshan; Zhang, Zhihua; Fan, Xinyi; Yuan, Hongyu; Li, Cheng; Guo, Yuduo; Ning, Weihai; Sun, Youliang; Song, Yongmei; Yu, Chunjiang

2017-04-04

Medulloblastoma is the most common malignant brain tumor in children. Folate receptor 1 (Folr1) was abundantly expressed in some epithelial malignancies. However the expression profile and the role of clinicopathological significance and therapeutic target potential in medulloblastoma still remain elusive. Currently we detected the expression of Folr1 in medulloblastoma and identified the diagnostic application by evaluating the clinical, pathological and neuroimaging values. Then we developed a target therapeutic compound with Folr1, which exhibited promising efficiency in treatment of medulloblastoma. Folr1 expression was up-regulated in medulloblastoma and positively correlated with percentage of Ki-67 and MMP9 labeling, pathological subtypes, serum Folr1 levels and CSF spreading on MRI. The level of serum Folr1 showed rational sensitivity and specificity in predicting histological subgroups. Strong Folr1 expression was recommended as the independent value regarding the prognosis of patients with medulloblastoma. Folr1 targeted therapy attenuated the tumor growth and metastasis with down-regulation of MMPs proteins and activation of apoptosis. Immunostaining analysis in the xenograft samples showed the decreased Ki-67 and MMP9 index providing the strong evidences that Folr1 targeted application can suppress the proliferation and invasion. Our findings uncovered in Folr1 a predictive candidate and therapeutic target for medulloblastoma.

VARIATIONS IN SOLAR WIND FRACTIONATION AS SEEN BY ACE/SWICS AND THE IMPLICATIONS FOR GENESIS MISSION RESULTS

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

Pilleri, P.; Wiens, R. C.; Reisenfeld, D. B.

We use Advanced Composition Explorer (ACE)/Solar Wind Ion Composition Spectrometer (SWICS) elemental composition data to compare the variations in solar wind (SW) fractionation as measured by SWICS during the last solar maximum (1999–2001), the solar minimum (2006–2009), and the period in which the Genesis spacecraft was collecting SW (late 2001—early 2004). We differentiate our analysis in terms of SW regimes (i.e., originating from interstream or coronal hole flows, or coronal mass ejecta). Abundances are normalized to the low-first ionization potential (low-FIP) ion magnesium to uncover correlations that are not apparent when normalizing to high-FIP ions. We find that relative tomore » magnesium, the other low-FIP elements are measurably fractionated, but the degree of fractionation does not vary significantly over the solar cycle. For the high-FIP ions, variation in fractionation over the solar cycle is significant: greatest for Ne/Mg and C/Mg, less so for O/Mg, and the least for He/Mg. When abundance ratios are examined as a function of SW speed, we find a strong correlation, with the remarkable observation that the degree of fractionation follows a mass-dependent trend. We discuss the implications for correcting the Genesis sample return results to photospheric abundances.« less

Serglycin as a potential biomarker for glioma: association of serglycin expression, extent of mast cell recruitment and glioblastoma progression

PubMed Central

Roy, Ananya; Attarha, Sanaz; Weishaupt, Holger; Edqvist, Per-Henrik; Swartling, Fredrik J.; Bergqvist, Michael; Siebzehnrubl, Florian A.; Smits, Anja; Pontén, Fredrik; Tchougounova, Elena

2017-01-01

Serglycin is an intracellular proteoglycan with a unique ability to adopt highly divergent structures by glycosylation with variable types of glycosaminoglycans (GAGs) when expressed by different cell types. Serglycin is overexpressed in aggressive cancers suggesting its protumorigenic role. In this study, we explored the expression of serglycin in human glioma and its correlation with survival and immune cell infiltration. We demonstrate that serglycin is expressed in glioma and that increased expression predicts poor survival of patients. Analysis of serglycin expression in a large cohort of low- and high-grade human glioma samples reveals that its expression is grade dependent and is positively correlated with mast cell (MC) infiltration. Moreover, serglycin expression in patient-derived glioma cells is significantly increased upon MC co-culture. This is also accompanied by increased expression of CXCL12, CXCL10, as well as markers of cancer progression, including CD44, ZEB1 and vimentin. In conclusion, these findings indicate the importance of infiltrating MCs in glioma by modulating signaling cascades involving serglycin, CD44 and ZEB1. The present investigation reveals serglycin as a potential prognostic marker for glioma and demonstrates an association with the extent of MC recruitment and glioma progression, uncovering potential future therapeutic opportunities for patients. PMID:28445977

Correlation of EMR and optical spectroscopy data for Cr3+ and Mn2+ ions doped into yttrium aluminum borate YAl3(BO3)4 crystal - Extracting low symmetry aspects

NASA Astrophysics Data System (ADS)

Rudowicz, Czesław; Gnutek, Paweł; Açıkgöz, Muhammed

2015-08-01

In this study, the crystal field analysis for Cr3+ and Mn2+ ions doped into yttrium aluminum borate YAl3(BO3)4, for short YAB, crystal has been carried out to complement earlier study of the zero-field splitting (ZFS) parameters (ZFSPs). This analysis utilizes data on the distortion models obtained from analysis of the ZFSPs obtained experimentally by EMR for Cr3+ and Mn2+ ions at the Y3+ and Al3+ sites in YAB. This approach enables to verify and enhance reliability of the ZFSP modeling based on superposition model (SPM) analysis and the distortion models predicted previously. Subsequently, modeling of the crystal field parameters (CFPs) based on SPM analysis is carried out for Cr3+ and Mn2+ ions located at possible cation sites in YAB. The SPM predicted CFP values serve as input for the Crystal Field Analysis (CFA) package to calculate the CF energy levels. The predicted physical ZFS of the ground spin state, i.e. the 4A2 state for Cr3+ ion and the 6S state Mn2+ ions, enable calculation of the theoretical ZFSP values, D and D & (a-F), respectively, using the microscopic spin Hamiltonian (MSH) module in the CFA package. In this way, data on the distortions around the Cr3+ centers in YAB (and to a certain extent also for Mn2+ centers) obtained using the ZFSP data from EMR measurements may be correlated with data on the CF energy levels measured by optical spectroscopy. This modeling approach uncovers certain incompatibilities in the existing data for Cr3+:YAB, which call for reanalysis of the previous assignments of the energy levels observed in optical spectra and more accurate experimental data.

Partially covered metal stents have longer patency than uncovered and fully covered metal stents in the management of distal malignant biliary obstruction: a retrospective study.

PubMed

Yokota, Yudai; Fukasawa, Mitsuharu; Takano, Shinichi; Kadokura, Makoto; Shindo, Hiroko; Takahashi, Ei; Hirose, Sumio; Kawakami, Satoshi; Fukasawa, Yoshimitsu; Sato, Tadashi; Enomoto, Nobuyuki

2017-10-11

Self-expandable metal stents (SEMSs) are widely used for malignant biliary obstructions. Nitinol-covered SEMSs have been developed to improve stent patency. Currently, SEMSs may be uncovered, partially covered, or fully covered; however, there is no consensus on the best stent type for the management of malignant distal biliary obstruction (MDBO). Patients with unresectable MDBO receiving SEMS (Wallflex™) were retrospectively analyzed. Time to recurrent biliary obstruction (TRBO) and survival time were compared among the three types of SEMSs. Univariate and multivariate analyses were performed to identify risk factors for stent dysfunction. In total, 101 patients received SEMSs for unresectable MDBO (44 uncovered, 28 partially covered, and 29 fully covered SEMSs). Median survival time was 200, 168, and 276 days in the uncovered, partially covered, and fully covered SEMSs groups, respectively. There were no differences in survival among the three groups. Median TRBO was 199, 444, and 194 days in the uncovered, partially covered, and fully covered SEMSs groups, respectively. Partially covered SEMSs had longer TRBO than uncovered (p = 0.013) and fully covered (p = 0.010) SEMSs. Tumor ingrowth occurred only with uncovered SEMSs and stent migration occurred only with fully covered SEMSs. Multivariate analyses confirmed that partially covered SEMSs have lower risk of dysfunction. Partially covered SEMSs with a proximal uncovered flared end have longer patency than uncovered and fully covered SEMSs by preventing tumor ingrowth and stent migration.

The Neural Basis of Postural Instability Gait Disorder Subtype of Parkinson's Disease: A PET and fMRI Study.

PubMed

Zhang, Li; Li, Tian-Nv; Yuan, Yong-Sheng; Jiang, Si-Ming; Tong, Qing; Wang, Min; Wang, Jian-Wei; Chen, Hua-Jun; Ding, Jian; Xu, Qin-Rong; Zhang, Ke-Zhong

2016-05-01

The aim of this study is to further uncover the neural basis of postural instability gait disorder (PIGD) subtype of Parkinson's disease. With F-18 fluorodeoxyglucose PET (FDG-PET), brain glucose metabolism of patients with PIGD (n = 15) was compared with healthy controls (n = 17) and tremor-dominant (TD) patients (n = 15), and the correlation between metabolism and PIGD symptoms was also assessed. Within PIGD symptom-correlated hypometabolic areas, the relationship of functional connectivity (FC) with motor and cognitive symptoms was examined by using functional MRI. Compared with controls, patients with PIGD displayed a distributed pattern of brain hypometabolism including striatal, frontal, and parietal areas. Relative to the pattern of TD patients, the pattern of patients with PIGD had additional metabolic decreases in caudate and inferior parietal lobule (IPL, Brodmann area [BA] 40). In PIGD group, the metabolic reductions in IPL (BA 40), middle frontal gyrus (MFG, BA 9) and fusiform gyrus (FG, BA 20) were associated with severe PIGD symptoms. Regions showing such correlation were chosen for further seed-based FC analysis. Decreased FC within the prefrontal-parietal network (between the MFG and IPL) was associated with severe PIGD symptoms. The involvement of the caudate, FG, and prefrontal-parietal network may be associated with the prominent gait impairments of PIGD subtype. Our findings expand the pathophysiological knowledge of PIGD subtype and provide valuable information for potential neuromodulation therapies alleviating gait disorders. © 2016 John Wiley & Sons Ltd.

Uncovering the influence of social skills and psychosociological factors on pain sensitivity using structural equation modeling

PubMed Central

Tanaka, Yoichi; Nishi, Yuki; Nishi, Yuki; Osumi, Michihiro; Morioka, Shu

2017-01-01

Pain is a subjective emotional experience that is influenced by psychosociological factors such as social skills, which are defined as problem-solving abilities in social interactions. This study aimed to reveal the relationships among pain, social skills, and other psychosociological factors by using structural equation modeling. A total of 101 healthy volunteers (41 men and 60 women; mean age: 36.6±12.7 years) participated in this study. To evoke participants’ sense of inner pain, we showed them images of painful scenes on a PC screen and asked them to evaluate the pain intensity by using the visual analog scale (VAS). We examined the correlation between social skills and VAS, constructed a hypothetical model based on results from previous studies and the current correlational analysis results, and verified the model’s fit using structural equation modeling. We found significant positive correlations between VAS and total social skills values, as well as between VAS and the “start of relationships” subscales. Structural equation modeling revealed that the values for “start of relationships” had a direct effect on VAS values (path coefficient =0.32, p<0.01). In addition, the “start of relationships” had both a direct and an indirect effect on psychological factors via social support. The results indicated that extroverted people are more sensitive to inner pain and tend to get more social support and maintain a better psychological condition. PMID:28979161

Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds

PubMed Central

Zhang, Liangzhi; Jia, Shangang; Plath, Martin; Huang, Yongzhen; Li, Congjun; Lei, Chuzhao; Zhao, Xin; Chen, Hong

2015-01-01

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression. PMID:26260653

Electrodermal complexity during the Stroop colour word test.

PubMed

Svetlak, Miroslav; Bob, Petr; Cernik, Michal; Kukleta, Miloslav

2010-01-15

Several recent studies suggest that quantitative description of signal complexity using algorithms of nonlinear analysis could uncover new information about the autonomic system that is not reflected using common methods applied to measures of autonomic activity. With this aim we have performed complexity analysis of electrodermal activity (EDA) assessed in 106 healthy university students during rest conditions and non-conflicting and conflicting Stroop task. Complexity analysis applied to EDA was performed using Skinner's algorithm for pointwise correlation dimension (PD2). Results have shown that EDA responses during the Stroop Colour Word test are related to significantly increased or decreased complexity. Particularly significant result is that PD2 has a unique ability to predict to an extent the change in EDA response to stress i.e. that subjects with low initial PD2 tended to respond to experimental stress by its increase and subjects with high initial PD2 values tended to respond by its decrease. This response was not found in EDA measures where increase of the EDA presented predominant response to experimental stress in majority of the subjects. These findings suggest that PD2 is more sensitive to subtle aspects of functionally and spatially distributed modulatory influences of various parts of the brain that are involved in the EDA modulation and provides novel information in comparison to traditional methods.

Childhood temperament: passive gene-environment correlation, gene-environment interaction, and the hidden importance of the family environment.

PubMed

Lemery-Chalfant, Kathryn; Kao, Karen; Swann, Gregory; Goldsmith, H Hill

2013-02-01

Biological parents pass on genotypes to their children, as well as provide home environments that correlate with their genotypes; thus, the association between the home environment and children's temperament can be genetically (i.e., passive gene-environment correlation) or environmentally mediated. Furthermore, family environments may suppress or facilitate the heritability of children's temperament (i.e., gene-environment interaction). The sample comprised 807 twin pairs (mean age = 7.93 years) from the longitudinal Wisconsin Twin Project. Important passive gene-environment correlations emerged, such that home environments were less chaotic for children with high effortful control, and this association was genetically mediated. Children with high extraversion/surgency experienced more chaotic home environments, and this correlation was also genetically mediated. In addition, heritability of children's temperament was moderated by home environments, such that effortful control and extraversion/surgency were more heritable in chaotic homes, and negative affectivity was more heritable under crowded or unsafe home conditions. Modeling multiple types of gene-environment interplay uncovered the complex role of genetic factors and the hidden importance of the family environment for children's temperament and development more generally.

Analysis of the synaptotagmin family during reconstituted membrane fusion. Uncovering a class of inhibitory isoforms.

PubMed

Bhalla, Akhil; Chicka, Michael C; Chapman, Edwin R

2008-08-01

Ca(2+)-triggered exocytosis in neurons and neuroendocrine cells is regulated by the Ca(2+)-binding protein synaptotagmin (syt) I. Sixteen additional isoforms of syt have been identified, but little is known concerning their biochemical or functional properties. Here, we assessed the abilities of fourteen syt isoforms to directly regulate SNARE (soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor)-catalyzed membrane fusion. One group of isoforms stimulated neuronal SNARE-mediated fusion in response to Ca(2+), while another set inhibited SNARE catalyzed fusion in both the absence and presence of Ca(2+). Biochemical analysis revealed a strong correlation between the ability of syt isoforms to bind 1,2-dioleoyl phosphatidylserine (PS) and t-SNAREs in a Ca(2+)-promoted manner with their abilities to enhance fusion, further establishing PS and SNAREs as critical effectors for syt action. The ability of syt I to efficiently stimulate fusion was specific for certain SNARE pairs, suggesting that syts might contribute to the specificity of intracellular membrane fusion reactions. Finally, a subset of inhibitory syts down-regulated the ability of syt I to activate fusion, demonstrating that syt isoforms can modulate the function of each other.

High Prevalence and Partner Correlates of Physical and Sexual Violence by Intimate Partners among Street and Off-Street Sex Workers

PubMed Central

Argento, Elena; Muldoon, Katherine A.; Duff, Putu; Simo, Annick; Deering, Kathleen N.; Shannon, Kate

2014-01-01

Objectives Intimate partner violence (IPV) is associated with increased risk of HIV among women globally. There is limited evidence and understanding about IPV and potential HIV risk pathways among sex workers (SWs). This study aims to longitudinally evaluate prevalence and correlates of IPV among street and off-street SWs over two-years follow-up. Methods Longitudinal data were drawn from an open prospective cohort, AESHA (An Evaluation of Sex Workers Health Access) in Metro Vancouver, Canada (2010–2012). Prevalence of physical and sexual IPV was measured using the WHO standardized IPV scale (version 9.9). Bivariate and multivariable logistic regression using Generalized Estimating Equations (GEE) were used to examine interpersonal and structural correlates of IPV over two years. Results At baseline, 387 SWs had a male, intimate sexual partner and were eligible for this analysis. One-fifth (n = 83, 21.5%) experienced recent physical/sexual IPV at baseline and 26.2% over two-years follow-up. In multivariable GEE analysis, factors independently correlated with physical/sexual IPV in the last six months include: childhood (<18 years) sexual/physical abuse (adjusted odds ratio [AOR] = 2.05, 95% confidence interval [CI]: 1.14–3.69), inconsistent condom use for vaginal and/or anal sex with intimate partner (AOR = 1.84, 95% CI: 1.07–3.16),

BMP and TGFbeta pathways in human central chondrosarcoma: enhanced endoglin and Smad 1 signaling in high grade tumors

PubMed Central

2012-01-01

Background As major regulators of normal chondrogenesis, the bone morphogenic protein (BMP) and transforming growth factor β (TGFB) signaling pathways may be involved in the development and progression of central chondrosarcoma. In order to uncover their possible implication, the aim of this study was to perform a systematic quantitative study of the expression of BMPs, TGFBs and their receptors and to assess activity of the corresponding pathways in central chondrosarcoma. Methods Gene expression analysis was performed by quantitative RT-PCR in 26 central chondrosarcoma and 6 healthy articular cartilage samples. Expression of endoglin and nuclear localization of phosphorylated Smad1/5/8 and Smad2 was assessed by immunohistochemical analysis. Results The expression of TGFB3 and of the activin receptor-like kinase ALK2 was found to be significantly higher in grade III compared to grade I chondrosarcoma. Nuclear phosphorylated Smad1/5/8 and Smad2 were found in all tumors analyzed and the activity of both signaling pathways was confirmed by functional reporter assays in 2 chondrosarcoma cell lines. Immunohistochemical analysis furthermore revealed that phosphorylated Smad1/5/8 and endoglin expression were significantly higher in high-grade compared to low-grade chondrosarcoma and correlated to each other. Conclusions The BMP and TGFβ signaling pathways were found to be active in central chondrosarcoma cells. The correlation of Smad1/5/8 activity to endoglin expression suggests that, as described in other cell types, endoglin could enhance Smad1/5/8 signaling in high-grade chondrosarcoma cells. Endoglin expression coupled to Smad1/5/8 activation could thus represent a functionally important signaling axis for the progression of chondrosarcoma and a regulator of the undifferentiated phenotype of high-grade tumor cells. PMID:23088614

Analysis of Design and Delivery of Critical Incident Workshops for Elementary School English as a Foreign Language Teachers in Community of Practice

ERIC Educational Resources Information Center

Chien, Chin-Wen

2018-01-01

Language teachers can uncover new understanding of the teaching and learning process through reflecting on critical incidents [Richard, J.C., and T.S.C. Farrell. 2005. "Professional Development for Language Teachers." New York, NY: Cambridge University Press]. Based on the data analysis of workshop handouts, observation notes, and…

Disambiguating with Bourdieu: Unravelling Policy from Practice in the Teaching of Children with English as an Additional Language

ERIC Educational Resources Information Center

Flynn, Naomi

2015-01-01

This article explores the use of Bourdieusian analysis for examining how policy and practice interact in the teaching of English and therefore in the development of children's language and literacy, in particular how. Bourdieusian analysis uncovers the ways in which teachers' practice has been influenced unconsciously by centralised shaping of the…

Confirmatory Factor Analysis of U.S. Merit Systems Protection Board's Survey of Sexual Harassment: The Fit of a Three-Factor Model.

ERIC Educational Resources Information Center

Stockdale, Margaret S.; Hope, Kathryn G.

1997-01-01

Factor analysis of data from 1,070 federal employees, 575 undergraduates and 575 graduate students, faculty, and staff uncovered some weaknesses in the Merit Systems Protection Board's sexual harassment survey instrument. This type of survey does not adequately measure sexual coercion or quid pro quo forms of harassment. (SK)

The Analysis of Likert Scales Using State Multipoles: An Application of Quantum Methods to Behavioral Sciences Data

ERIC Educational Resources Information Center

Camparo, James; Camparo, Lorinda B.

2013-01-01

Though ubiquitous, Likert scaling's traditional mode of analysis is often unable to uncover all of the valid information in a data set. Here, the authors discuss a solution to this problem based on methodology developed by quantum physicists: the state multipole method. The authors demonstrate the relative ease and value of this method by…

Comparison between uncovered and covered self-expandable metal stent placement in malignant duodenal obstruction.

PubMed

Kim, Ji Won; Jeong, Ji Bong; Lee, Kook Lae; Kim, Byeong Gwan; Ahn, Dong Won; Lee, Jae Kyung; Kim, Su Hwan

2015-02-07

To compare the clinical outcomes of uncovered and covered self-expandable metal stent placements in patients with malignant duodenal obstruction. A total of 67 patients were retrospectively enrolled from January 2003 to June 2013. All patients had symptomatic obstruction characterized by nausea, vomiting, reduced oral intake, and weight loss. The exclusion criteria included asymptomatic duodenal obstruction, perforation or peritonitis, concomitant small bowel obstruction, or duodenal obstruction caused by benign strictures. The technical and clinical success rate, complication rate, and stent patency were compared according to the placement of uncovered (n = 38) or covered (n = 29) stents. The technical and clinical success rates did not differ between the uncovered and covered stent groups (100% vs 96.6% and 89.5% vs 82.8%). There were no differences in the overall complication rates between the uncovered and covered stent groups (31.6% vs 41.4%). However, stent migration occurred more frequently with covered than uncovered stents [20.7% (6/29) vs 0% (0/38), P < 0.05]. Moreover, the overall cumulative median duration of stent patency was longer in uncovered than in covered stents [251 d (95%CI: 149.8 d-352.2 d) vs 139 d (95%CI: 45.5 d-232.5 d), P < 0.05 by log-rank test] The overall cumulative median survival period was not different between the uncovered stent (70 d) and covered stent groups (60 d). Uncovered stents may be preferable in malignant duodenal obstruction because of their greater resistance to stent migration and longer stent patency than covered stents.

Comparison between uncovered and covered self-expandable metal stent placement in malignant duodenal obstruction

PubMed Central

Kim, Ji Won; Jeong, Ji Bong; Lee, Kook Lae; Kim, Byeong Gwan; Ahn, Dong Won; Lee, Jae Kyung; Kim, Su Hwan

2015-01-01

AIM: To compare the clinical outcomes of uncovered and covered self-expandable metal stent placements in patients with malignant duodenal obstruction. METHODS: A total of 67 patients were retrospectively enrolled from January 2003 to June 2013. All patients had symptomatic obstruction characterized by nausea, vomiting, reduced oral intake, and weight loss. The exclusion criteria included asymptomatic duodenal obstruction, perforation or peritonitis, concomitant small bowel obstruction, or duodenal obstruction caused by benign strictures. The technical and clinical success rate, complication rate, and stent patency were compared according to the placement of uncovered (n = 38) or covered (n = 29) stents. RESULTS: The technical and clinical success rates did not differ between the uncovered and covered stent groups (100% vs 96.6% and 89.5% vs 82.8%). There were no differences in the overall complication rates between the uncovered and covered stent groups (31.6% vs 41.4%). However, stent migration occurred more frequently with covered than uncovered stents [20.7% (6/29) vs 0% (0/38), P < 0.05]. Moreover, the overall cumulative median duration of stent patency was longer in uncovered than in covered stents [251 d (95%CI: 149.8 d-352.2 d) vs 139 d (95%CI: 45.5 d-232.5 d), P < 0.05 by log-rank test] The overall cumulative median survival period was not different between the uncovered stent (70 d) and covered stent groups (60 d). CONCLUSION: Uncovered stents may be preferable in malignant duodenal obstruction because of their greater resistance to stent migration and longer stent patency than covered stents. PMID:25663777

Diagnosing Communication Pathologies.

ERIC Educational Resources Information Center

Mueller, Carol J.

This paper addresses the concept of the communication audit, i.e., a fact-finding analysis, interpretation, and reporting process that studies the communication philosophy, structure, flow, and practice of the organization. Reasons for doing a communication audit are identified: (1) to uncover information blockages and organizational hindrances;…

Who Was the Real William Shakespeare?

ERIC Educational Resources Information Center

Edwards, Michael Todd

2009-01-01

This article highlights a project that encourages students to connect reading and mathematics instruction by using a data analysis approach. Students analyze sonnets from statistical, literary, and historical points of view in an effort to uncover the true identity of William Shakespeare. (Contains 10 figures.)

Genomics of Nitrogen Cycle in Freshwater Lakes with Focus on Methylotrophic Bacteria

NASA Astrophysics Data System (ADS)

Chistoserdova, L.

2014-12-01

Data will be presented on communities of microbes active in methane oxidation in Lake Washington, Seattle. Metagenomic sequencing of sediment samples reveals dominant presence of Methylobacter, contrary to prior understanding based on cultivation of methanotrophs. Stable isotope probing of microcosms incubated with methane at varying concentrations of oxygen and nitrate uncover a dominant response by Methylobacter species and a correlation between the populations of Methylobacter and Methylotenera, both responding positively to nitrate. We also uncover a propensity of Methylobacter to act in microoxic conditions, in this case transferring carbon down a food chain represented by a variety of bacteria. Functional gene profiling detects upwards shifts in the abundances of nitrogen metabolism genes in response to nitrate, with Methylococcaceae and Methylophilaceae genes being most abundant. We test a hypothesis of cooperative behavior between Methylobacter, Methylotenera and other species using two alternative approaches: a top-down approach in which we incubate native lake sediments under different conditions and observe trajectories of community simplification, and a bottom-up approach in which we construct synthetic communities from pure cultures of bacteria and observe their behavior. We also cultivate Methylobacter as well as multiple species of Methylophilaceae and analyze their genomes. Among the Methylophilaceae, we uncover a remarkable flexibility in terms of both central carbon and nitrogen metabolic pathways. We hypothesize that this diversity may be driven by microniche conditions along the methane and oxygen countergradients, as well as by the availability of nitrogen sources. Our future plans include deciphering the mechanistic details of cooperative behavior in methane oxidation, using Lake Washington communities as a model.

Uncovering Hidden Layers of Cell Cycle Regulation through Integrative Multi-omic Analysis

PubMed Central

Aviner, Ranen; Shenoy, Anjana; Elroy-Stein, Orna; Geiger, Tamar

2015-01-01

Studying the complex relationship between transcription, translation and protein degradation is essential to our understanding of biological processes in health and disease. The limited correlations observed between mRNA and protein abundance suggest pervasive regulation of post-transcriptional steps and support the importance of profiling mRNA levels in parallel to protein synthesis and degradation rates. In this work, we applied an integrative multi-omic approach to study gene expression along the mammalian cell cycle through side-by-side analysis of mRNA, translation and protein levels. Our analysis sheds new light on the significant contribution of both protein synthesis and degradation to the variance in protein expression. Furthermore, we find that translation regulation plays an important role at S-phase, while progression through mitosis is predominantly controlled by changes in either mRNA levels or protein stability. Specific molecular functions are found to be co-regulated and share similar patterns of mRNA, translation and protein expression along the cell cycle. Notably, these include genes and entire pathways not previously implicated in cell cycle progression, demonstrating the potential of this approach to identify novel regulatory mechanisms beyond those revealed by traditional expression profiling. Through this three-level analysis, we characterize different mechanisms of gene expression, discover new cycling gene products and highlight the importance and utility of combining datasets generated using different techniques that monitor distinct steps of gene expression. PMID:26439921

Dimensions of belonging as an aspect of racial-ethnic-cultural identity: an exploration of indigenous Australians.

PubMed

Neville, Helen A; Oyama, Kathleen E; Odunewu, Latifat O; Huggins, Jackie G

2014-07-01

Sense of belonging is a key aspect of racial and ethnic identity. Interestingly, there is little exploration of the multiple characteristics of belongingness within the racial and ethnic identity literature. Through individual interviews and a focus group, we explored the sense of racial-ethnic-cultural (REC) belonging among 19 self-identified Black Indigenous Australians (Aborigines and Torres Strait Islanders). Using dimensional analysis, we uncovered 5 core interrelated dimensions of REC belonging: History/Memory, Place, and Peoplehood; Sense of Community; Acceptance and Pride; Shared Language and Culture; and Interconnections. We also uncovered 3 main barriers undermining participants' sense of REC belonging: phenotype, social identity, and history of colonization. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Comparative Transcriptomic Analysis Reveals Similarities and Dissimilarities in Saccharomyces cerevisiae Wine Strains Response to Nitrogen Availability

PubMed Central

Barbosa, Catarina; García-Martínez, José; Pérez-Ortín, José E.; Mendes-Ferreira, Ana

2015-01-01

Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12h, 24h and 96h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape-musts and the development of strategies to optimize yeast performance in industrial fermentations. PMID:25884705

Theory of the special Smith-Purcell radiation from a rectangular grating

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

Liu, Weihao, E-mail: liuwhao@ustc.edu.cn; He, Zhigang, E-mail: hezhg@ustc.edu.cn; Jia, Qika

2015-12-15

The recently uncovered special Smith-Purcell radiation (S-SPR) from the rectangular grating has significantly higher intensity than the ordinary Smith-Purcell radiation (SPR). Its monochromaticity and directivity are also much better. Here we explored the mechanism of the S-SPR by applying the fundamental electromagnetic theory and simulations. We have confirmed that the S-SPR is exactly from the radiating eigen modes of the grating. Its frequency and direction are well correlated with the beam velocity and structure parameters, which indicates its promising applications in tunable wave generation and beam diagnostic.

Evolutionary anomalies among the aminoacyl-tRNA synthetases

NASA Technical Reports Server (NTRS)

Doolittle, R. F.; Handy, J.; Bada, J. L. (Principal Investigator)

1998-01-01

Unexpected relationships among the various aminoacyl-tRNA synthetases continue to be uncovered. The question arises - is this mainly the result of promiscuous exchange, or is the confusion really a reflection of the differential loss of past duplications? Phylogenetic analysis may yet provide the answer.

Carnage interrupted : an analysis of fifteen terrorist plots against public surface transportation.

DOT National Transportation Integrated Search

2012-04-01

This report examines 13 terrorist plots against public surface transportation that were uncovered and foiled by authorities between 1997 and 2010 and two failed attempts to carry out attacks. Certainly, this is not the total universe of foiled or fai...

Uncovering Ways of Thinking, Practicing, and Being through Decoding across Disciplines

ERIC Educational Resources Information Center

Miller-Young, Janice; Boman, Jennifer

2017-01-01

This chapter presents the bottlenecks identified by seven faculty members from diverse disciplines and an inductive content analysis of their Decoding interviews. Representative quotations illustrate themes in the interviews and we consider the implications for both faculty development and pedagogical research.

Using brain stimulation to disentangle neural correlates of conscious vision

PubMed Central

de Graaf, Tom A.; Sack, Alexander T.

2014-01-01

Research into the neural correlates of consciousness (NCCs) has blossomed, due to the advent of new and increasingly sophisticated brain research tools. Neuroimaging has uncovered a variety of brain processes that relate to conscious perception, obtained in a range of experimental paradigms. But methods such as functional magnetic resonance imaging or electroencephalography do not always afford inference on the functional role these brain processes play in conscious vision. Such empirical NCCs could reflect neural prerequisites, neural consequences, or neural substrates of a conscious experience. Here, we take a closer look at the use of non-invasive brain stimulation (NIBS) techniques in this context. We discuss and review how NIBS methodology can enlighten our understanding of brain mechanisms underlying conscious vision by disentangling the empirical NCCs. PMID:25295015

Uncovering the effective interval of resolution parameter across multiple community optimization measures

NASA Astrophysics Data System (ADS)

Li, Hui-Jia; Cheng, Qing; Mao, He-Jin; Wang, Huanian; Chen, Junhua

2017-03-01

The study of community structure is a primary focus of network analysis, which has attracted a large amount of attention. In this paper, we focus on two famous functions, i.e., the Hamiltonian function H and the modularity density measure D, and intend to uncover the effective thresholds of their corresponding resolution parameter γ without resolution limit problem. Two widely used example networks are employed, including the ring network of lumps as well as the ad hoc network. In these two networks, we use discrete convex analysis to study the interval of resolution parameter of H and D that will not cause the misidentification. By comparison, we find that in both examples, for Hamiltonian function H, the larger the value of resolution parameter γ, the less resolution limit the network suffers; while for modularity density D, the less resolution limit the network suffers when we decrease the value of γ. Our framework is mathematically strict and efficient and can be applied in a lot of scientific fields.

Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues.

PubMed

Kadoki, Motohiko; Patil, Ashwini; Thaiss, Cornelius C; Brooks, Donald J; Pandey, Surya; Deep, Deeksha; Alvarez, David; von Andrian, Ulrich H; Wagers, Amy J; Nakai, Kenta; Mikkelsen, Tarjei S; Soumillon, Magali; Chevrier, Nicolas

2017-10-05

A fundamental challenge in immunology is to decipher the principles governing immune responses at the whole-organism scale. Here, using a comparative infection model, we observe immune signal propagation within and between organs to obtain a dynamic map of immune processes at the organism level. We uncover two inter-organ mechanisms of protective immunity mediated by soluble and cellular factors. First, analyzing ligand-receptor connectivity across tissues reveals that type I IFNs trigger a whole-body antiviral state, protecting the host within hours after skin vaccination. Second, combining parabiosis, single-cell analyses, and gene knockouts, we uncover a multi-organ web of tissue-resident memory T cells that functionally adapt to their environment to stop viral spread across the organism. These results have implications for manipulating tissue-resident memory T cells through vaccination and open up new lines of inquiry for the analysis of immune responses at the organism level. Copyright © 2017 Elsevier Inc. All rights reserved.

The Incremental Multiresolution Matrix Factorization Algorithm

PubMed Central

Ithapu, Vamsi K.; Kondor, Risi; Johnson, Sterling C.; Singh, Vikas

2017-01-01

Multiresolution analysis and matrix factorization are foundational tools in computer vision. In this work, we study the interface between these two distinct topics and obtain techniques to uncover hierarchical block structure in symmetric matrices – an important aspect in the success of many vision problems. Our new algorithm, the incremental multiresolution matrix factorization, uncovers such structure one feature at a time, and hence scales well to large matrices. We describe how this multiscale analysis goes much farther than what a direct “global” factorization of the data can identify. We evaluate the efficacy of the resulting factorizations for relative leveraging within regression tasks using medical imaging data. We also use the factorization on representations learned by popular deep networks, providing evidence of their ability to infer semantic relationships even when they are not explicitly trained to do so. We show that this algorithm can be used as an exploratory tool to improve the network architecture, and within numerous other settings in vision. PMID:29416293

Exploring the Dimensionality of Ethnic Minority Adaptation in Britain: An Analysis across Ethnic and Generational Lines

PubMed Central

Lessard-Phillips, Laurence

2015-01-01

In this article I explore the dimensionality of the long-term experiences of the main ethnic minority groups (their adaptation) in Britain. Using recent British data, I apply factor analysis to uncover the underlying number of factors behind variables deemed to be representative of the adaptation experience within the literature. I then attempt to assess the groupings of adaptation present in the data, to see whether a typology of adaptation exists (i.e. whether adaptation in different dimensions can be concomitant with others). The analyses provide an empirical evidence base to reflect on: (1) the extent of group differences in the adaptation process, which may cut across ethnic and generational lines; and (2) whether the uncovered dimensions of adaptation match existing theoretical views and empirical evidence. Results suggest that adaptation should be regarded as a multi-dimensional phenomenon where clear typologies of adaptation based on specific trade-offs (mostly cultural) appear to exist. PMID:28502998

Multiple-locus variable number of tandem repeat analysis (MLVA) of Irish verocytotoxigenic Escherichia coli O157 from feedlot cattle: uncovering strain dissemination routes.

PubMed

Murphy, Mary; Minihan, Donal; Buckley, James F; O'Mahony, Micheál; Whyte, Paul; Fanning, Séamus

2008-01-24

The identification of the routes of dissemination of Escherichia coli (E. coli) O157 through a cohort of cattle is a critical step to control this pathogen at farm level. The aim of this study was to identify potential routes of dissemination of E. coli O157 using Multiple-Locus Variable number of tandem repeat Analysis (MLVA). Thirty-eight environmental and sixteen cattle faecal isolates, which were detected in four adjacent pens over a four-month period were sub-typed. MLVA could separate these isolates into broadly defined clusters consisting of twelve MLVA types. Strain diversity was observed within pens, individual cattle and the environment. Application of MLVA is a broadly useful and convenient tool when applied to uncover the dissemination of E. coli O157 in the environment and in supporting improved on-farm management of this important pathogen. These data identified diverse strain types based on amplification of VNTR markers in each case.

78 FR 41784 - Uncovered Innerspring Units From the People's Republic of China: Affirmative Preliminary...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-11

... DEPARTMENT OF COMMERCE International Trade Administration [A-570-928] Uncovered Innerspring Units... Commerce. Preliminary Determination The Department has preliminarily determined that uncovered innerspring... Commerce, 14th Street and Constitution Avenue NW., Washington, DC 20230; telephone: (202) [[Page 41785...

Uncovering Heavily Obscured AGN with WISE and NuSTAR

NASA Astrophysics Data System (ADS)

Hickox, Ryan C.; Carroll, Christopher M.; Yan, Wei; DiPompeo, Michael A.; Hainline, Kevin N.; NuSTAR Obscured AGN Team

2018-01-01

Supermassive black holes gain their mass through accretion as active galactic nuclei (AGN), but it is now clear that a large fraction of this growth is "hidden" behind large columns of gas and dust. Of particular interest are Compton-thick (CT) AGN, with columns NH > 1024 cm-2, that have been difficult to identify using optical or soft X-ray surveys. We will present two studies of heavily obscured AGN that aim to uncover more of the full population of "hidden" growing black holes: (1) Analysis of the spectral energy distributions of millions of galaxies with photometry from WISE (mid-IR), UKIDSS (near-IR), and SDSS (optical), that uncovers large populations of weak or heavily buried AGN, and (2) NuSTAR observations of a sample of candidate highly obscured AGN, selected from WISE and SDSS photometry,and confirmed using SALT and Keck spectroscopy. The NuSTAR data reveal the existence of powerful CT quasars with extremely large columns NH > 1025 cm-2, which may represent a significant fraction of previously hidden black hole growth. This work is supported by NASA grant numbers NNX16AN48G and NNX15AP24G, and the NSF through grant numbers 1515364 and 1554584.

High levels of cryptic species diversity uncovered in Amazonian frogs

PubMed Central

Funk, W. Chris; Caminer, Marcel; Ron, Santiago R.

2012-01-01

One of the greatest challenges for biodiversity conservation is the poor understanding of species diversity. Molecular methods have dramatically improved our ability to uncover cryptic species, but the magnitude of cryptic diversity remains unknown, particularly in diverse tropical regions such as the Amazon Basin. Uncovering cryptic diversity in amphibians is particularly pressing because amphibians are going extinct globally at an alarming rate. Here, we use an integrative analysis of two independent Amazonian frog clades, Engystomops toadlets and Hypsiboas treefrogs, to test whether species richness is underestimated and, if so, by how much. We sampled intensively in six countries with a focus in Ecuador (Engystomops: 252 individuals from 36 localities; Hypsiboas: 208 individuals from 65 localities) and combined mitochondrial DNA, nuclear DNA, morphological, and bioacoustic data to detect cryptic species. We found that in both clades, species richness was severely underestimated, with more undescribed species than described species. In Engystomops, the two currently recognized species are actually five to seven species (a 150–250% increase in species richness); in Hypsiboas, two recognized species represent six to nine species (a 200–350% increase). Our results suggest that Amazonian frog biodiversity is much more severely underestimated than previously thought. PMID:22130600

Vocabulary Glossing: A Meta-Analysis of the Relative Effectiveness of Different Gloss Types on L2 Vocabulary Acquisition

ERIC Educational Resources Information Center

Vahedi, Vahideh Sadat; Ghonsooly, Behzad; Pishghadam, Reza

2016-01-01

In recent years there has been a growing interest to incorporate hypertext glosses into L2 reading materials and accordingly, it has provoked researchers to uncover to what extent and under which moderator variables a specific type of gloss yields more effective outcomes than other types of glossing. The present meta-analysis attempts to examine…

Hearing the Signal in the Noise: A Software-Based Content Analysis of Patterns in Responses by Experts and Students to a New Venture Investment Proposal

ERIC Educational Resources Information Center

Hostager, Todd J.; Voiovich, Jason; Hughes, Raymond K.

2013-01-01

The authors apply a software-based content analysis method to uncover differences in responses by expert entrepreneurs and undergraduate entrepreneur majors to a new venture investment proposal. Data analyzed via the Leximancer software package yielded conceptual maps highlighting key differences in the nature of these responses. Study methods and…

Haptic contents of a movie dynamically engage the spectator's sensorimotor cortex.

PubMed

Lankinen, Kaisu; Smeds, Eero; Tikka, Pia; Pihko, Elina; Hari, Riitta; Koskinen, Miika

2016-11-01

Observation of another person's actions and feelings activates brain areas that support similar functions in the observer, thereby facilitating inferences about the other's mental and bodily states. In real life, events eliciting this kind of vicarious brain activations are intermingled with other complex, ever-changing stimuli in the environment. One practical approach to study the neural underpinnings of real-life vicarious perception is to image brain activity during movie viewing. Here the goal was to find out how observed haptic events in a silent movie would affect the spectator's sensorimotor cortex. The functional state of the sensorimotor cortex was monitored by analyzing, in 16 healthy subjects, magnetoencephalographic (MEG) responses to tactile finger stimuli that were presented once per second throughout the session. Using canonical correlation analysis and spatial filtering, consistent single-trial responses across subjects were uncovered, and their waveform changes throughout the movie were quantified. The long-latency (85-175 ms) parts of the responses were modulated in concordance with the participants' average moment-by-moment ratings of own engagement in the haptic content of the movie (correlation r = 0.49; ratings collected after the MEG session). The results, obtained by using novel signal-analysis approaches, demonstrate that the functional state of the human sensorimotor cortex fluctuates in a fine-grained manner even during passive observation of temporally varying haptic events. Hum Brain Mapp 37:4061-4068, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

A practical guide to environmental association analysis in landscape genomics.

PubMed

Rellstab, Christian; Gugerli, Felix; Eckert, Andrew J; Hancock, Angela M; Holderegger, Rolf

2015-09-01

Landscape genomics is an emerging research field that aims to identify the environmental factors that shape adaptive genetic variation and the gene variants that drive local adaptation. Its development has been facilitated by next-generation sequencing, which allows for screening thousands to millions of single nucleotide polymorphisms in many individuals and populations at reasonable costs. In parallel, data sets describing environmental factors have greatly improved and increasingly become publicly accessible. Accordingly, numerous analytical methods for environmental association studies have been developed. Environmental association analysis identifies genetic variants associated with particular environmental factors and has the potential to uncover adaptive patterns that are not discovered by traditional tests for the detection of outlier loci based on population genetic differentiation. We review methods for conducting environmental association analysis including categorical tests, logistic regressions, matrix correlations, general linear models and mixed effects models. We discuss the advantages and disadvantages of different approaches, provide a list of dedicated software packages and their specific properties, and stress the importance of incorporating neutral genetic structure in the analysis. We also touch on additional important aspects such as sampling design, environmental data preparation, pooled and reduced-representation sequencing, candidate-gene approaches, linearity of allele-environment associations and the combination of environmental association analyses with traditional outlier detection tests. We conclude by summarizing expected future directions in the field, such as the extension of statistical approaches, environmental association analysis for ecological gene annotation, and the need for replication and post hoc validation studies. © 2015 John Wiley & Sons Ltd.

Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data

PubMed Central

Bryan, Kenneth; Cunningham, Pádraig

2008-01-01

Background Microarrays have the capacity to measure the expressions of thousands of genes in parallel over many experimental samples. The unsupervised classification technique of bicluster analysis has been employed previously to uncover gene expression correlations over subsets of samples with the aim of providing a more accurate model of the natural gene functional classes. This approach also has the potential to aid functional annotation of unclassified open reading frames (ORFs). Until now this aspect of biclustering has been under-explored. In this work we illustrate how bicluster analysis may be extended into a 'semi-supervised' ORF annotation approach referred to as BALBOA. Results The efficacy of the BALBOA ORF classification technique is first assessed via cross validation and compared to a multi-class k-Nearest Neighbour (kNN) benchmark across three independent gene expression datasets. BALBOA is then used to assign putative functional annotations to unclassified yeast ORFs. These predictions are evaluated using existing experimental and protein sequence information. Lastly, we employ a related semi-supervised method to predict the presence of novel functional modules within yeast. Conclusion In this paper we demonstrate how unsupervised classification methods, such as bicluster analysis, may be extended using of available annotations to form semi-supervised approaches within the gene expression analysis domain. We show that such methods have the potential to improve upon supervised approaches and shed new light on the functions of unclassified ORFs and their co-regulation. PMID:18831786

Reaching ABE Students: Lessons from the Iowa Studies.

ERIC Educational Resources Information Center

Beder, Hal

1990-01-01

An Iowa survey of 351 adult basic education participants uncovered 10 motivations for participation, which were used to develop a cluster-analysis market segmentation. Another Iowa study found 4 basic causes for nonparticipation: low perception of need, perceived difficulty, dislike of school, and situational barriers. (SK)

Transitional Patterns of Adolescent Females in Non-Traditional Career Paths.

ERIC Educational Resources Information Center

Ciccocioppo, Anna-Lisa; Stewin, Leonard L.; Madill, Helen M.; Montgomerie, T. Craig; Tovell, Dorothy R.; Armour, Margaret-Ann; Fitzsimmons, George W.

2002-01-01

Examines the factors that affected the career decision-making of adolescent females and young women in undergraduate science, engineering, and technology programs. Qualitative analysis was used to uncover seven themes: transition from high school, educational influences, family influences, academic issues, coursework management, gender issues, and…

Use of chemoinformatics tools- nuts and bolts; Challenges in their regulatory application

EPA Science Inventory

Cheminformatics spans a continuum of components from data storage to uncovering new insights that are useful for different decision making contexts. It covers the input, retrieval of data, the manipulation and integration of data through to the visualisation and analysis to trans...

Proteomic analysis of propiconazole responses in mouse liver: comparison of genomic and proteomic profiles

EPA Science Inventory

We have performed for the first time a comprehensive profiling of changes in protein expression of soluble proteins in livers from mice treated with the mouse liver tumorigen, propiconazole, to uncover the pathways and networks altered by this fungicide. Utilizing twodimensional...

The Surprising Persistence of Biglan's Classification Scheme

ERIC Educational Resources Information Center

Simpson, Adrian

2017-01-01

Within higher education systems, different institutions deliver different patterns of disciplines. A simple analysis of the structure of that pattern of disciplines across institutions in one higher education system uncovers a surprising relationship. That is, the key dimensions which describe that structure align nearly perfectly with dimensions…

Hippocampal α-Synuclein in Dementia with Lewy Bodies Contributes to Memory Impairment and Is Consistent with Spread of Pathology

PubMed Central

Roy, Subhojit; Galasko, Douglas R.; Hansen, Lawrence A.; Masliah, Eliezer

2017-01-01

Despite considerable research to uncover them, the anatomic and neuropathologic correlates of memory impairment in dementia with Lewy bodies (DLB) remain unclear. While some studies have implicated Lewy bodies in the neocortex, others have pointed to α-synuclein pathology in the hippocampus. We systematically examined hippocampal Lewy pathology and its distribution in hippocampal subfields in 95 clinically and neuropathologically characterized human cases of DLB, finding that α-synuclein pathology was highest in two hippocampal-related subregions: the CA2 subfield and the entorhinal cortex (EC). While the EC had numerous classic somatic Lewy bodies, CA2 contained mainly Lewy neurites in presumed axon terminals, suggesting the involvement of the EC → CA2 circuitry in the pathogenesis of DLB symptoms. Clinicopathological correlations with measures of verbal and visual memory supported a role for EC Lewy pathology, but not CA2, in causing these memory deficits. Lewy pathology in CA1—the main output region for CA2—correlated best with results from memory testing despite a milder pathology. This result indicates that CA1 may be more functionally relevant than CA2 in the context of memory impairment in DLB. These correlations remained significant after controlling for several factors, including concurrent Alzheimer's pathology (neuritic plaques and neurofibrillary tangles) and the interval between time of testing and time of death. Our data suggest that although hippocampal Lewy pathology in DLB is predominant in CA2 and EC, memory performance correlates most strongly with CA1 burden. SIGNIFICANCE STATEMENT This study provides a detailed neuropathologic analysis of hippocampal Lewy pathology in human patients with autopsy-confirmed dementia with Lewy bodies. The approach—informed by regional molecular markers, concurrent Alzheimer's pathology analysis, and relevant clinical data—helps tease out the relative contribution of Lewy pathology to memory dysfunction in the disease. Levels of Lewy pathology were found to be highest in the hippocampal CA2 subregion and entorhinal cortex, implicating a potentially overlooked circuit in disease pathogenesis. However, correlation with memory performance was strongest with CA1. This unexpected finding suggests that Lewy pathology must reach a critical burden across hippocampal circuitry to contribute to memory dysfunction beyond that related to other factors, notably coexisting Alzheimer's disease tau pathology. PMID:28039370

State-plane analysis of parallel resonant converter

NASA Technical Reports Server (NTRS)

Oruganti, R.; Lee, F. C.

1985-01-01

A method for analyzing the complex operation of a parallel resonant converter is developed, utilizing graphical state-plane techniques. The comprehensive mode analysis uncovers, for the first time, the presence of other complex modes besides the continuous conduction mode and the discontinuous conduction mode and determines their theoretical boundaries. Based on the insight gained from the analysis, a novel, high-frequency resonant buck converter is proposed. The voltage conversion ratio of the new converter is almost independent of load.

Uncovering underlying processes of semantic priming by correlating item-level effects.

PubMed

Heyman, Tom; Hutchison, Keith A; Storms, Gert

2016-04-01

The current study examines the underlying processes of semantic priming using the largest priming database available (i.e., Semantic Priming Project, Hutchison et al. Behavior Research Methods, 45(4), 1099-1114, 2013). Specifically, it compares priming effects in two tasks: lexical decision and pronunciation. Task similarities were assessed at two different stimulus onset asynchronies (SOAs) (i.e., 200 and 1,200 ms) and for both primary and other associates. To evaluate how consistent priming is across these two tasks, item-level priming effects obtained in each task were correlated for each condition separately. The results revealed significant correlations at the short SOA for both primary and other associates. The correlations at the long SOA were significantly smaller and only reached significance when z-transformed response times were used. Furthermore, this pattern remained essentially the same when only asymmetric forward associates (e.g., panda-bear) were considered, suggesting that the cross-task stability at the short SOA was not merely caused by retrospective processes such as semantic matching. Instead, these findings provide evidence for a rapidly operating, item-based, relational characteristic such as spreading activation.

Correlation between diffuse interstellar bands (DIBs) and interstellar extinction using data from Bosscha Compact Spectrograph

NASA Astrophysics Data System (ADS)

Puspitarini, L.; Malasan, H. L.; Aprilia; Arifyanto, M. I.; Lallement, R.; Irfan, M.; Puspitaningrum, E.

2018-04-01

A longstanding challenge in astronomical spectroscopy is to uncover the carriers of diffuse interstellar bands (DIBs). They are broad absorption features due to the interstellar matter (ISM). They are seen in stellar spectra of background stars or other astronomical objects. Although we do not know utterly the carriers of the DIBs, they can be a promising tracer of the ISM. One of the interesting properties is their correlations with the interstellar (IS) extinction. For each band, the correlation has considerable dispersion and differences that possibly due to the IS physical conditions. Some DIBs are sensitive to the stellar radiation field, and some are not. To study the effect, we measured the DIB observed in Be/B stars spectra. The stars were observed by using Bosscha Compact Spectrograph at the Bosscha Observatory, Lembang, Indonesia. We performed an automated fitting of a combination of a smooth stellar continuum, the DIB profile, and a synthetic telluric transmission to the spectrum. The DIB measurements were compared to the general DIBs-extinction relationship. The correlation is found to be in good agreement with previous determinations.

Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

PubMed

Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

2016-04-01

To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes.

Cost Per Additional Responder Associated With Ixekizumab and Etanercept in the Treatment of Moderate-to-Severe Psoriasis.

PubMed

Feldman, Steven R; Foster, Shonda A; Zhu, Baojin; Burge, Russel; Al Sawah, Sarah; Goldblum, Orin M

2017-12-01

BACKGROUND: Newer psoriasis treatments can achieve greater levels of efficacy than older systemic therapies; however, current psoriasis costs are substantial. We sought to estimate costs per additional responder associated with ixekizumab and etanercept, versus placebo, using efficacy data from phase 3 clinical trials (UNCOVER-2 and UNCOVER-3). METHODS: In UNCOVER-2/UNCOVER-3, patients received subcutaneous placebo, etanercept 50 mg twice weekly (BIW), or ixekizumab one 80 mg injection every 2 weeks (Q2W) after a 160-mg starting dose. Twelve-week induction-phase Psoriasis Area and Severity Index (PASI) 75, PASI 90, and PASI 100 response rates for ixekizumab, etanercept, and placebo were obtained from pooled data from the overall and United States (US) subgroup intention-to-treat (ITT) populations, and used to calculate numbers needed to treat (NNTs) to achieve one additional PASI 75, PASI 90, or PASI 100 response for ixekizumab Q2W and etanercept BIW versus placebo. Twelve-week drug costs per patient were calculated based on the UNCOVER-2/UNCOVER-3 dosing schedule and wholesale acquisition costs. Mean costs per additional responder for PASI 75, PASI 90, and PASI 100 for each treatment versus placebo were calculated for pooled UN-COVER-2/UNCOVER-3 overall and US subgroup ITT populations. RESULTS: Pooled overall ITT population: costs per additional PASI 75, PASI 90, or PASI 100 responder were US $37,540, US $46,299, or US $80,710 for ixekizumab Q2W and US $57,533, US $120,720, or US $404,695 for etanercept BIW, respectively. US subgroup ITT population: costs per additional PASI 75, PASI 90, or PASI 100 responder were US $38,165, US $49,740, or US $93,536 for ixekizumab Q2W and US $69,580, US $140,881, or US $631,875 for etanercept BIW, respectively. CONCLUSIONS: Twelve-week costs per additional responder were lower for ixekizumab Q2W than for etanercept BIW across all levels of clearance (PASI 75, PASI 90, and PASI 100) in the pooled UNCOVER-2/UNCOVER-3 overall and US subgroup ITT populations.

Association analysis for loci regulating grain quality traits and marker development in the USDA rice collection

USDA-ARS?s Scientific Manuscript database

Uncovering underlying genetics associated with grain quality is important to world food security. Rice is consumed as a whole grain, therefore cooked rice texture, stickiness, chewiness, grain dimensions and grain appearance can affect palatability and marketability. Amylose and protein content play...

Robust Detection of Examinees with Aberrant Answer Changes

ERIC Educational Resources Information Center

Belov, Dmitry I.

2015-01-01

The statistical analysis of answer changes (ACs) has uncovered multiple testing irregularities on large-scale assessments and is now routinely performed at testing organizations. However, AC data has an uncertainty caused by technological or human factors. Therefore, existing statistics (e.g., number of wrong-to-right ACs) used to detect examinees…

Uncovering trends in gene naming

PubMed Central

Seringhaus, Michael R; Cayting, Philip D; Gerstein, Mark B

2008-01-01

We take stock of current genetic nomenclature and attempt to organize strange and notable gene names. We categorize, for instance, those that involve a naming system transferred from another context (for example, Pavlov’s dogs). We hope this analysis provides clues to better steer gene naming in the future. PMID:18254929

A Study of Early Childhood Teachers' Conceptions of Creativity in Hong Kong

ERIC Educational Resources Information Center

Cheung, Rebecca Hun Ping; Mok, Magdalena Mo Ching

2013-01-01

The study aimed to uncover the conceptions of creativity among early childhood teachers in Hong Kong. The sample comprised 563 early childhood teachers. Factor analysis supported the multidimensional hypothesis of teachers' conceptions of creativity. Five dimensions were found: novelty, product, problem solving, cognitive processes and personal…

Empirical Identification of the Major Facets of Conscientiousness

ERIC Educational Resources Information Center

MacCann, Carolyn; Duckworth, Angela Lee; Roberts, Richard D.

2009-01-01

Conscientiousness is often found to predict academic outcomes, but is defined differently by different models of personality. High school students (N = 291) completed a large number of Conscientiousness items from different models and the Big Five Inventory (BFI). Exploratory and confirmatory factor analysis of the items uncovered eight facets:…

Dimensions of Social Capital among High School Mathematics Teachers

ERIC Educational Resources Information Center

Koebley, Sarah Cotton

2013-01-01

This study sought to uncover teacher perceptions of social capital within a high school mathematics department utilizing a research design that acknowledged the complex environment faced by high school teachers and their subsequent interpretations of how and from whom they sought access to professional resources. Through an analysis of narratives…

Proteomic Analysis of Propiconazole Responses in Mouse Liver-Comparison of Genomic and Proteomic Profiles

EPA Science Inventory

We have performed for the first time a comprehensive profiling of changes in protein expression of soluble proteins in livers from mice treated with the mouse liver tumorigen, propiconazole, to uncover the pathways and networks altered by this commonly used fungicide. Utilizing t...

Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

USDA-ARS?s Scientific Manuscript database

Decades of intensive tomato breeding using wild germplasm has resulted in genomes of domesticated accessions (Solanum lycopersicum) to be intertwined with introgressions from their wild relatives. Here we present the first whole genome sequences of two tomato inbreds Gh13 and BTI87, both carrying a ...

Mapping the Field of Educational Administration Research: A Journal Citation Network Analysis

ERIC Educational Resources Information Center

Wang, Yinying; Bowers, Alex J.

2016-01-01

Purpose: The purpose of this paper is to uncover how knowledge is exchanged and disseminated in the educational administration research literature through the journal citation network. Design/ Methodology/Approach: Drawing upon social network theory and citation network studies in other disciplines, the authors constructed an educational…

Uncovering Portuguese Teachers' Difficulties in Implementing Sciences Curriculum

ERIC Educational Resources Information Center

Vasconcelos, Clara; Torres, Joana; Moutinho, Sara; Martins, Idalina; Costa, Nilza

2015-01-01

Many countries recognize the positive and effective results of improving science education through the introduction of reforms in the sciences curriculum. However, some important issues are generally neglected like, for example, the involvement of the teachers in the reform process. Taking the sciences curriculum reform under analysis and…

Chaos and insect ecology

Treesearch

Jesse A. Logan; Fred P. Hain

1990-01-01

Recent advances in applied mathematical analysis have uncovered a fascinating and unexpected dynamical richness that underlies behavior of even the simplest non-linear mathematical models. Due to the complexity of solutions to these non-linear equations, a new mathematical term, chaos, has been coined to describe the resulting dynamics. This term captures the notion...

The Complexity of One-Step Equations

ERIC Educational Resources Information Center

Ngu, Bing

2014-01-01

An analysis of one-step equations from a cognitive load theory perspective uncovers variation within one-step equations. The complexity of one-step equations arises from the element interactivity across the operational and relational lines. The higher the number of operational and relational lines, the greater the complexity of the equations.…

Managing Student Affairs Programs: Methods, Models, Muddles.

ERIC Educational Resources Information Center

Deegan, William L.

Management processes and problems are examined in a variety of student affairs contexts. This book (1) proposes a theoretical framework for the analysis of management functions in colleges and universities, (2) studies the practice of management in several different student affairs contexts to uncover current practices, issues, problems, and…

Preservice and Early Career Teachers' Preconceptions and Misconceptions about Making in Education

ERIC Educational Resources Information Center

Cohen, Jonathan D.; Jones, W. Monty; Smith, Shaunna

2018-01-01

This qualitative study examined preservice and early career teachers' preconceptions and misconceptions about making in education. Eighty-two preservice and early career teachers participated in brief, one-time maker workshops, then wrote reflections on their experiences. Using constant comparative analysis, researchers uncovered two common…

What Effects Do Social Movements Have on Curricular Reform?

ERIC Educational Resources Information Center

Apple, Michael W.

2003-01-01

A review of "Contentious Curricula: Afrocentrism and Creationism in American Public Schools," by Amy Binder, claims it is a valuable analysis that employs a social movement perspective to uncover the dynamics involved in proposals for and the politics of curriculum change, especially in highly contested curriculum areas. (Contains 13…

Uncovering the Hidden Dimensions of Meaning in Descriptions of Educational Practice.

ERIC Educational Resources Information Center

Harris, Ilene B.

Descriptions of educational practice offer an array of important, but typically hidden dimensions of meaning which provide potentially rich resources for understanding the practices. This paper illustrates: (1) how analysis, interpretations, and assessments interpenetrate what appear to be descriptions and suggest how readers can tease out these…

Emergence and temporal structure of Lead-Lag correlations in collective stock dynamics

NASA Astrophysics Data System (ADS)

Xia, Lisi; You, Daming; Jiang, Xin; Chen, Wei

2018-07-01

Understanding the correlations among stock returns is crucial for reducing the risk of investment in stock markets. As an important stylized correlation, lead-lag effect plays a major role in analyzing market volatility and deriving trading strategies. Here, we explore historical lead-lag relationships among stocks in the Chinese stock market. Strongly positive lagged correlations can be empirically observed. We demonstrate this lead-lag phenomenon is not constant but temporally emerges during certain periods. By introducing moving time window method, we transform the lead-lag dynamics into a series of asymmetric lagged correlation matrices. Dynamic lead-lag structures are uncovered in the form of temporal network structures. We find that the size of lead-lag group experienced a rapid drop during the year 2012, which signaled a re-balance of the stock market. On the daily timescale, we find the lead-lag structure exhibits several persistent patterns, which can be characterized by the Jaccard matrix. We show significant market events can be distinguished in the Jaccard matrix diagram. Taken together, we study an integration of all the temporal networks and identify several leading stock sectors, which are in accordance with the common Chinese economic fundamentals.

Childhood Temperament: Passive Gene-Environment Correlation, Gene-Environment Interaction, and the Hidden Importance of the Family Environment

PubMed Central

Lemery-Chalfant, Kathryn; Kao, Karen; Swann, Gregory; Goldsmith, H. Hill

2013-01-01

Biological parents pass on genotypes to their children, as well as provide home environments that correlate with their genotypes; thus, the association between the home environment and children's temperament can be genetically (i.e. passive gene-environment correlation) or environmentally mediated. Furthermore, family environments may suppress or facilitate the heritability of children's temperament (i.e. gene-environment interaction). The sample comprised 807 twin pairs (M age = 7.93 years) from the longitudinal Wisconsin Twin Project. Important passive gene-environment correlations emerged, such that home environments were less chaotic for children with high Effortful Control, and this association was genetically mediated. Children with high Extraversion/Surgency experienced more chaotic home environments, and this correlation was also genetically mediated. In addition, heritability of children's temperament was moderated by home environments, such that Effortful Control and Extraversion/Surgency were more heritable in chaotic homes, and Negative Affectivity was more heritable under crowded or unsafe home conditions. Modeling multiple types of gene-environment interplay uncovered the complex role of genetic factors and the hidden importance of the family environment for children's temperament and development more generally. PMID:23398752

Self-amplified photo-induced gap quenching in a correlated electron material

DOE PAGES

Mathias, S.; Eich, S.; Urbancic, J.; ...

2016-10-04

Capturing the dynamic electronic band structure of a correlated material presents a powerful capability for uncovering the complex couplings between the electronic and structural degrees of freedom. When combined with ultrafast laser excitation, new phases of matter can result, since far-from-equilibrium excited states are instantaneously populated. Here, we elucidate a general relation between ultrafast non-equilibrium electron dynamics and the size of the characteristic energy gap in a correlated electron material. Here, we show that carrier multiplication via impact ionization can be one of the most important processes in a gapped material, and that the speed of carrier multiplication critically dependsmore » on the size of the energy gap. In the case of the charge-density wave material 1T-TiSe 2, our data indicate that carrier multiplication and gap dynamics mutually amplify each other, which explains—on a microscopic level—the extremely fast response of this material to ultrafast optical excitation.« less

Aberration hubs in protein interaction networks highlight actionable targets in cancer.

PubMed

Karimzadeh, Mehran; Jandaghi, Pouria; Papadakis, Andreas I; Trainor, Sebastian; Rung, Johan; Gonzàlez-Porta, Mar; Scelo, Ghislaine; Vasudev, Naveen S; Brazma, Alvis; Huang, Sidong; Banks, Rosamonde E; Lathrop, Mark; Najafabadi, Hamed S; Riazalhosseini, Yasser

2018-05-18

Despite efforts for extensive molecular characterization of cancer patients, such as the international cancer genome consortium (ICGC) and the cancer genome atlas (TCGA), the heterogeneous nature of cancer and our limited knowledge of the contextual function of proteins have complicated the identification of targetable genes. Here, we present Aberration Hub Analysis for Cancer (AbHAC) as a novel integrative approach to pinpoint aberration hubs, i.e. individual proteins that interact extensively with genes that show aberrant mutation or expression. Our analysis of the breast cancer data of the TCGA and the renal cancer data from the ICGC shows that aberration hubs are involved in relevant cancer pathways, including factors promoting cell cycle and DNA replication in basal-like breast tumors, and Src kinase and VEGF signaling in renal carcinoma. Moreover, our analysis uncovers novel functionally relevant and actionable targets, among which we have experimentally validated abnormal splicing of spleen tyrosine kinase as a key factor for cell proliferation in renal cancer. Thus, AbHAC provides an effective strategy to uncover novel disease factors that are only identifiable by examining mutational and expression data in the context of biological networks.

Automatic Image Processing Workflow for the Keck/NIRC2 Vortex Coronagraph

NASA Astrophysics Data System (ADS)

Xuan, Wenhao; Cook, Therese; Ngo, Henry; Zawol, Zoe; Ruane, Garreth; Mawet, Dimitri

2018-01-01

The Keck/NIRC2 camera, equipped with the vortex coronagraph, is an instrument targeted at the high contrast imaging of extrasolar planets. To uncover a faint planet signal from the overwhelming starlight, we utilize the Vortex Image Processing (VIP) library, which carries out principal component analysis to model and remove the stellar point spread function. To bridge the gap between data acquisition and data reduction, we implement a workflow that 1) downloads, sorts, and processes data with VIP, 2) stores the analysis products into a database, and 3) displays the reduced images, contrast curves, and auxiliary information on a web interface. Both angular differential imaging and reference star differential imaging are implemented in the analysis module. A real-time version of the workflow runs during observations, allowing observers to make educated decisions about time distribution on different targets, hence optimizing science yield. The post-night version performs a standardized reduction after the observation, building up a valuable database that not only helps uncover new discoveries, but also enables a statistical study of the instrument itself. We present the workflow, and an examination of the contrast performance of the NIRC2 vortex with respect to factors including target star properties and observing conditions.

Comprehensive analysis of mouse retinal mononuclear phagocytes.

PubMed

Lückoff, Anika; Scholz, Rebecca; Sennlaub, Florian; Xu, Heping; Langmann, Thomas

2017-06-01

The innate immune system is activated in a number of degenerative and inflammatory retinal disorders such as age-related macular degeneration (AMD). Retinal microglia, choroidal macrophages, and recruited monocytes, collectively termed 'retinal mononuclear phagocytes', are critical determinants of ocular disease outcome. Many publications have described the presence of these cells in mouse models for retinal disease; however, only limited aspects of their behavior have been uncovered, and these have only been uncovered using a single detection method. The workflow presented here describes a comprehensive analysis strategy that allows characterization of retinal mononuclear phagocytes in vivo and in situ. We present standardized working steps for scanning laser ophthalmoscopy of microglia from MacGreen reporter mice (mice expressing the macrophage colony-stimulating factor receptor GFP transgene throughout the mononuclear phagocyte system), quantitative analysis of Iba1-stained retinal sections and flat mounts, CD11b-based retinal flow cytometry, and qRT-PCR analysis of key microglia markers. The protocol can be completed within 3 d, and we present data from retinas treated with laser-induced choroidal neovascularization (CNV), bright white-light exposure, and Fam161a-associated inherited retinal degeneration. The assays can be applied to any of the existing mouse models for retinal disorders and may be valuable for documenting immune responses in studies for immunomodulatory therapies.

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

PubMed Central

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-01-01

Within the framework of ‘Network Physiology’, we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain–heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain–heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems. PMID:27044991

nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary.

PubMed

Lisa, Jessica A; Jayakumar, Amal; Ward, Bess B; Song, Bongkeun

2017-12-01

Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 8%-29% of the abundant NRE archetypes. Archetypes found in a particular site, 'specialists', were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe 2+ . A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H 2 S respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among nirS-type denitrifying communities and supports the essential role of individual community members in overall ecosystem function. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Transient and permanent changes in DNA methylation patterns in inorganic arsenic-mediated epithelial-to-mesenchymal transition

PubMed Central

Eckstein, Meredith; Rea, Matthew; Fondufe-Mittendorf, Yvonne N.

2017-01-01

Chronic low dose inorganic arsenic exposure causes cells to take on an epithelial-to-mesenchymal phenotype, which is a crucial process in carcinogenesis. Inorganic arsenic is not a mutagen and thus epigenetic alterations have been implicated in this process. Indeed, during the epithelial-to-mesenchymal transition, morphologic changes to cells correlate with changes in chromatin structure and gene expression, ultimately driving this process. However, studies on the effects of inorganic arsenic exposure/withdrawal on the epithelial-to-mesenchymal transition and the impact of epigenetic alterations in this process are limited. In this study we used high-resolution microarray analysis to measure the changes in DNA methylation in cells undergoing inorganic arsenic-induced epithelial-to-mesenchymal transition, and on the reversal of this process, after removal of the inorganic arsenic exposure. We found that cells exposed to chronic, low-dose inorganic arsenic exposure showed 30,530 sites were differentially methylated, and with inorganic arsenic withdrawal several differential methylated sites were reversed, albeit not completely. Furthermore, these changes in DNA methylation mainly correlated with changes in gene expression at most sites tested but not at all. This study suggests that DNA methylation changes on gene expression are not clear-cut and provide a platform to begin to uncover the relationship between DNA methylation and gene expression, specifically within the context of inorganic arsenic treatment. PMID:28336213

Genome-wide DNA Methylation Profiles and Their Relationships with mRNA and the microRNA Transcriptome in Bovine Muscle Tissue (Bos taurine)

PubMed Central

Huang, Yong-Zhen; Sun, Jia-Jie; Zhang, Liang-Zhi; Li, Cong-Jun; Womack, James E.; Li, Zhuan-Jian; Lan, Xian-Yong; Lei, Chu-Zhao; Zhang, Chun-Lei; Zhao, Xin; Chen, Hong

2014-01-01

DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampled longissimus dorsi muscle (LDM) from a well-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development. PMID:25306978

Non-random occurrence of Robertsonian translocations in the house mouse (Mus musculus domesticus): is it related to quantitative variation in the minor satellite?

PubMed

Cazaux, Benoîte; Catalan, Josette; Claude, Julien; Britton-Davidian, Janice

2014-01-01

The house mouse, Mus musculus domesticus, shows extraordinary chromosomal diversity driven by fixation of Robertsonian (Rb) translocations. The high frequency of this rearrangement, which involves the centromeric regions, has been ascribed to the architecture of the satellite sequence (high quantity and homogeneity). This promotes centromere-related translocations through unequal recombination and gene conversion. A characteristic feature of Rb variation in this subspecies is the non-random contribution of different chromosomes to the translocation frequency, which, in turn, depends on the chromosome size. Here, the association between satellite quantity and Rb frequency was tested by PRINS of the minor satellite which is the sequence involved in the translocation breakpoints. Five chromosomes with different translocation frequencies were selected and analyzed among wild house mice from 8 European localities. Using a relative quantitative measurement per chromosome, the analysis detected a large variability in signal size most of which was observed between individuals and/or localities. The chromosomes differed significantly in the quantity of the minor satellite, but these differences were not correlated with their translocation frequency. However, the data uncovered a marginally significant correlation between the quantity of the minor satellite and chromosome size. The implications of these results on the evolution of the chromosomal architecture in the house mouse are discussed. © 2014 S. Karger AG, Basel.

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

NASA Astrophysics Data System (ADS)

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-05-01

Within the framework of `Network Physiology', we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain-heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain-heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems.

Information-dependent enrichment analysis reveals time-dependent transcriptional regulation of the estrogen pathway of toxicity.

PubMed

Pendse, Salil N; Maertens, Alexandra; Rosenberg, Michael; Roy, Dipanwita; Fasani, Rick A; Vantangoli, Marguerite M; Madnick, Samantha J; Boekelheide, Kim; Fornace, Albert J; Odwin, Shelly-Ann; Yager, James D; Hartung, Thomas; Andersen, Melvin E; McMullen, Patrick D

2017-04-01

The twenty-first century vision for toxicology involves a transition away from high-dose animal studies to in vitro and computational models (NRC in Toxicity testing in the 21st century: a vision and a strategy, The National Academies Press, Washington, DC, 2007). This transition requires mapping pathways of toxicity by understanding how in vitro systems respond to chemical perturbation. Uncovering transcription factors/signaling networks responsible for gene expression patterns is essential for defining pathways of toxicity, and ultimately, for determining the chemical modes of action through which a toxicant acts. Traditionally, transcription factor identification is achieved via chromatin immunoprecipitation studies and summarized by calculating which transcription factors are statistically associated with up- and downregulated genes. These lists are commonly determined via statistical or fold-change cutoffs, a procedure that is sensitive to statistical power and may not be as useful for determining transcription factor associations. To move away from an arbitrary statistical or fold-change-based cutoff, we developed, in the context of the Mapping the Human Toxome project, an enrichment paradigm called information-dependent enrichment analysis (IDEA) to guide identification of the transcription factor network. We used a test case of activation in MCF-7 cells by 17β estradiol (E2). Using this new approach, we established a time course for transcriptional and functional responses to E2. ERα and ERβ were associated with short-term transcriptional changes in response to E2. Sustained exposure led to recruitment of additional transcription factors and alteration of cell cycle machinery. TFAP2C and SOX2 were the transcription factors most highly correlated with dose. E2F7, E2F1, and Foxm1, which are involved in cell proliferation, were enriched only at 24 h. IDEA should be useful for identifying candidate pathways of toxicity. IDEA outperforms gene set enrichment analysis (GSEA) and provides similar results to weighted gene correlation network analysis, a platform that helps to identify genes not annotated to pathways.

Test-retest and between-site reliability in a multicenter fMRI study.

PubMed

Friedman, Lee; Stern, Hal; Brown, Gregory G; Mathalon, Daniel H; Turner, Jessica; Glover, Gary H; Gollub, Randy L; Lauriello, John; Lim, Kelvin O; Cannon, Tyrone; Greve, Douglas N; Bockholt, Henry Jeremy; Belger, Aysenil; Mueller, Bryon; Doty, Michael J; He, Jianchun; Wells, William; Smyth, Padhraic; Pieper, Steve; Kim, Seyoung; Kubicki, Marek; Vangel, Mark; Potkin, Steven G

2008-08-01

In the present report, estimates of test-retest and between-site reliability of fMRI assessments were produced in the context of a multicenter fMRI reliability study (FBIRN Phase 1, www.nbirn.net). Five subjects were scanned on 10 MRI scanners on two occasions. The fMRI task was a simple block design sensorimotor task. The impulse response functions to the stimulation block were derived using an FIR-deconvolution analysis with FMRISTAT. Six functionally-derived ROIs covering the visual, auditory and motor cortices, created from a prior analysis, were used. Two dependent variables were compared: percent signal change and contrast-to-noise-ratio. Reliability was assessed with intraclass correlation coefficients derived from a variance components analysis. Test-retest reliability was high, but initially, between-site reliability was low, indicating a strong contribution from site and site-by-subject variance. However, a number of factors that can markedly improve between-site reliability were uncovered, including increasing the size of the ROIs, adjusting for smoothness differences, and inclusion of additional runs. By employing multiple steps, between-site reliability for 3T scanners was increased by 123%. Dropping one site at a time and assessing reliability can be a useful method of assessing the sensitivity of the results to particular sites. These findings should provide guidance toothers on the best practices for future multicenter studies.

Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds.

PubMed

Zhang, Liangzhi; Jia, Shangang; Plath, Martin; Huang, Yongzhen; Li, Congjun; Lei, Chuzhao; Zhao, Xin; Chen, Hong

2015-08-10

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

An Analysis of Earth Science Data Analytics Use Cases

NASA Technical Reports Server (NTRS)

Shie, Chung-Lin; Kempler, Steve

2014-01-01

The increase in the number and volume, and sources, of globally available Earth science data measurements and datasets have afforded Earth scientists and applications researchers unprecedented opportunities to study our Earth in ever more sophisticated ways. In fact, the NASA Earth Observing System Data Information System (EOSDIS) archives have doubled from 2007 to 2014, to 9.1 PB (Ramapriyan, 2009; and https:earthdata.nasa.govaboutsystem-- performance). In addition, other US agency, international programs, field experiments, ground stations, and citizen scientists provide a plethora of additional sources for studying Earth. Co--analyzing huge amounts of heterogeneous data to glean out unobvious information is a daunting task. Earth science data analytics (ESDA) is the process of examining large amounts of data of a variety of types to uncover hidden patterns, unknown correlations and other useful information. It can include Data Preparation, Data Reduction, and Data Analysis. Through work associated with the Earth Science Information Partners (ESIP) Federation, a collection of Earth science data analytics use cases have been collected and analyzed for the purpose of extracting the types of Earth science data analytics employed, and requirements for data analytics tools and techniques yet to be implemented, based on use case needs. ESIP generated use case template, ESDA use cases, use case types, and preliminary use case analysis (this is a work in progress) will be presented.

Exploring anti-correlated radio/X-ray modes in transitional millisecond pulsars

NASA Astrophysics Data System (ADS)

Jaodand, Amruta

2017-09-01

Recently, using coordinated VLA+Chandra observations, Bogdanov et al.(2017) have uncovered a stunning anti-correlation in the LMXB state of the tMSP PSR J1023+0038. They see that radio luminosity consistently peaks during the X-ray `low' luminosity modes. Also, we have found a promising candidate tMSP, 3FGL J1544-1125(J1544) (Bogdanov and Halpern 2015; currently only tMSP candidate apart from J1023 in a persistent LMXB state). Using VLA and simultaneous Swift observations we see that it lies on the proposed tMSP track in radio vs. X-ray luminosity (L_ R/L_X) diagram. This finding strengthens its classification as a tMSP and provides an excellent opportunity to a)determine universality of radio/X-ray brightness anti-correlatio and b)understand jet/outflow formation in tMSPs.

Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation.

PubMed

El-Sharkawy, Islam; Liang, Dong; Xu, Kenong

2015-12-01

Using RNA-seq, this study analysed an apple (Malus×domestica) anthocyanin-deficient yellow-skin somatic mutant 'Blondee' (BLO) and its red-skin parent 'Kidd's D-8' (KID), the original name of 'Gala', to understand the molecular mechanisms underlying the mutation. A total of 3299 differentially expressed genes (DEGs) were identified between BLO and KID at four developmental stages and/or between two adjacent stages within BLO and/or KID. A weighted gene co-expression network analysis (WGCNA) of the DEGs uncovered a network module of 34 genes highly correlated (r=0.95, P=9.0×10(-13)) with anthocyanin contents. Although 12 of the 34 genes in the WGCNA module were characterized and known of roles in anthocyanin, the remainder 22 appear to be novel. Examining the expression of ten representative genes in the module in 14 diverse apples revealed that at least eight were significantly correlated with anthocyanin variation. MdMYB10 (MDP0000259614) and MdGST (MDP0000252292) were among the most suppressed module member genes in BLO despite being undistinguishable in their corresponding sequences between BLO and KID. Methylation assay of MdMYB10 and MdGST in fruit skin revealed that two regions (MR3 and MR7) in the MdMYB10 promoter exhibited remarkable differences between BLO and KID. In particular, methylation was high and progressively increased alongside fruit development in BLO while was correspondingly low and constant in KID. The methylation levels in both MR3 and MR7 were negatively correlated with anthocyanin content as well as the expression of MdMYB10 and MdGST. Clearly, the collective repression of the 34 genes explains the loss-of-colour in BLO while the methylation in MdMYB10 promoter is likely causal for the mutation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation

PubMed Central

El-Sharkawy, Islam; Liang, Dong; Xu, Kenong

2015-01-01

Using RNA-seq, this study analysed an apple (Malus×domestica) anthocyanin-deficient yellow-skin somatic mutant ‘Blondee’ (BLO) and its red-skin parent ‘Kidd’s D-8’ (KID), the original name of ‘Gala’, to understand the molecular mechanisms underlying the mutation. A total of 3299 differentially expressed genes (DEGs) were identified between BLO and KID at four developmental stages and/or between two adjacent stages within BLO and/or KID. A weighted gene co-expression network analysis (WGCNA) of the DEGs uncovered a network module of 34 genes highly correlated (r=0.95, P=9.0×10–13) with anthocyanin contents. Although 12 of the 34 genes in the WGCNA module were characterized and known of roles in anthocyanin, the remainder 22 appear to be novel. Examining the expression of ten representative genes in the module in 14 diverse apples revealed that at least eight were significantly correlated with anthocyanin variation. MdMYB10 (MDP0000259614) and MdGST (MDP0000252292) were among the most suppressed module member genes in BLO despite being undistinguishable in their corresponding sequences between BLO and KID. Methylation assay of MdMYB10 and MdGST in fruit skin revealed that two regions (MR3 and MR7) in the MdMYB10 promoter exhibited remarkable differences between BLO and KID. In particular, methylation was high and progressively increased alongside fruit development in BLO while was correspondingly low and constant in KID. The methylation levels in both MR3 and MR7 were negatively correlated with anthocyanin content as well as the expression of MdMYB10 and MdGST. Clearly, the collective repression of the 34 genes explains the loss-of-colour in BLO while the methylation in MdMYB10 promoter is likely causal for the mutation. PMID:26417021

Single-Cell Analysis Uncovers Extensive Biological Noise in Poliovirus Replication

PubMed Central

Schulte, Michael B.

2014-01-01

ABSTRACT Viral infections often begin with a very small number of initiating particles. Accordingly, the outcome of an infection is likely to be affected by variability in the initial molecular interactions between virus and host. In this study, we investigated the range of outcomes upon infection of single cells. We isolated individual cells infected with poliovirus at low or high multiplicities of infection (MOI) and measured viral genomic replication and infectious viral progeny in each cell. We first determined that at 7 h postinfection, the ratio of positive to negative strands in individual cells varies from 5:1 to more than 190:1, with and average of 20:1, suggesting a significant variability in RNA synthesis. We further found that while virus genome production is higher in cells infected at a high multiplicity, the production of infectious particles is largely independent of the number of viruses infecting each cell. Strikingly, by correlating RNA and particle production within individual infections, we uncovered a significant contribution of stochastic noise to the outcome of infection. At low MOI, stochastic influences appear as kinetic effects which are most critical at the initial steps in infection. At high MOI, stochastic influences appear to dictate the virus's ability to harness cellular resources. We conclude that biological noise is a critical determinant of the overall productivity of viral infections. The distinct nature of stochasticity in the outcome of infection by low and high numbers of viral particles may have important implications for our understanding of the determinants of successful viral infections. IMPORTANCE By correlating genome and particle production in single-cell infections, we elucidated sources of noise in viral infections. When a cell was infected by only a single infectious particle, variation in the kinetics of the initial steps of replication contributed significantly to the overall productivity of the infection. Additionally, variation in the distribution of subcellular resources impacted infections initiated by one or many infectious particles. We also observed that when a cell was infected with multiple particles, more genomes were produced, while particle production was hindered by an apparent cellular resource limit. Understanding variations in viral infections may illuminate the dynamics of infection and pathogenesis and has implications for virus adaptation and evolution. PMID:24648454

Low-Resolution Radial-Velocity Monitoring of Pulsating sdBs in the Kepler Field

NASA Astrophysics Data System (ADS)

Telting, J.; Östensen, R.; Reed, M.; Kiæerad, F.; Farris, L.; Baran, A.; Oreiro, R.; O'Toole, S.

2014-04-01

We present preliminary results from an ongoing spectroscopic campaign to uncover the binary status of the 18 known pulsating subdwarf B stars and the one pulsating BHB star observed with the Kepler spacecraft. During the 2010-2012 observing seasons, we have used the KP4m Mayall, NOT, and WHT telescopes to obtain low-resolution (R˜2000-2500) Balmer-line spectroscopy of our sample stars. We applied a standard cross-correlation technique to derive radial velocities, and find clear evidence for binarity in several of the pulsators, some of which were not previously known to be binaries.

Local Variation of Hashtag Spike Trains and Popularity in Twitter

PubMed Central

Sanlı, Ceyda; Lambiotte, Renaud

2015-01-01

We draw a parallel between hashtag time series and neuron spike trains. In each case, the process presents complex dynamic patterns including temporal correlations, burstiness, and all other types of nonstationarity. We propose the adoption of the so-called local variation in order to uncover salient dynamical properties, while properly detrending for the time-dependent features of a signal. The methodology is tested on both real and randomized hashtag spike trains, and identifies that popular hashtags present regular and so less bursty behavior, suggesting its potential use for predicting online popularity in social media. PMID:26161650

Mapping the nanoscale energetic landscape in conductive polymer films with spatially super-resolved exciton dynamics

NASA Astrophysics Data System (ADS)

Ginsberg, Naomi

2015-03-01

The migration of Frenkel excitons, tightly-bound electron-hole pairs, in polymeric organic semiconducting films is critical to the efficiency of bulk heterojunction solar cells. While these materials exhibit a high degree of structural heterogeneity on the nanoscale, traditional measurements of exciton diffusion lengths are performed on bulk samples. Since both the characteristic length scales of structural heterogeneity and the reported bulk diffusion lengths are smaller than the optical diffraction limit, we adapt far-field super-resolution fluorescence imaging to uncover the correlations between the structural and energetic landscapes that the excitons explore.

The Nun Study and Alzheimer's disease: Quality of vocation as a potential protective factor?

PubMed

Keohane, Kieran; Balfe, Myles

2017-01-01

Data from the Nun Study, the most famous longitudinal epidemiology of Alzheimer's disease to date, are analyzed and reformulated in terms of Max Weber's discussion of the centrality of beruf - "calling" - fulfilling a life task in pursuit of a vocation. Qualitative differences in the Nuns' vocations are uncovered, which are correlated to their resilience to dementia. Extrapolating, we argue that Alzheimer's disease and the dementia reputed to it should be understood as a social pathology of contemporary civilization related to the loss of moral foundations from which coherent, meaningful life-projects can be conducted.

Transcriptome difference and potential crosstalk between liver and mammary tissue in mid-lactation primiparous dairy cows.

PubMed

Bu, Dengpan; Bionaz, Massimo; Wang, Mengzhi; Nan, Xuemei; Ma, Lu; Wang, Jiaqi

2017-01-01

Liver and mammary gland are among the most important organs during lactation in dairy cows. With the purpose of understanding both the different and the complementary roles and the crosstalk of those two organs during lactation, a transcriptome analysis was performed on liver and mammary tissues of 10 primiparous dairy cows in mid-lactation. The analysis was performed using a 4×44K Bovine Agilent microarray chip. The transcriptome difference between the two tissues was analyzed using SAS JMP Genomics using ANOVA with a false discovery rate correction (FDR). The analysis uncovered >9,000 genes differentially expressed (DEG) between the two tissues with a FDR<0.001. The functional analysis of the DEG uncovered a larger metabolic (especially related to lipid) and inflammatory response capacity in liver compared with mammary tissue while the mammary tissue had a larger protein synthesis and secretion, proliferation/differentiation, signaling, and innate immune system capacity compared with the liver. A plethora of endogenous compounds, cytokines, and transcription factors were estimated to control the DEG between the two tissues. Compared with mammary tissue, the liver transcriptome appeared to be under control of a large array of ligand-dependent nuclear receptors and, among endogenous chemical, fatty acids and bacteria-derived compounds. Compared with liver, the transcriptome of the mammary tissue was potentially under control of a large number of growth factors and miRNA. The in silico crosstalk analysis between the two tissues revealed an overall large communication with a reciprocal control of lipid metabolism, innate immune system adaptation, and proliferation/differentiation. In summary the transcriptome analysis confirmed prior known differences between liver and mammary tissue, especially considering the indication of a larger metabolic activity in liver compared with the mammary tissue and the larger protein synthesis, communication, and proliferative capacity in mammary tissue compared with the liver. Relatively novel is the indication by the data that the transcriptome of the liver is highly regulated by dietary and bacteria-related compounds while the mammary transcriptome is more under control of hormones, growth factors, and miRNA. A large crosstalk between the two tissues with a reciprocal control of metabolism and innate immune-adaptation was indicated by the network analysis that allowed uncovering previously unknown crosstalk between liver and mammary tissue for several signaling molecules.

Transcriptome difference and potential crosstalk between liver and mammary tissue in mid-lactation primiparous dairy cows

PubMed Central

Bu, Dengpan; Bionaz, Massimo; Wang, Mengzhi; Nan, Xuemei; Ma, Lu; Wang, Jiaqi

2017-01-01

Liver and mammary gland are among the most important organs during lactation in dairy cows. With the purpose of understanding both the different and the complementary roles and the crosstalk of those two organs during lactation, a transcriptome analysis was performed on liver and mammary tissues of 10 primiparous dairy cows in mid-lactation. The analysis was performed using a 4×44K Bovine Agilent microarray chip. The transcriptome difference between the two tissues was analyzed using SAS JMP Genomics using ANOVA with a false discovery rate correction (FDR). The analysis uncovered >9,000 genes differentially expressed (DEG) between the two tissues with a FDR<0.001. The functional analysis of the DEG uncovered a larger metabolic (especially related to lipid) and inflammatory response capacity in liver compared with mammary tissue while the mammary tissue had a larger protein synthesis and secretion, proliferation/differentiation, signaling, and innate immune system capacity compared with the liver. A plethora of endogenous compounds, cytokines, and transcription factors were estimated to control the DEG between the two tissues. Compared with mammary tissue, the liver transcriptome appeared to be under control of a large array of ligand-dependent nuclear receptors and, among endogenous chemical, fatty acids and bacteria-derived compounds. Compared with liver, the transcriptome of the mammary tissue was potentially under control of a large number of growth factors and miRNA. The in silico crosstalk analysis between the two tissues revealed an overall large communication with a reciprocal control of lipid metabolism, innate immune system adaptation, and proliferation/differentiation. In summary the transcriptome analysis confirmed prior known differences between liver and mammary tissue, especially considering the indication of a larger metabolic activity in liver compared with the mammary tissue and the larger protein synthesis, communication, and proliferative capacity in mammary tissue compared with the liver. Relatively novel is the indication by the data that the transcriptome of the liver is highly regulated by dietary and bacteria-related compounds while the mammary transcriptome is more under control of hormones, growth factors, and miRNA. A large crosstalk between the two tissues with a reciprocal control of metabolism and innate immune-adaptation was indicated by the network analysis that allowed uncovering previously unknown crosstalk between liver and mammary tissue for several signaling molecules. PMID:28291785

Nearing saturation of cancer driver gene discovery.

PubMed

Hsiehchen, David; Hsieh, Antony

2018-06-15

Extensive sequencing efforts of cancer genomes such as The Cancer Genome Atlas (TCGA) have been undertaken to uncover bona fide cancer driver genes which has enhanced our understanding of cancer and revealed therapeutic targets. However, the number of driver gene mutations is bounded, indicating that there must be a point when further sequencing efforts will be excessive. We found that there was a significant positive correlation between sample size and identified driver gene mutations across 33 cancers sequenced by the TCGA, which is expected if additional sequencing is still leading to the identification of more driver genes. However, the rate of new cancer driver genes being discovered with larger samples is declining rapidly. Our analysis provides a general guide for determining which cancer types would likely benefit from additional sequencing efforts, particularly those with relatively high rates of cancer driver gene discovery. Our results argue that past strategies of indiscriminately sequencing as many specimens as possible for all cancer types is becoming inefficient. In addition, without significant investments into applying our knowledge of cancer genomes, we risk sequencing more cancer genomes for the sake of sequencing rather than meaningful patient benefit.

Tunable plasmonic toroidal terahertz metamodulator

NASA Astrophysics Data System (ADS)

Gerislioglu, Burak; Ahmadivand, Arash; Pala, Nezih

2018-04-01

Optical modulators are essential and strategic parts of micro- and nanophotonic circuits to encode electro-optical signals in the optical domain. Here, by using arrays of multipixel toroidal plasmonic terahertz (THz) metamolecules, we developed a functional plasmonic metamodulator with high efficiency and tunability. Technically, the dynamic toroidal dipole induces nonradiating charge-current arrangements leading to have an exquisite role in defining the inherent spectral features of various materials. By categorizing in a different family of multipoles far from the traditional electromagnetic multipoles, the toroidal dipole corresponds to poloidal currents flowing on the surface of a closed-loop torus. Utilizing the sensitivity of the optically driven toroidal momentum to the incident THz beam power and by employing both numerical tools and experimental analysis, we systematically studied the spectral response of the proposed THz plasmonic metadevice. In this Rapid Communication, we uncover a correlation between the existence and the excitation of the toroidal response and the incident beam power. This mechanism is employed to develop THz toroidal metamodulators with a strong potential to be employed for practical advanced and next-generation communication, filtering, and routing applications.

Molecular docking study, synthesis and biological evaluation of Mannich bases as Hsp90 inhibitors.

PubMed

Gupta, Sayan Dutta; Bommaka, Manish Kumar; Mazaira, Gisela I; Galigniana, Mario D; Subrahmanyam, Chavali Venkata Satya; Gowrishankar, Naryanasamy Lachmana; Raghavendra, Nulgumnalli Manjunathaiah

2015-09-01

The ubiquitously expressed heat shock protein 90 is an encouraging target for the development of novel anticancer agents. In a program directed towards uncovering novel chemical scaffolds against Hsp90, we performed molecular docking studies using Tripos-Sybyl drug designing software by including the required conserved water molecules. The results of the docking studies predicted Mannich bases derived from 2,4-dihydroxy acetophenone/5-chloro 2,4-dihydroxy acetophenone as potential Hsp90 inhibitors. Subsequently, a few of them were synthesized (1-6) and characterized by IR, (1)H NMR, (13)C NMR and mass spectral analysis. The synthesized Mannich compounds were evaluated for their potential to suppress Hsp90 ATPase activity by the colorimetric Malachite green assay. Subsequently, the molecules were screened for their antiproilferative effect against PC3 pancreatic carcinoma cells by adopting the 3-(4,5-dimethythiazol- 2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay method. The activity profile of the identified derivatives correlated well with their docking results. Copyright © 2015 Elsevier B.V. All rights reserved.

Effect of Particulate Matter Mineral Composition on Environmentally Persistent Free Radical (EPFR) Formation.

PubMed

Feld-Cook, Elisabeth E; Bovenkamp-Langlois, Lisa; Lomnicki, Slawo M

2017-09-19

Environmentally Persistent Free Radicals (EPFRs) are newly discovered, long-lived surface bound radicals that form on particulate matter and combustion borne particulates, such as fly ash. Human exposure to such particulates lead to translocation into the lungs and heart resulting in cardio-vascular and respiratory disease through the production of reactive oxygen species. Analysis of some waste incinerator fly ashes revealed a significant difference between their EPFR contents. Although EPFR formation occurs on the metal domains, these differences were correlated with the altering concentration of calcium and sulfur. To analyze these phenomena, surrogate fly ashes were synthesized to mimic the presence of their major mineral components, including metal oxides, calcium, and sulfur. The results of this study led to the conclusion that the presence of sulfates limits formation of EPFRs due to inhibition or poisoning of the transition metal active sites necessary for their formation. These findings provide a pathway toward understanding differences in EPFR presence on particulate matter and uncover the possibility of remediating EPFRs from incineration and hazardous waste sites.

Magnetic field tunability of spin polarized excitations in a high temperature magnet

NASA Astrophysics Data System (ADS)

Holinsworth, Brian; Sims, Hunter; Cherian, Judy; Mazumdar, Dipanjan; Harms, Nathan; Chapman, Brandon; Gupta, Arun; McGill, Steve; Musfeldt, Janice

Magnetic semiconductors are at the heart of modern device physics because they naturally provide a non-zero magnetic moment below the ordering temperature, spin-dependent band gap, and spin polarization that originates from exchange-coupled magnetization or an applied field creating a spin-split band structure. Strongly correlated spinel ferrites are amongst the most noteworthy contenders for semiconductor spintronics. NiFe2O4, in particular, displays spin-filtering, linear magnetoresistance, and wide application in the microwave regime. To unravel the spin-charge interaction in NiFe2O4, we bring together magnetic circular dichroism, photoconductivity, and prior optical absorption with complementary first principles calculations. Analysis uncovers a metamagnetic transition modifying electronic structure in the minority channel below the majority channel gap, exchange splittings emerging from spin-split bands, anisotropy of excitons surrounding the indirect gap, and magnetic-field dependent photoconductivity. These findings open the door for the creation and control of spin-polarized excitations from minority channel charge charge transfer in NiFe2O4 and other members of the spinel ferrite family.

Differential Gene Expression (DEX) and Alternative Splicing Events (ASE) for Temporal Dynamic Processes Using HMMs and Hierarchical Bayesian Modeling Approaches.

PubMed

Oh, Sunghee; Song, Seongho

2017-01-01

In gene expression profile, data analysis pipeline is categorized into four levels, major downstream tasks, i.e., (1) identification of differential expression; (2) clustering co-expression patterns; (3) classification of subtypes of samples; and (4) detection of genetic regulatory networks, are performed posterior to preprocessing procedure such as normalization techniques. To be more specific, temporal dynamic gene expression data has its inherent feature, namely, two neighboring time points (previous and current state) are highly correlated with each other, compared to static expression data which samples are assumed as independent individuals. In this chapter, we demonstrate how HMMs and hierarchical Bayesian modeling methods capture the horizontal time dependency structures in time series expression profiles by focusing on the identification of differential expression. In addition, those differential expression genes and transcript variant isoforms over time detected in core prerequisite steps can be generally further applied in detection of genetic regulatory networks to comprehensively uncover dynamic repertoires in the aspects of system biology as the coupled framework.

Uncovering stable and occasional human mobility patterns: A case study of the Beijing subway

NASA Astrophysics Data System (ADS)

Yong, Nuo; Ni, Shunjiang; Shen, Shifei; Chen, Peng; Ji, Xuewei

2018-02-01

There have generally been two kinds of approaches to the empirical study of human mobility. At the group level, some valuable information might be submerged in statistical noise, while due to the diversity of individual purpose and preference, there is still no general statistical regularity of human mobility at the individual level. In this paper, we considered group-level human mobility as the combination of several basic patterns and analyzed the collective mobility by category. Utilizing matrix factorization and correlation analysis, we extracted some of the stable/occasional components from the collective human mobility in the Beijing subway and found that the departure and arrival mobility patterns have different characteristics, both in time and space, under various conditions. We classified individual records into different patterns and analyzed the most likely trip distance by category. The proposed method can decompose stable/occasional mobility patterns from the collective mobility and identify passengers belonging to different patterns, helping us to better understand the origin of different mobility patterns and provide guidance for emergency management of large crowds.

Label-Free Proteomic Analysis of Protein Changes in the Striatum during Chronic Ethanol Use and Early Withdrawal

PubMed Central

Ayers-Ringler, Jennifer R.; Oliveros, Alfredo; Qiu, Yanyan; Lindberg, Daniel M.; Hinton, David J.; Moore, Raymond M.; Dasari, Surendra; Choi, Doo-Sup

2016-01-01

The molecular mechanisms underlying the neuronal signaling changes in alcohol addiction and withdrawal are complex and multifaceted. The cortico-striatal circuit is highly implicated in these processes, and the striatum plays a significant role not only in the early stages of addiction, but in the developed-addictive state as well, including withdrawal symptoms. Transcriptional analysis is a useful method for determining changes in gene expression, however, the results do not always accurately correlate with protein levels. In this study, we employ label-free proteomic analysis to determine changes in protein expression within the striatum during chronic ethanol use and early withdrawal. The striatum, composed primarily of medium spiny GABAergic neurons, glutamatergic and dopaminergic nerve terminals and astrocytes, is relatively homogeneous for proteomic analysis. We were able to analyze more than 5000 proteins from both the dorsal (caudate and putamen) and ventral (nucleus accumbens) striatum and identified significant changes following chronic intermittent ethanol exposure and acute (8 h) withdrawal compared to ethanol naïve and ethanol exposure groups respectively. Our results showed significant changes in proteins involved in glutamate and opioid peptide signaling, and also uncovered novel pathways including mitochondrial function and lipid/cholesterol metabolism, as revealed by changes in electron transport chain proteins and RXR activation pathways. These results will be useful in the development of novel treatments for alcohol withdrawal and thereby aid in recovery from alcohol use disorder. PMID:27014007

Percutaneous Transhepatic Biliary Stenting with Uncovered Self-Expandable Metallic Stents in Patients with Malignant Biliary Obstruction – Efficacy and Survival Analysis

PubMed Central

Pranculis, Andrius; Kievišienė, Lina; Vaičius, Artūras; Vanagas, Tomas; Kaupas, Rytis Stasys; Dambrauskas, Žilvinas

2017-01-01

Summary Background The aim of this study was to assess short- and long-term outcomes of malignant biliary obstruction (MBO) treatment by percutaneous transhepatic biliary stenting (PTBS) with uncovered selfexpandable metallic stents (SEMS), and to identify predictors of survival. Material/Methods A nine-year, single-centre study from a prospectively collected database included 222 patients with inoperable MBO treated by PTBS with uncovered nitinol SEMS. Results Technical and clinical success rates were 95.9% and 82.4%, respectively. The total rate of postprocedural complications was 14.4%. The mean durations of the primary and secondary stent patency were 114.7±15.1 and 146.4±21.2 days, respectively. The 30-day mortality rate was 15.3% with no procedure-related deaths. The mean estimated length of survival was 143.3±20.6 days. Independent predictors increasing the risk of death included higher than 115 μmol/L serum bilirubin 2–5 days after biliary stenting (HR 3.274, P=0.019), distal (non-hilar) obstruction of the bile ducts (HR 3.711, P=0.008), Bismuth-Corlette type IV stricture (HR 2.082, P=0.008), obstruction due to gallbladder cancer (HR 31.029, P=0.012) and only partial drainage of liver parenchyma (HR 4.158, P=0.040). Conclusions PTBS with uncovered SEMS is an effective and safe method for palliative treatment of MBO. Serum bilirubin higher than 115 μmol/L 2–5 days after the procedure has a significant negative impact on patients’ survival. Lower survival is also determined by distal bile duct obstruction, Bismuth– Corlette type IV stricture, biliary obstruction caused by gallbladder cancer and when only partial liver drainage is applied. PMID:29662569

Percutaneous Transhepatic Biliary Stenting with Uncovered Self-Expandable Metallic Stents in Patients with Malignant Biliary Obstruction - Efficacy and Survival Analysis.

PubMed

Pranculis, Andrius; Kievišas, Mantas; Kievišienė, Lina; Vaičius, Artūras; Vanagas, Tomas; Kaupas, Rytis Stasys; Dambrauskas, Žilvinas

2017-01-01

The aim of this study was to assess short- and long-term outcomes of malignant biliary obstruction (MBO) treatment by percutaneous transhepatic biliary stenting (PTBS) with uncovered selfexpandable metallic stents (SEMS), and to identify predictors of survival. A nine-year, single-centre study from a prospectively collected database included 222 patients with inoperable MBO treated by PTBS with uncovered nitinol SEMS. Technical and clinical success rates were 95.9% and 82.4%, respectively. The total rate of postprocedural complications was 14.4%. The mean durations of the primary and secondary stent patency were 114.7±15.1 and 146.4±21.2 days, respectively. The 30-day mortality rate was 15.3% with no procedure-related deaths. The mean estimated length of survival was 143.3±20.6 days. Independent predictors increasing the risk of death included higher than 115 μmol/L serum bilirubin 2-5 days after biliary stenting (HR 3.274, P =0.019), distal (non-hilar) obstruction of the bile ducts (HR 3.711, P =0.008), Bismuth-Corlette type IV stricture (HR 2.082, P =0.008), obstruction due to gallbladder cancer (HR 31.029, P =0.012) and only partial drainage of liver parenchyma (HR 4.158, P =0.040). PTBS with uncovered SEMS is an effective and safe method for palliative treatment of MBO. Serum bilirubin higher than 115 μmol/L 2-5 days after the procedure has a significant negative impact on patients' survival. Lower survival is also determined by distal bile duct obstruction, Bismuth- Corlette type IV stricture, biliary obstruction caused by gallbladder cancer and when only partial liver drainage is applied.

Percutaneous unilateral biliary metallic stent placement in patients with malignant obstruction of the biliary hila and contralateral portal vein steno-occlusion.

PubMed

Son, Rak Chae; Gwon, Dong Il; Ko, Heung Kyu; Kim, Jong Woo; Ko, Gi-Young

2015-01-01

To investigate the outcomes of percutaneous unilateral metallic stent placement in patients with a malignant obstruction of the biliary hila and a contralateral portal vein steno-occlusion. Sixty patients with a malignant hilar obstruction and unilobar portal vein steno-occlusion caused by tumor invasion or preoperative portal vein embolization were enrolled in this retrospective study from October 2010 to October 2013. All patients were treated with percutaneous placement of a biliary metallic stent, including expanded polytetrafluoroethylene (ePTFE)-covered stents in 27 patients and uncovered stents in 33 patients. A total of 70 stents were successfully placed in 60 patients. Procedural-related minor complications, including self-limiting hemobilia (n = 2) and cholangitis (n = 4) occurred in six (10%) patients. Acute cholecystitis occurred in two patients. Successful internal drainage was achieved in 54 (90%) of the 60 patients. According to a Kaplan-Meier analysis, median survival time was 210 days (95% confidence interval [CI], 135-284 days), and median stent patency time was 133 days (95% CI, 94-171 days). No significant difference in stent patency was observed between covered and uncovered stents (p = 0.646). Stent dysfunction occurred in 16 (29.6%) of 54 patients after a mean of 159 days (range, 65-321 days). Unilateral placement of ePTFE-covered and uncovered stents in the hepatic lobe with a patent portal vein is a safe and effective method for palliative treatment of patients with a contralateral portal vein steno-occlusion caused by an advanced hilar malignancy or portal vein embolization. No significant difference in stent patency was detected between covered and uncovered metallic stents.

Percutaneous Unilateral Biliary Metallic Stent Placement in Patients with Malignant Obstruction of the Biliary Hila and Contralateral Portal Vein Steno-Occlusion

PubMed Central

Son, Rak Chae; Ko, Heung Kyu; Kim, Jong Woo; Ko, Gi-Young

2015-01-01

Objective To investigate the outcomes of percutaneous unilateral metallic stent placement in patients with a malignant obstruction of the biliary hila and a contralateral portal vein steno-occlusion. Materials and Methods Sixty patients with a malignant hilar obstruction and unilobar portal vein steno-occlusion caused by tumor invasion or preoperative portal vein embolization were enrolled in this retrospective study from October 2010 to October 2013. All patients were treated with percutaneous placement of a biliary metallic stent, including expanded polytetrafluoroethylene (ePTFE)-covered stents in 27 patients and uncovered stents in 33 patients. Results A total of 70 stents were successfully placed in 60 patients. Procedural-related minor complications, including self-limiting hemobilia (n = 2) and cholangitis (n = 4) occurred in six (10%) patients. Acute cholecystitis occurred in two patients. Successful internal drainage was achieved in 54 (90%) of the 60 patients. According to a Kaplan-Meier analysis, median survival time was 210 days (95% confidence interval [CI], 135-284 days), and median stent patency time was 133 days (95% CI, 94-171 days). No significant difference in stent patency was observed between covered and uncovered stents (p = 0.646). Stent dysfunction occurred in 16 (29.6%) of 54 patients after a mean of 159 days (range, 65-321 days). Conclusion Unilateral placement of ePTFE-covered and uncovered stents in the hepatic lobe with a patent portal vein is a safe and effective method for palliative treatment of patients with a contralateral portal vein steno-occlusion caused by an advanced hilar malignancy or portal vein embolization. No significant difference in stent patency was detected between covered and uncovered metallic stents. PMID:25995688

Self-spinning nanoparticle laden microdroplets for sensing and energy harvesting

NASA Astrophysics Data System (ADS)

Bhattacharjee, Mitradip; Pasumarthi, Viswanath; Chaudhuri, Joydip; Singh, Amit Kumar; Nemade, Harshal; Bandyopadhyay, Dipankar

2016-03-01

Exposure of a volatile organic vapour could set in powerful rotational motion a microdroplet composed of an aqueous salt solution loaded with metal nanoparticles. The solutal Marangoni motion on the surface originating from the sharp difference in the surface tension of water and organic vapour stimulated the strong vortices inside the droplet. The vapour sources of methanol, ethanol, diethyl ether, toluene, and chloroform stimulated motions of different magnitudes could easily be correlated to the surface tension gradient on the drop surface. Interestingly, when the nanoparticle laden droplet of aqueous salt solution was connected to an external electric circuit through a pair of electrodes, an ~85-95% reduction in the electrical resistance was observed across the spinning droplet. The extent of reduction in the resistance was found to have a correlation with the difference in the surface tension of the vapour source and the water droplet, which could be employed to distinguish the vapour sources. Remarkably, the power density of the same prototype was estimated to be around 7 μW cm-2, which indicated the potential of the phenomenon in converting surface energy into electrical in a non-destructive manner and under ambient conditions. Theoretical analysis uncovered that the difference in the ζ-potential near the electrodes was the major reason for the voltage generation. The prototype could also detect the repeated exposure and withdrawal of vapour sources, which helped in the development of a proof-of-concept detector to sense alcohol issuing out of the human breathing system.Exposure of a volatile organic vapour could set in powerful rotational motion a microdroplet composed of an aqueous salt solution loaded with metal nanoparticles. The solutal Marangoni motion on the surface originating from the sharp difference in the surface tension of water and organic vapour stimulated the strong vortices inside the droplet. The vapour sources of methanol, ethanol, diethyl ether, toluene, and chloroform stimulated motions of different magnitudes could easily be correlated to the surface tension gradient on the drop surface. Interestingly, when the nanoparticle laden droplet of aqueous salt solution was connected to an external electric circuit through a pair of electrodes, an ~85-95% reduction in the electrical resistance was observed across the spinning droplet. The extent of reduction in the resistance was found to have a correlation with the difference in the surface tension of the vapour source and the water droplet, which could be employed to distinguish the vapour sources. Remarkably, the power density of the same prototype was estimated to be around 7 μW cm-2, which indicated the potential of the phenomenon in converting surface energy into electrical in a non-destructive manner and under ambient conditions. Theoretical analysis uncovered that the difference in the ζ-potential near the electrodes was the major reason for the voltage generation. The prototype could also detect the repeated exposure and withdrawal of vapour sources, which helped in the development of a proof-of-concept detector to sense alcohol issuing out of the human breathing system. Electronic supplementary information (ESI) available: Discussion of simulation with results, characterization and movies of particle motion inside droplets along with detailed explanation. See DOI: 10.1039/c6nr00217j

Molecular profiling identifies prognostic markers of stage IA lung adenocarcinoma.

PubMed

Zhang, Jie; Shao, Jinchen; Zhu, Lei; Zhao, Ruiying; Xing, Jie; Wang, Jun; Guo, Xiaohui; Tu, Shichun; Han, Baohui; Yu, Keke

2017-09-26

We previously showed that different pathologic subtypes were associated with different prognostic values in patients with stage IA lung adenocarcinoma (AC). We hypothesize that differential gene expression profiles of different subtypes may be valuable factors for prognosis in stage IA lung adenocarcinoma. We performed microarray gene expression profiling on tumor tissues micro-dissected from patients with acinar and solid predominant subtypes of stage IA lung adenocarcinoma. These patients had undergone a lobectomy and mediastinal lymph node dissection at the Shanghai Chest Hospital, Shanghai, China in 2012. No patient had preoperative treatment. We performed the Gene Set Enrichment Analysis (GSEA) analysis to look for gene expression signatures associated with tumor subtypes. The histologic subtypes of all patients were classified according to the 2015 WHO lung Adenocarcinoma classification. We found that patients with the solid predominant subtype are enriched for genes involved in RNA polymerase activity as well as inactivation of the p53 pathway. Further, we identified a list of genes that may serve as prognostic markers for stage IA lung adenocarcinoma. Validation in the TCGA database shows that these genes are correlated with survival, suggesting that they are novel prognostic factors for stage IA lung adenocarcinoma. In conclusion, we have uncovered novel prognostic factors for stage IA lung adenocarcinoma using gene expression profiling in combination with histopathology subtyping.

Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum.

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

Reddy, Anireddy; Ben-Hur, Asa

Abiotic stresses including drought are major limiting factors of crop yields and cause significant crop losses. Acquisition of stress tolerance to abiotic stresses requires coordinated regulation of a multitude of biochemical and physiological changes, and most of these changes depend on alterations in gene expression. The goal of this work is to perform global analysis of differential regulation of gene expression and alternative splicing, and their relationship with chromatin landscape in drought sensitive and tolerant cultivars. our Iso-Seq study revealed transcriptome-wide full-length isoforms at an unprecedented scale with over 11000 novel splice isoforms. Additionally, we uncovered alternative polyadenylation sites ofmore » ~11000 expressed genes and many novel genes. Overall, Iso-Seq results greatly enhanced sorghum gene annotations that are not only useful in analyzing all our RNA-seq, ChIP-seq and ATAC-seq data but also serve as a great resource to the plant biology community. Our studies identified differentially expressed genes and splicing events that are correlated with the drought-resistant phenotype. An association between alternative splicing and chromatin accessibility was also revealed. Several computational tools developed here (TAPIS and iDiffIR) have been made freely available to the research community in analyzing alternative splicing and differential alternative splicing.« less

A singular value decomposition approach for improved taxonomic classification of biological sequences

PubMed Central

2011-01-01

Background Singular value decomposition (SVD) is a powerful technique for information retrieval; it helps uncover relationships between elements that are not prima facie related. SVD was initially developed to reduce the time needed for information retrieval and analysis of very large data sets in the complex internet environment. Since information retrieval from large-scale genome and proteome data sets has a similar level of complexity, SVD-based methods could also facilitate data analysis in this research area. Results We found that SVD applied to amino acid sequences demonstrates relationships and provides a basis for producing clusters and cladograms, demonstrating evolutionary relatedness of species that correlates well with Linnaean taxonomy. The choice of a reasonable number of singular values is crucial for SVD-based studies. We found that fewer singular values are needed to produce biologically significant clusters when SVD is employed. Subsequently, we developed a method to determine the lowest number of singular values and fewest clusters needed to guarantee biological significance; this system was developed and validated by comparison with Linnaean taxonomic classification. Conclusions By using SVD, we can reduce uncertainty concerning the appropriate rank value necessary to perform accurate information retrieval analyses. In tests, clusters that we developed with SVD perfectly matched what was expected based on Linnaean taxonomy. PMID:22369633

Covered self-expandable metal stents with an anti-migration system improve patency duration without increased complications compared with uncovered stents for distal biliary obstruction caused by pancreatic carcinoma: a randomized multicenter trial.

PubMed

Kitano, Masayuki; Yamashita, Yukitaka; Tanaka, Kiyohito; Konishi, Hideyuki; Yazumi, Shujiro; Nakai, Yoshitaka; Nishiyama, Osamu; Uehara, Hiroyuki; Mitoro, Akira; Sanuki, Tsuyoshi; Takaoka, Makoto; Koshitani, Tatsuya; Arisaka, Yoshifumi; Shiba, Masatsugu; Hoki, Noriyuki; Sato, Hideki; Sasaki, Yuichi; Sato, Masako; Hasegawa, Kazunori; Kawabata, Hideaki; Okabe, Yoshihiro; Mukai, Hidekazu

2013-11-01

The requirements of biliary stents used in the palliation of malignant biliary obstruction are a long duration of patency and minimal adverse effects. Covered self-expandable metal stents (SEMSs) have been shown to prevent tumor ingrowth, which is the most frequent complication of uncovered SEMSs. However, because they are prone to migration, the superiority of covered SEMS has yet to be convincingly demonstrated. The aim of this study was to evaluate the superiority of covered over uncovered SEMSs in the palliation of distal biliary obstruction due to unresectable pancreatic carcinoma, using both stent types with relatively low axial force and uncovered flared ends to prevent their migration. From April 2009 to December 2010, 120 patients who were admitted to 22 tertiary-care centers because of distal biliary obstruction from unresectable pancreatic carcinomas were enrolled in this prospective randomized multicenter study. Patients were randomly assigned to receive a covered or uncovered SEMS deployed at the site of the biliary stricture during endoscopic retrograde cholangiopancreatography. Stent patency time, patient survival time, patient survival time without stent dysfunction (time to stent dysfunction or patient death), cause of stent dysfunction (ingrowth, overgrowth, migration, or sludge formation), and serious adverse events were compared between covered and uncovered SEMS groups. Patient survival time in the two groups did not significantly differ (median: 285 and 223 days, respectively; P=0.68). Patient survival time without stent dysfunction was significantly longer in the covered than in the uncovered SEMS group (median: 187 vs. 132 days; P=0.043). Stent patency was also significantly longer in the covered than in the uncovered SEMS group (mean±s.d.: 219.3±159.1 vs. 166.9±124.9 days; P=0.047). Reintervention for stent dysfunction was performed in 14 of 60 patients with covered SEMSs (23%) and in 22 of 60 patients with uncovered SEMSs (37%; P=0.08). Stent dysfunction was caused by tumor ingrowth, tumor overgrowth, and sludge formation in 0 (0%), 3 (5%), and 11 (18%) patients in the covered SEMSs group, and in 15 (25%), 2 (3%), and 6 (10%) patients in the uncovered SEMSs group, respectively. Stent migration was not observed in either group. Rates of tumor overgrowth and sludge formation did not significantly differ between the two groups, whereas the rate of tumor ingrowth was significantly lower in the covered than in the uncovered SEMS group (P<0.01). Acute pancreatitis occurred in only one patient in the covered SEMS group. Acute cholecystitis occurred in one patient in the covered SEMS group and in two patients in the uncovered SEMS group. There was no significant difference between the two groups in the incidence of serious adverse events. By preventing tumor ingrowth and migration, covered SEMSs with an anti-migration system had a longer duration of patency than uncovered SEMSs, which recommends their use in the palliative treatment of patients with biliary obstruction due to pancreatic carcinomas.

How can knowledge discovery methods uncover spatio-temporal patterns in environmental data?

NASA Astrophysics Data System (ADS)

Wachowicz, Monica

2000-04-01

This paper proposes the integration of KDD, GVis and STDB as a long-term strategy, which will allow users to apply knowledge discovery methods for uncovering spatio-temporal patterns in environmental data. The main goal is to combine innovative techniques and associated tools for exploring very large environmental data sets in order to arrive at valid, novel, potentially useful, and ultimately understandable spatio-temporal patterns. The GeoInsight approach is described using the principles and key developments in the research domains of KDD, GVis, and STDB. The GeoInsight approach aims at the integration of these research domains in order to provide tools for performing information retrieval, exploration, analysis, and visualization. The result is a knowledge-based design, which involves visual thinking (perceptual-cognitive process) and automated information processing (computer-analytical process).

Uncovering an Existential Barrier to Breast Self-exam Behavior

PubMed Central

Goldenberg, Jamie L.; Arndt, Jamie; Hart, Joshua; Routledge, Clay

2008-01-01

The present research applies an analysis derived from terror management theory to the health domain of breast examination, and in doing so uncovers previously unrecognized factors that may contribute to women’s reluctance to perform breast self-examinations (BSEs). In Study 1, when concerns about mortality were primed, reminders of human beings’ physical nature (i.e., creatureliness) reduced intentions to conduct BSEs compared to reminders of humans’ uniqueness. In Study 2, women conducted shorter exams on a breast model (an experience found to increase death-thought accessibility) when creatureliness was primed compared to a uniqueness and no essay condition. In Study 3, after a creatureliness prime, women performed shorter BSEs when a placebo did not provide an alternative explanation for their discomfort compared to when it did. Advances for theory and breast self-exam promotion are discussed. PMID:19255593

Familial Brugada syndrome uncovered by hyperkalaemic diabetic ketoacidosis.

PubMed

Postema, Pieter G; Vlaar, Alexander P J; DeVries, J Hans; Tan, Hanno L

2011-10-01

We describe a case of diabetic ketoacidosis with concomitant hyperkalaemia that uncovered a typical Brugada syndrome electrocardiogram (ECG). Further provocation testing in the patient and his son confirmed familial Brugada syndrome. Diabetic ketoacidosis with hyperkalaemia may uncover an inheritable arrhythmia syndrome that may put the patient and his/her next of kin at risk for a sudden death, irrespective of diabetes mellitus.

Uncovering Student Values for Hiring in the Software Industry

ERIC Educational Resources Information Center

Chinn, Donald; Vandegrift, Tammy

2008-01-01

This article provides an analysis of student responses to an exercise used in a computer ethics and a software engineering course to raise awareness of issues related to hiring, including issues of professional responsibility and diversity. Students from two different universities were asked to evaluate four candidates for two positions in a…

Covering the Standards: Astronomy Teachers' Preparation and Beliefs

ERIC Educational Resources Information Center

Plummer, Julia D.; Zahm, Valerie M.

2010-01-01

An online survey of science teachers and interviews with curriculum directors were used to investigate the coverage of astronomy in middle and high schools in the greater Philadelphia region. Our analysis looked beyond astronomy elective courses to uncover all sources of astronomy education in secondary schools. We focused on coverage of state…

Integrated phospholipidomics and transcriptomics analysis of Saccharomyces cerevisiae with enhanced tolerance to a mixture of acetic acid, furfural, and phenol

USDA-ARS?s Scientific Manuscript database

A mixture of acetic acid, furfural and phenol (AFP), three representative lignocellulose derived inhibitors, significantly inhibited the growth and bioethanol production of Saccharomyces cerevisiae. In order to uncover mechanisms behind the enhanced tolerance of an inhibitor-tolerant S.cerevisiae s...

Social Network Analysis of International Student Mobility: Uncovering the Rise of Regional Hubs

ERIC Educational Resources Information Center

Kondakci, Yasar; Bedenlier, Svenja; Zawacki-Richter, Olaf

2018-01-01

Research on the patterns of international student mobility and the dynamics shaping these patterns has been dominated by studies reflecting a Western orientation, discourse, and understanding. Considering political, economic, cultural, historical, and ecological factors, this study argues that international student mobility is not only an issue of…

Swimming Upstream: The Experience of Academic Mothers of Young Children

ERIC Educational Resources Information Center

Hirakata, Pam E.; Daniluk, Judith C.

2009-01-01

A qualitative phenomenological approach was used to explore the experiences of 10 tenured and untenured women from various disciplines who were engaged in academic careers while mothering pre-teen children. Analysis of the in-depth interview data uncovered six themes common to the participants: (a) sense of vulnerability, (b) sense of isolation,…

Uncovering Multivariate Structure in Classroom Observations in the Presence of Rater Errors

ERIC Educational Resources Information Center

McCaffrey, Daniel F.; Yuan, Kun; Savitsky, Terrance D.; Lockwood, J. R.; Edelen, Maria O.

2015-01-01

We examine the factor structure of scores from the CLASS-S protocol obtained from observations of middle school classroom teaching. Factor analysis has been used to support both interpretations of scores from classroom observation protocols, like CLASS-S, and the theories about teaching that underlie them. However, classroom observations contain…

The Primacy of IQ Subtest Analysis to Understand Reading Performance for Culturally Diverse Groups

ERIC Educational Resources Information Center

Ortiz, Samuel O.; Johnston, Harriet N.; Wilcox, Gabrielle; Francis, Stella L.; Tomes, Yuma I.

2014-01-01

There is significant debate over the value and ethics of IQ testing for children, including those from diverse cultural groups, particularly in light of studies examining performance on various subtests that are uncovering important processing differences between cultural and linguistic groups (Sotelo-Dynega, Ortiz, Flanagan, & Chaplin, 2013).…

Same Plans, Different Strategies: The Multiple Faces of Resistance

ERIC Educational Resources Information Center

Mendoza Pérez, Karmele; Morgade Salgado, Marta

2016-01-01

This article reports an ethnographic study of resistance in an informal education context: an NGO Day Centre and Hostel for socially excluded adults in Bilbao, Spain. The purpose of this research is to contribute to the field of resistance theory by focusing on a non-school setting. Our analysis uncovered four resistance strategies ("The…

Morphological Processing of Ultraviolet Emissions of Electrical Corona Discharge for Analysis and Diagnostic Use

NASA Technical Reports Server (NTRS)

Schubert, Matthew R.; Moore, Andrew J.

2015-01-01

Electron cascades from electrical discharge produce secondary emissions from atmospheric plasma in the ultraviolet band. For a single point of discharge, these emissions exhibit a stereotypical discharge morphology, with latent information about the discharge location. Morphological processing can uncover the location and therefore can have diagnostic utility.

Morphological processing of ultraviolet emissions of electrical corona discharge for analysis and diagnostic use.

PubMed

Schubert, Matthew; Moore, Andrew J

2016-03-01

Electron cascades from electrical discharge produce secondary emissions from atmospheric plasma in the ultraviolet band. For a single point of discharge, these emissions exhibit a stereotypical discharge morphology, with latent information about the discharge location. Morphological processing can uncover the location and therefore have diagnostic utility.

Problem Solving in Swedish Mathematics Textbooks for Upper Secondary School

ERIC Educational Resources Information Center

Brehmer, Daniel; Ryve, Andreas; Van Steenbrugge, Hendrik

2016-01-01

The aim of this study is to analyse how mathematical problem solving is represented in mathematical textbooks for Swedish upper secondary school. The analysis comprises dominating Swedish textbook series, and relates to uncovering (a) the quantity of tasks that are actually mathematical problems, (b) their location in the chapter, (c) their…

Virtual Chironomia: A Multimodal Study of Verbal and Non-Verbal Communication in a Virtual World

ERIC Educational Resources Information Center

Verhulsdonck, Gustav

2010-01-01

This mixed methods study examined the various aspects of multimodal use of non-verbal communication in virtual worlds during dyadic negotiations. Quantitative analysis uncovered a treatment effect whereby people with more rhetorical certainty used more neutral non-verbal communication; whereas people that were rhetorically less certain used more…

The Role of Reading Strategies in Integrated L2 Writing Tasks

ERIC Educational Resources Information Center

Plakans, Lia

2009-01-01

Integrated second-language writing tasks elicit writing performances that involve other abilities such as reading or listening. Thus, understanding the role of these other abilities is necessary for interpreting performance on such tasks. This study used an inductive analysis of think-aloud protocol data and interviews to uncover the reading…

A Meta-Analysis on the Effectiveness of Bilingual Programs in Europe

ERIC Educational Resources Information Center

Reljic, Gabrijela; Ferring, Dieter; Martin, Romain

2015-01-01

The effectiveness of bilingual programs for promoting academic achievement of language minority children in the United States has been examined in six meta-analyses. The present meta-analytic study investigates this topic for the first time in the European context. Thorough literature searches uncovered 101 European studies, with only 7 meeting…

Leading Schools in Communities of Multiple Deprivation: Women Principals in South Africa

ERIC Educational Resources Information Center

Lumby, Jacky

2015-01-01

This article explores how leadership and gender are constructed by women principals of schools located in communities of multiple deprivation in two provinces of South Africa. Analysis of interview data uncovers a hierarchy of goals related to establishing a school, recruiting and retaining learners, ensuring they are ready to learn, developing…

Uncovering Dimensions of Culture in Underperforming Group Homes for People with Severe Intellectual Disability

ERIC Educational Resources Information Center

Bigby, Christine; Knox, Marie; Beadle-Brown, Julie; Clement, Tim; Mansell, Jim

2012-01-01

Culture recurs as an important but under-investigated variable associated with resident outcomes in supported accommodation for people with intellectual disability. This study aimed to conceptualize the potential dimensions of culture in all group homes and describe the culture in underperforming group homes. A secondary analysis, using an…

The Influence of Place-Based Communities on Information Behavior: A Comparative Grounded Theory Analysis

ERIC Educational Resources Information Center

Gibson, Amelia N.

2013-01-01

This study examines the effect of experiential place and local community on information access and behavior for two communities of parents of children with Down syndrome. It uncovers substantive issues associated with health information seeking, government and education-related information access, and information overload and avoidance within the…

Pan-cancer analysis of somatic copy number alterations implicates IRS4 and IGF2 in enhancer hijacking

PubMed Central

Weischenfeldt, Joachim; Dubash, Taronish; Drainas, Alexandros P.; Mardin, Balca R.; Chen, Yuanyuan; Stütz, Adrian M.; Waszak, Sebastian M.; Bosco, Graziella; Halvorsen, Ann Rita; Raeder, Benjamin; Efthymiopoulos, Theocharis; Erkek, Serap; Siegl, Christine; Brenner, Hermann; Brustugun, Odd Terje; Dieter, Sebastian M.; Northcott, Paul A.; Petersen, Iver; Pfister, Stefan M.; Schneider, Martin; Solberg, Steinar K.; Thunissen, Erik; Weichert, Wilko; Zichner, Thomas; Thomas, Roman; Peifer, Martin; Helland, Aslaug; Ball, Claudia R.; Jechlinger, Martin; Sotillo, Rocio; Glimm, Hanno; Korbel, Jan O.

2018-01-01

Extensive prior research has focused on somatic copy-number alterations (SCNAs) affecting cancer genes, yet the extent to which recurrent SCNAs exert their influence through rearranging cis-regulatory elements remains unclear. Here, we present a framework for inferring cancer-related gene overexpression resulting from cis-regulatory element reorganization (e.g., enhancer hijacking), by integrating SCNAs, gene expression data, and information on chromatin interaction domains. Analysis of 7,416 cancer genomes uncovered several pan-cancer candidate genes, including IRS4, SMARCA1 and TERT. We demonstrate that IRS4 overexpression in lung cancer associates with recurrent deletions in cis, and present evidence supporting a tumor-promoting role. We additionally pursued cancer type-specific analyses, uncovering IGF2 as a target for enhancer hijacking in colorectal cancer. IGF2-containing tandem duplications result in the de novo formation of a 3D contact domain comprising IGF2 and a lineage-specific super-enhancer, which mediates high-level gene activation. Our framework enables systematic inference of cis-regulatory element rearrangements mediating dysregulation in cancer. PMID:27869826

Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100K

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

Gerlits, Oksana O.; Keen, David A.; Blakeley, Matthew P.

HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly altermore » the drug–enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.« less

Room temperature neutron crystallography of drug resistant HIV-1 protease uncovers limitations of X-ray structural analysis at 100K

DOE PAGES

Gerlits, Oksana O.; Keen, David A.; Blakeley, Matthew P.; ...

2017-02-14

HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly altermore » the drug–enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.« less

The Multimodal Assessment of Adult Attachment Security: Developing the Biometric Attachment Test.

PubMed

Parra, Federico; Miljkovitch, Raphaële; Persiaux, Gwenaelle; Morales, Michelle; Scherer, Stefan

2017-04-06

Attachment theory has been proven essential for mental health, including psychopathology, development, and interpersonal relationships. Validated psychometric instruments to measure attachment abound but suffer from shortcomings common to traditional psychometrics. Recent developments in multimodal fusion and machine learning pave the way for new automated and objective psychometric instruments for adult attachment that combine psychophysiological, linguistic, and behavioral analyses in the assessment of the construct. The aim of this study was to present a new exposure-based, automatic, and objective adult-attachment assessment, the Biometric Attachment Test (BAT), which exposes participants to a short standardized set of visual and music stimuli, whereas their immediate reactions and verbal responses, captured by several computer sense modalities, are automatically analyzed for scoring and classification. We also aimed to empirically validate two of its assumptions: its capacity to measure attachment security and the viability of using themes as placeholders for rotating stimuli. A total of 59 French participants from the general population were assessed using the Adult Attachment Questionnaire (AAQ), the Adult Attachment Projective Picture System (AAP), and the Attachment Multiple Model Interview (AMMI) as ground truth for attachment security. They were then exposed to three different BAT stimuli sets, whereas their faces, voices, heart rate (HR), and electrodermal activity (EDA) were recorded. Psychophysiological features, such as skin-conductance response (SCR) and Bayevsky stress index; behavioral features, such as gaze and facial expressions; as well as linguistic and paralinguistic features, were automatically extracted. An exploratory analysis was conducted using correlation matrices to uncover the features that are most associated with attachment security. A confirmatory analysis was conducted by creating a single composite effects index and by testing it for correlations with attachment security. The stability of the theory-consistent features across three different stimuli sets was explored using repeated measures analysis of variances (ANOVAs). In total, 46 theory-consistent correlations were found during the exploration (out of 65 total significant correlations). For example, attachment security as measured by the AAP was correlated with positive facial expressions (r=.36, P=.01). AMMI's security with the father was inversely correlated with the low frequency (LF) of HRV (r=-.87, P=.03). Attachment security to partners as measured by the AAQ was inversely correlated with anger facial expression (r=-.43, P=.001). The confirmatory analysis showed that the composite effects index was significantly correlated to security in the AAP (r=.26, P=.05) and the AAQ (r=.30, P=.04) but not in the AMMI. Repeated measures ANOVAs conducted individually on each of the theory-consistent features revealed that only 7 of the 46 (15%) features had significantly different values among responses to three different stimuli sets. We were able to validate two of the instrument's core assumptions: its capacity to measure attachment security and the viability of using themes as placeholders for rotating stimuli. Future validation of other of its dimensions, as well as the ongoing development of its scoring and classification algorithms is discussed. ©Federico Parra, Raphaële Miljkovitch, Gwenaelle Persiaux, Michelle Morales, Stefan Scherer. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 06.04.2017.

The Multimodal Assessment of Adult Attachment Security: Developing the Biometric Attachment Test

PubMed Central

Miljkovitch, Raphaële; Persiaux, Gwenaelle; Morales, Michelle; Scherer, Stefan

2017-01-01

Background Attachment theory has been proven essential for mental health, including psychopathology, development, and interpersonal relationships. Validated psychometric instruments to measure attachment abound but suffer from shortcomings common to traditional psychometrics. Recent developments in multimodal fusion and machine learning pave the way for new automated and objective psychometric instruments for adult attachment that combine psychophysiological, linguistic, and behavioral analyses in the assessment of the construct. Objective The aim of this study was to present a new exposure-based, automatic, and objective adult-attachment assessment, the Biometric Attachment Test (BAT), which exposes participants to a short standardized set of visual and music stimuli, whereas their immediate reactions and verbal responses, captured by several computer sense modalities, are automatically analyzed for scoring and classification. We also aimed to empirically validate two of its assumptions: its capacity to measure attachment security and the viability of using themes as placeholders for rotating stimuli. Methods A total of 59 French participants from the general population were assessed using the Adult Attachment Questionnaire (AAQ), the Adult Attachment Projective Picture System (AAP), and the Attachment Multiple Model Interview (AMMI) as ground truth for attachment security. They were then exposed to three different BAT stimuli sets, whereas their faces, voices, heart rate (HR), and electrodermal activity (EDA) were recorded. Psychophysiological features, such as skin-conductance response (SCR) and Bayevsky stress index; behavioral features, such as gaze and facial expressions; as well as linguistic and paralinguistic features, were automatically extracted. An exploratory analysis was conducted using correlation matrices to uncover the features that are most associated with attachment security. A confirmatory analysis was conducted by creating a single composite effects index and by testing it for correlations with attachment security. The stability of the theory-consistent features across three different stimuli sets was explored using repeated measures analysis of variances (ANOVAs). Results In total, 46 theory-consistent correlations were found during the exploration (out of 65 total significant correlations). For example, attachment security as measured by the AAP was correlated with positive facial expressions (r=.36, P=.01). AMMI’s security with the father was inversely correlated with the low frequency (LF) of HRV (r=−.87, P=.03). Attachment security to partners as measured by the AAQ was inversely correlated with anger facial expression (r=−.43, P=.001). The confirmatory analysis showed that the composite effects index was significantly correlated to security in the AAP (r=.26, P=.05) and the AAQ (r=.30, P=.04) but not in the AMMI. Repeated measures ANOVAs conducted individually on each of the theory-consistent features revealed that only 7 of the 46 (15%) features had significantly different values among responses to three different stimuli sets. Conclusions We were able to validate two of the instrument’s core assumptions: its capacity to measure attachment security and the viability of using themes as placeholders for rotating stimuli. Future validation of other of its dimensions, as well as the ongoing development of its scoring and classification algorithms is discussed. PMID:28385683

Characterization of dependencies between growth and division in budding yeast

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

Mayhew, Michael B.; Iversen, Edwin S.; Hartemink, Alexander J.

Cell growth and division are processes vital to the proliferation and development of life. Coordination between these two processes has been recognized for decades in a variety of organisms. In the budding yeast Saccharomyces cerevisiae, this coordination or ‘size control’ appears as an inverse correlation between cell size and the rate of cell-cycle progression, routinely observed in G1 prior to cell division commitment. Beyond this point, cells are presumed to complete S/G 2/M at similar rates and in a size-independent manner. As such, studies of dependence between growth and division have focused on G1. Moreover, in unicellular organisms, coordination betweenmore » growth and division has commonly been analyzed within the cycle of a single cell without accounting for correlations in growth and division characteristics between cycles of related cells. In a comprehensive analysis of three published time-lapse microscopy datasets, we analyze both intra- and inter-cycle dependencies between growth and division, revisiting assumptions about the coordination between these two processes. Interestingly, we find evidence (1) that S/G 2/M durations are systematically longer in daughters than in mothers, (2) of dependencies between S/G2/M and size at budding that echo the classical G1 dependencies, and, (3) in contrast with recent bacterial studies, of negative dependencies between size at birth and size accumulated during the cell cycle. In addition, we develop a novel hierarchical model to uncover inter-cycle dependencies, and we find evidence for such dependencies in cells growing in sugar-poor environments. Our analysis highlights the need for experimentalists and modelers to account for new sources of cell-to-cell variation in growth and division, and our model provides a formal statistical framework for the continued study of dependencies between biological processes.« less

Characterization of dependencies between growth and division in budding yeast

DOE PAGES

Mayhew, Michael B.; Iversen, Edwin S.; Hartemink, Alexander J.

2017-02-01

Cell growth and division are processes vital to the proliferation and development of life. Coordination between these two processes has been recognized for decades in a variety of organisms. In the budding yeast Saccharomyces cerevisiae, this coordination or ‘size control’ appears as an inverse correlation between cell size and the rate of cell-cycle progression, routinely observed in G1 prior to cell division commitment. Beyond this point, cells are presumed to complete S/G 2/M at similar rates and in a size-independent manner. As such, studies of dependence between growth and division have focused on G1. Moreover, in unicellular organisms, coordination betweenmore » growth and division has commonly been analyzed within the cycle of a single cell without accounting for correlations in growth and division characteristics between cycles of related cells. In a comprehensive analysis of three published time-lapse microscopy datasets, we analyze both intra- and inter-cycle dependencies between growth and division, revisiting assumptions about the coordination between these two processes. Interestingly, we find evidence (1) that S/G 2/M durations are systematically longer in daughters than in mothers, (2) of dependencies between S/G2/M and size at budding that echo the classical G1 dependencies, and, (3) in contrast with recent bacterial studies, of negative dependencies between size at birth and size accumulated during the cell cycle. In addition, we develop a novel hierarchical model to uncover inter-cycle dependencies, and we find evidence for such dependencies in cells growing in sugar-poor environments. Our analysis highlights the need for experimentalists and modelers to account for new sources of cell-to-cell variation in growth and division, and our model provides a formal statistical framework for the continued study of dependencies between biological processes.« less

Uncovering the Nutritional Landscape of Food

PubMed Central

Kim, Seunghyeon; Sung, Jaeyun; Foo, Mathias; Jin, Yong-Su; Kim, Pan-Jun

2015-01-01

Recent progresses in data-driven analysis methods, including network-based approaches, are revolutionizing many classical disciplines. These techniques can also be applied to food and nutrition, which must be studied to design healthy diets. Using nutritional information from over 1,000 raw foods, we systematically evaluated the nutrient composition of each food in regards to satisfying daily nutritional requirements. The nutrient balance of a food was quantified and termed nutritional fitness; this measure was based on the food’s frequency of occurrence in nutritionally adequate food combinations. Nutritional fitness offers a way to prioritize recommendable foods within a global network of foods, in which foods are connected based on the similarities of their nutrient compositions. We identified a number of key nutrients, such as choline and α-linolenic acid, whose levels in foods can critically affect the nutritional fitness of the foods. Analogously, pairs of nutrients can have the same effect. In fact, two nutrients can synergistically affect the nutritional fitness, although the individual nutrients alone may not have an impact. This result, involving the tendency among nutrients to exhibit correlations in their abundances across foods, implies a hidden layer of complexity when exploring for foods whose balance of nutrients within pairs holistically helps meet nutritional requirements. Interestingly, foods with high nutritional fitness successfully maintain this nutrient balance. This effect expands our scope to a diverse repertoire of nutrient-nutrient correlations, which are integrated under a common network framework that yields unexpected yet coherent associations between nutrients. Our nutrient-profiling approach combined with a network-based analysis provides a more unbiased, global view of the relationships between foods and nutrients, and can be extended towards nutritional policies, food marketing, and personalized nutrition. PMID:25768022

Characterization of dependencies between growth and division in budding yeast

PubMed Central

Iversen, Edwin S.; Hartemink, Alexander J.

2017-01-01

Cell growth and division are processes vital to the proliferation and development of life. Coordination between these two processes has been recognized for decades in a variety of organisms. In the budding yeast Saccharomyces cerevisiae, this coordination or ‘size control’ appears as an inverse correlation between cell size and the rate of cell-cycle progression, routinely observed in G1 prior to cell division commitment. Beyond this point, cells are presumed to complete S/G2/M at similar rates and in a size-independent manner. As such, studies of dependence between growth and division have focused on G1. Moreover, in unicellular organisms, coordination between growth and division has commonly been analysed within the cycle of a single cell without accounting for correlations in growth and division characteristics between cycles of related cells. In a comprehensive analysis of three published time-lapse microscopy datasets, we analyse both intra- and inter-cycle dependencies between growth and division, revisiting assumptions about the coordination between these two processes. Interestingly, we find evidence (i) that S/G2/M durations are systematically longer in daughters than in mothers, (ii) of dependencies between S/G2/M and size at budding that echo the classical G1 dependencies, and (iii) in contrast with recent bacterial studies, of negative dependencies between size at birth and size accumulated during the cell cycle. In addition, we develop a novel hierarchical model to uncover inter-cycle dependencies, and we find evidence for such dependencies in cells growing in sugar-poor environments. Our analysis highlights the need for experimentalists and modellers to account for new sources of cell-to-cell variation in growth and division, and our model provides a formal statistical framework for the continued study of dependencies between biological processes. PMID:28228543

Characterization of dependencies between growth and division in budding yeast.

PubMed

Mayhew, Michael B; Iversen, Edwin S; Hartemink, Alexander J

2017-02-01

Cell growth and division are processes vital to the proliferation and development of life. Coordination between these two processes has been recognized for decades in a variety of organisms. In the budding yeast Saccharomyces cerevisiae , this coordination or 'size control' appears as an inverse correlation between cell size and the rate of cell-cycle progression, routinely observed in G 1 prior to cell division commitment. Beyond this point, cells are presumed to complete S/G 2 /M at similar rates and in a size-independent manner. As such, studies of dependence between growth and division have focused on G 1 Moreover, in unicellular organisms, coordination between growth and division has commonly been analysed within the cycle of a single cell without accounting for correlations in growth and division characteristics between cycles of related cells. In a comprehensive analysis of three published time-lapse microscopy datasets, we analyse both intra- and inter-cycle dependencies between growth and division, revisiting assumptions about the coordination between these two processes. Interestingly, we find evidence (i) that S/G 2 /M durations are systematically longer in daughters than in mothers, (ii) of dependencies between S/G 2 /M and size at budding that echo the classical G 1 dependencies, and (iii) in contrast with recent bacterial studies, of negative dependencies between size at birth and size accumulated during the cell cycle. In addition, we develop a novel hierarchical model to uncover inter-cycle dependencies, and we find evidence for such dependencies in cells growing in sugar-poor environments. Our analysis highlights the need for experimentalists and modellers to account for new sources of cell-to-cell variation in growth and division, and our model provides a formal statistical framework for the continued study of dependencies between biological processes. © 2017 The Author(s).

Induction of acute hepatic injury by endotoxin in mice.

PubMed

Xie, Guo-Qi; Jiang, Jian-Xin; Chen, Yong-Hua; Liu, Da-Wei; Zhu, Pei-Fang; Wang, Zheng-Guo

2002-11-01

To investigate the changes of scavenger receptor (SR) and CD14 in Kupffer cells in endotoxemia in order to uncover the mechanism of the liver to turn a defense organ into effector one in sepsis. Mouse models of endotoxemia of different severity were reproduced by injection of different doses of lipopolysaccharide (LPS) via the tail vein. The expression of SR and CD14 in the liver was assayed by immunohistochemistry and was subsequently analyzed with an image analysis system. The levels of TNF-alpha and IL-6 in liver tissue were determined with ELISA. The expression of SR in the liver in the high-dose group was markedly decreased one hour after injection of LPS, and also in the low-dose group at 3 hours. The expression of SR in the liver in the two groups was shown to be progressively decreased with the time prolonged. There was significant difference in average optical density (OD) values of SR between the two groups. The expression of CD14 in the two groups was shown to be significantly increased one hour after injection of LPS, and more significantly with the time prolonged. But there was no significant difference in OD values of CD14 between the two groups. The contents of intrahepatic proinflammatory mediators TNF-alpha, IL-6, ALT and TBIL were significantly increased after injection of LPS. Correlation analysis revealed that the changes of TNF-alpha, IL-6, ALT, and TBIL were negatively correlated with the expression of SR, and positively with the expression of CD14. The up-regulation of CD14 expression and down-regulation of SR expression on Kupffer cells might be one of the important mechanisms for the conversion of Kupffer cells from immune defensive to inflammatory response cells in acute hepatic injury.

Earth Science Data Analytics: Preparing for Extracting Knowledge from Information

NASA Technical Reports Server (NTRS)

Kempler, Steven; Barbieri, Lindsay

2016-01-01

Data analytics is the process of examining large amounts of data of a variety of types to uncover hidden patterns, unknown correlations and other useful information. Data analytics is a broad term that includes data analysis, as well as an understanding of the cognitive processes an analyst uses to understand problems and explore data in meaningful ways. Analytics also include data extraction, transformation, and reduction, utilizing specific tools, techniques, and methods. Turning to data science, definitions of data science sound very similar to those of data analytics (which leads to a lot of the confusion between the two). But the skills needed for both, co-analyzing large amounts of heterogeneous data, understanding and utilizing relevant tools and techniques, and subject matter expertise, although similar, serve different purposes. Data Analytics takes on a practitioners approach to applying expertise and skills to solve issues and gain subject knowledge. Data Science, is more theoretical (research in itself) in nature, providing strategic actionable insights and new innovative methodologies. Earth Science Data Analytics (ESDA) is the process of examining, preparing, reducing, and analyzing large amounts of spatial (multi-dimensional), temporal, or spectral data using a variety of data types to uncover patterns, correlations and other information, to better understand our Earth. The large variety of datasets (temporal spatial differences, data types, formats, etc.) invite the need for data analytics skills that understand the science domain, and data preparation, reduction, and analysis techniques, from a practitioners point of view. The application of these skills to ESDA is the focus of this presentation. The Earth Science Information Partners (ESIP) Federation Earth Science Data Analytics (ESDA) Cluster was created in recognition of the practical need to facilitate the co-analysis of large amounts of data and information for Earth science. Thus, from a to advance science point of view: On the continuum of ever evolving data management systems, we need to understand and develop ways that allow for the variety of data relationships to be examined, and information to be manipulated, such that knowledge can be enhanced, to facilitate science. Recognizing the importance and potential impacts of the unlimited ways to co-analyze heterogeneous datasets, now and especially in the future, one of the objectives of the ESDA cluster is to facilitate the preparation of individuals to understand and apply needed skills to Earth science data analytics. Pinpointing and communicating the needed skills and expertise is new, and not easy. Information technology is just beginning to provide the tools for advancing the analysis of heterogeneous datasets in a big way, thus, providing opportunity to discover unobvious scientific relationships, previously invisible to the science eye. And it is not easy It takes individuals, or teams of individuals, with just the right combination of skills to understand the data and develop the methods to glean knowledge out of data and information. In addition, whereas definitions of data science and big data are (more or less) available (summarized in Reference 5), Earth science data analytics is virtually ignored in the literature, (barring a few excellent sources).

A Modularity-Based Method Reveals Mixed Modules from Chemical-Gene Heterogeneous Network

PubMed Central

Song, Jianglong; Tang, Shihuan; Liu, Xi; Gao, Yibo; Yang, Hongjun; Lu, Peng

2015-01-01

For a multicomponent therapy, molecular network is essential to uncover its specific mode of action from a holistic perspective. The molecular system of a Traditional Chinese Medicine (TCM) formula can be represented by a 2-class heterogeneous network (2-HN), which typically includes chemical similarities, chemical-target interactions and gene interactions. An important premise of uncovering the molecular mechanism is to identify mixed modules from complex chemical-gene heterogeneous network of a TCM formula. We thus proposed a novel method (MixMod) based on mixed modularity to detect accurate mixed modules from 2-HNs. At first, we compared MixMod with Clauset-Newman-Moore algorithm (CNM), Markov Cluster algorithm (MCL), Infomap and Louvain on benchmark 2-HNs with known module structure. Results showed that MixMod was superior to other methods when 2-HNs had promiscuous module structure. Then these methods were tested on a real drug-target network, in which 88 disease clusters were regarded as real modules. MixMod could identify the most accurate mixed modules from the drug-target 2-HN (normalized mutual information 0.62 and classification accuracy 0.4524). In the end, MixMod was applied to the 2-HN of Buchang naoxintong capsule (BNC) and detected 49 mixed modules. By using enrichment analysis, we investigated five mixed modules that contained primary constituents of BNC intestinal absorption liquid. As a matter of fact, the findings of in vitro experiments using BNC intestinal absorption liquid were found to highly accord with previous analysis. Therefore, MixMod is an effective method to detect accurate mixed modules from chemical-gene heterogeneous networks and further uncover the molecular mechanism of multicomponent therapies, especially TCM formulae. PMID:25927435

Clustering high-dimensional mixed data to uncover sub-phenotypes: joint analysis of phenotypic and genotypic data.

PubMed

McParland, D; Phillips, C M; Brennan, L; Roche, H M; Gormley, I C

2017-12-10

The LIPGENE-SU.VI.MAX study, like many others, recorded high-dimensional continuous phenotypic data and categorical genotypic data. LIPGENE-SU.VI.MAX focuses on the need to account for both phenotypic and genetic factors when studying the metabolic syndrome (MetS), a complex disorder that can lead to higher risk of type 2 diabetes and cardiovascular disease. Interest lies in clustering the LIPGENE-SU.VI.MAX participants into homogeneous groups or sub-phenotypes, by jointly considering their phenotypic and genotypic data, and in determining which variables are discriminatory. A novel latent variable model that elegantly accommodates high dimensional, mixed data is developed to cluster LIPGENE-SU.VI.MAX participants using a Bayesian finite mixture model. A computationally efficient variable selection algorithm is incorporated, estimation is via a Gibbs sampling algorithm and an approximate BIC-MCMC criterion is developed to select the optimal model. Two clusters or sub-phenotypes ('healthy' and 'at risk') are uncovered. A small subset of variables is deemed discriminatory, which notably includes phenotypic and genotypic variables, highlighting the need to jointly consider both factors. Further, 7 years after the LIPGENE-SU.VI.MAX data were collected, participants underwent further analysis to diagnose presence or absence of the MetS. The two uncovered sub-phenotypes strongly correspond to the 7-year follow-up disease classification, highlighting the role of phenotypic and genotypic factors in the MetS and emphasising the potential utility of the clustering approach in early screening. Additionally, the ability of the proposed approach to define the uncertainty in sub-phenotype membership at the participant level is synonymous with the concepts of precision medicine and nutrition. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

A bibliometric analysis of natural language processing in medical research.

PubMed

Chen, Xieling; Xie, Haoran; Wang, Fu Lee; Liu, Ziqing; Xu, Juan; Hao, Tianyong

2018-03-22

Natural language processing (NLP) has become an increasingly significant role in advancing medicine. Rich research achievements of NLP methods and applications for medical information processing are available. It is of great significance to conduct a deep analysis to understand the recent development of NLP-empowered medical research field. However, limited study examining the research status of this field could be found. Therefore, this study aims to quantitatively assess the academic output of NLP in medical research field. We conducted a bibliometric analysis on NLP-empowered medical research publications retrieved from PubMed in the period 2007-2016. The analysis focused on three aspects. Firstly, the literature distribution characteristics were obtained with a statistics analysis method. Secondly, a network analysis method was used to reveal scientific collaboration relations. Finally, thematic discovery and evolution was reflected using an affinity propagation clustering method. There were 1405 NLP-empowered medical research publications published during the 10 years with an average annual growth rate of 18.39%. 10 most productive publication sources together contributed more than 50% of the total publications. The USA had the highest number of publications. A moderately significant correlation between country's publications and GDP per capita was revealed. Denny, Joshua C was the most productive author. Mayo Clinic was the most productive affiliation. The annual co-affiliation and co-country rates reached 64.04% and 15.79% in 2016, respectively. 10 main great thematic areas were identified including Computational biology, Terminology mining, Information extraction, Text classification, Social medium as data source, Information retrieval, etc. CONCLUSIONS: A bibliometric analysis of NLP-empowered medical research publications for uncovering the recent research status is presented. The results can assist relevant researchers, especially newcomers in understanding the research development systematically, seeking scientific cooperation partners, optimizing research topic choices and monitoring new scientific or technological activities.

Robust validation of approximate 1-matrix functionals with few-electron harmonium atoms

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

Cioslowski, Jerzy, E-mail: jerzy@wmf.univ.szczecin.pl; Piris, Mario; Matito, Eduard

2015-12-07

A simple comparison between the exact and approximate correlation components U of the electron-electron repulsion energy of several states of few-electron harmonium atoms with varying confinement strengths provides a stringent validation tool for 1-matrix functionals. The robustness of this tool is clearly demonstrated in a survey of 14 known functionals, which reveals their substandard performance within different electron correlation regimes. Unlike spot-testing that employs dissociation curves of diatomic molecules or more extensive benchmarking against experimental atomization energies of molecules comprising some standard set, the present approach not only uncovers the flaws and patent failures of the functionals but, even moremore » importantly, also allows for pinpointing their root causes. Since the approximate values of U are computed at exact 1-densities, the testing requires minimal programming and thus is particularly suitable for rapid screening of new functionals.« less

Survival of influenza A virus on contaminated student clothing

PubMed Central

IKEDA, KEIKO; TSUJIMOTO, KAZUKO; SUZUKI, YUKIKO; KOYAMA, AUGUSTINE HAJIME

2015-01-01

The role of contaminated clothing in the transmission of influenza A virus during an epidemic period was investigated by examining the recovery of infectious influenza virus from experimentally virus-contaminated clothing, which had been subejected to routine wearing and washing for several months or years. The amount of infectious virus recovered from the nine types of clothing decreased with time and was shown to differ widely between clothing samples, when the contaminated clothing samples were maintained in uncovered glass Petri dishes in a safety cabinet under air blowing. These results indicate a dependence of virus transmissibility on the nature of the contaminated clothes. The difference in recovery was shown to have no significant correlation with the thickness or the materials of the clothing; however, a correlation was observed with the residual amount of water in the deposited virus preparation on the test clothing. PMID:25780410

Three-stage stochastic pump: Another type of Onsager-Casimir symmetry and results far from equilibrium

NASA Astrophysics Data System (ADS)

Rosas, Alexandre; Van den Broeck, Christian; Lindenberg, Katja

2018-06-01

The stochastic thermodynamic analysis of a time-periodic single particle pump sequentially exposed to three thermochemical reservoirs is presented. The analysis provides explicit results for flux, thermodynamic force, entropy production, work, and heat. These results apply near equilibrium as well as far from equilibrium. In the linear response regime, a different type of Onsager-Casimir symmetry is uncovered. The Onsager matrix becomes symmetric in the limit of zero dissipation.

Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling

PubMed Central

Li, Xia; Rao, Shaoqi; Jiang, Wei; Li, Chuanxing; Xiao, Yun; Guo, Zheng; Zhang, Qingpu; Wang, Lihong; Du, Lei; Li, Jing; Li, Li; Zhang, Tianwen; Wang, Qing K

2006-01-01

Background It is one of the ultimate goals for modern biological research to fully elucidate the intricate interplays and the regulations of the molecular determinants that propel and characterize the progression of versatile life phenomena, to name a few, cell cycling, developmental biology, aging, and the progressive and recurrent pathogenesis of complex diseases. The vast amount of large-scale and genome-wide time-resolved data is becoming increasing available, which provides the golden opportunity to unravel the challenging reverse-engineering problem of time-delayed gene regulatory networks. Results In particular, this methodological paper aims to reconstruct regulatory networks from temporal gene expression data by using delayed correlations between genes, i.e., pairwise overlaps of expression levels shifted in time relative each other. We have thus developed a novel model-free computational toolbox termed TdGRN (Time-delayed Gene Regulatory Network) to address the underlying regulations of genes that can span any unit(s) of time intervals. This bioinformatics toolbox has provided a unified approach to uncovering time trends of gene regulations through decision analysis of the newly designed time-delayed gene expression matrix. We have applied the proposed method to yeast cell cycling and human HeLa cell cycling and have discovered most of the underlying time-delayed regulations that are supported by multiple lines of experimental evidence and that are remarkably consistent with the current knowledge on phase characteristics for the cell cyclings. Conclusion We established a usable and powerful model-free approach to dissecting high-order dynamic trends of gene-gene interactions. We have carefully validated the proposed algorithm by applying it to two publicly available cell cycling datasets. In addition to uncovering the time trends of gene regulations for cell cycling, this unified approach can also be used to study the complex gene regulations related to the development, aging and progressive pathogenesis of a complex disease where potential dependences between different experiment units might occurs. PMID:16420705

Using a system of differential equations that models cattle growth to uncover the genetic basis of complex traits.

PubMed

Freua, Mateus Castelani; Santana, Miguel Henrique de Almeida; Ventura, Ricardo Vieira; Tedeschi, Luis Orlindo; Ferraz, José Bento Sterman

2017-08-01

The interplay between dynamic models of biological systems and genomics is based on the assumption that genetic variation of the complex trait (i.e., outcome of model behavior) arises from component traits (i.e., model parameters) in lower hierarchical levels. In order to provide a proof of concept of this statement for a cattle growth model, we ask whether model parameters map genomic regions that harbor quantitative trait loci (QTLs) already described for the complex trait. We conducted a genome-wide association study (GWAS) with a Bayesian hierarchical LASSO method in two parameters of the Davis Growth Model, a system of three ordinary differential equations describing DNA accretion, protein synthesis and degradation, and fat synthesis. Phenotypic and genotypic data were available for 893 Nellore (Bos indicus) cattle. Computed values for parameter k 1 (DNA accretion rate) ranged from 0.005 ± 0.003 and for α (constant for energy for maintenance requirement) 0.134 ± 0.024. The expected biological interpretation of the parameters is confirmed by QTLs mapped for k 1 and α. QTLs within genomic regions mapped for k 1 are expected to be correlated with the DNA pool: body size and weight. Single nucleotide polymorphisms (SNPs) which were significant for α mapped QTLs that had already been associated with residual feed intake, feed conversion ratio, average daily gain (ADG), body weight, and also dry matter intake. SNPs identified for k 1 were able to additionally explain 2.2% of the phenotypic variability of the complex ADG, even when SNPs for k 1 did not match the genomic regions associated with ADG. Although improvements are needed, our findings suggest that genomic analysis on component traits may help to uncover the genetic basis of more complex traits, particularly when lower biological hierarchies are mechanistically described by mathematical simulation models.

On interrelations of recurrences and connectivity trends between stock indices

NASA Astrophysics Data System (ADS)

Goswami, B.; Ambika, G.; Marwan, N.; Kurths, J.

2012-09-01

Financial data has been extensively studied for correlations using Pearson's cross-correlation coefficient ρ as the point of departure. We employ an estimator based on recurrence plots - the correlation of probability of recurrence (CPR) - to analyze connections between nine stock indices spread worldwide. We suggest a slight modification of the CPR approach in order to get more robust results. We examine trends in CPR for an approximately 19-month window moved along the time series and compare them to trends in ρ. Binning CPR into three levels of connectedness (strong, moderate, and weak), we extract the trends in number of connections in each bin over time. We also look at the behavior of CPR during the dot-com bubble by shifting the time series to align their peaks. CPR mainly uncovers that the markets move in and out of periods of strong connectivity erratically, instead of moving monotonically towards increasing global connectivity. This is in contrast to ρ, which gives a picture of ever-increasing correlation. CPR also exhibits that time-shifted markets have high connectivity around the dot-com bubble of 2000. We use significance tests using twin surrogates to interpret all the measures estimated in the study.

Consistency relations for sharp inflationary non-Gaussian features

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

Mooij, Sander; Palma, Gonzalo A.; Panotopoulos, Grigoris

If cosmic inflation suffered tiny time-dependent deviations from the slow-roll regime, these would induce the existence of small scale-dependent features imprinted in the primordial spectra, with their shapes and sizes revealing information about the physics that produced them. Small sharp features could be suppressed at the level of the two-point correlation function, making them undetectable in the power spectrum, but could be amplified at the level of the three-point correlation function, offering us a window of opportunity to uncover them in the non-Gaussian bispectrum. In this article, we show that sharp features may be analyzed using only data coming frommore » the three point correlation function parametrizing primordial non-Gaussianity. More precisely, we show that if features appear in a particular non-Gaussian triangle configuration (e.g. equilateral, folded, squeezed), these must reappear in every other configuration according to a specific relation allowing us to correlate features across the non-Gaussian bispectrum. As a result, we offer a method to study scale-dependent features generated during inflation that depends only on data coming from measurements of non-Gaussianity, allowing us to omit data from the power spectrum.« less

General and Domain-Specific Contributions to Creative Ideation and Creative Performance

PubMed Central

An, Donggun; Runco, Mark A.

2016-01-01

The general objective of this study was to reexamine two views of creativity, one positing that there is a general creative capacity or talent and the other that creativity is domain-specific. These two views were compared by (a) testing correlations among measures of domain-general and domain-specific creativity and (b) examining how the general and the specific measures was each related to indices of knowledge, motivation, and personality. Participants were 147 college students enrolled in a foreign language course. Data were collected on participants’ domain knowledge, motivation, and creative personality, as well as four measures representing “General or Domain-Specific Creative Ideation” or “Creative Performance and Activity”. Results indicated that the four measures of creativity were correlated with one another, except for “General Performance and Activity” and “Domain-Specific Ideation.” A canonical correlation indicated that knowledge, motivation, and personality were significantly correlated with the four creativity measures (Rc = .49, p < .01). Multiple regressions uncovered particular relationships consistent with the view that creativity has both general and domain-specific contributions. Limitations, such as the focus on one domain, and future directions are discussed. PMID:27872664

Partially covered versus uncovered self-expandable nitinol stents with anti-migration properties for the palliation of malignant distal biliary obstruction: A randomized controlled trial.

PubMed

Yang, Min Jae; Kim, Jin Hong; Yoo, Byung Moo; Hwang, Jae Chul; Yoo, Jun Hwan; Lee, Ki Seong; Kang, Joon Koo; Kim, Soon Sun; Lim, Sun Gyo; Shin, Sung Jae; Cheong, Jae Youn; Lee, Kee Myung; Lee, Kwang Jae; Cho, Sung Won

2015-01-01

Covered self-expandable metal stents (SEMSs) are increasingly used as alternatives to uncovered SEMSs for the palliation of inoperable malignant distal biliary obstruction to counteract tumor ingrowth. We aimed to compare the outcomes of partially covered and uncovered SEMSs with identical mesh structures and anti-migration properties, such as low axial force and flared ends. One hundred and three patients who were diagnosed with inoperable malignant distal biliary obstruction between January 2006 and August 2013 were randomly assigned to either the partially covered (n = 51) or uncovered (n = 52) SEMS group. There were no significant differences in the cumulative stent patency, overall patient survival, stent dysfunction-free survival and overall adverse events, including pancreatitis and cholecystitis, between the two groups. Compared to the uncovered group, stent migration (5.9% vs. 0%, p = 0.118) and tumor overgrowth (7.8% vs. 1.9%, p = 0.205) were non-significantly more frequent in the partially covered group, whereas tumor ingrowth showed a significantly higher incidence in the uncovered group (5.9% vs. 19.2%, p = 0.041). Stent migration in the partially covered group occurred only in patients with short stenosis of the utmost distal bile duct (two in ampullary cancer, one in bile duct cancer), and did not occur in any patients with pancreatic cancer. For the palliation of malignant distal biliary obstruction, endoscopic placement of partially covered SEMSs with anti-migration designs and identical mesh structures to uncovered SEMSs failed to prolong cumulative stent patency or reduce stent migration.

Intellectual property analysis of holographic materials business

NASA Astrophysics Data System (ADS)

Reingand, Nadya; Hunt, David

2006-02-01

The paper presents an overview of intellectual property in the field of holographic photosensitive materials and highlights the possibilities offered by patent searching and analysis. Thousands of patent documents relevant to holographic materials have been uncovered by the study. The search was performed in the following databases: U.S. Patent Office, European Patent Office, and Japanese Patent Office for the time frame of 1971 through November 2005. The patent analysis has unveiled trends in patent temporal distribution, leading IP portfolios, companies competition within the holographic materials market and other interesting insights.

Intellectual property (IP) analysis of embossed hologram business

NASA Astrophysics Data System (ADS)

Hunt, David; Reingand, Nadya; Cantrell, Robert

2006-02-01

This paper presents an overview of patents and patent applications on security embossed holograms, and highlights the possibilities offered by patent searching and analysis. Thousands of patent documents relevant to embossed holograms were uncovered by the study. The search was performed in the following databases: U.S. Patent Office, European Patent Office, Japanese Patent Office and Korean Patent Office for the time frame from 1971 through November 2005. The patent analysis unveils trends in patent temporal distribution, patent families formation, significant technological coverage within the embossed holography market and other interesting insights.

An Optimization-Driven Analysis Pipeline to Uncover Biomarkers and Signaling Paths: Cervix Cancer.

PubMed

Lorenzo, Enery; Camacho-Caceres, Katia; Ropelewski, Alexander J; Rosas, Juan; Ortiz-Mojer, Michael; Perez-Marty, Lynn; Irizarry, Juan; Gonzalez, Valerie; Rodríguez, Jesús A; Cabrera-Rios, Mauricio; Isaza, Clara

2015-06-01

Establishing how a series of potentially important genes might relate to each other is relevant to understand the origin and evolution of illnesses, such as cancer. High-throughput biological experiments have played a critical role in providing information in this regard. A special challenge, however, is that of trying to conciliate information from separate microarray experiments to build a potential genetic signaling path. This work proposes a two-step analysis pipeline, based on optimization, to approach meta-analysis aiming to build a proxy for a genetic signaling path.

Comparative analysis reveals the underlying mechanism of vertebrate seasonal reproduction.

PubMed

Ikegami, Keisuke; Yoshimura, Takashi

2016-02-01

Animals utilize photoperiodic changes as a calendar to regulate seasonal reproduction. Birds have highly sophisticated photoperiodic mechanisms and functional genomics analysis in quail uncovered the signal transduction pathway regulating avian seasonal reproduction. Birds detect light with deep brain photoreceptors. Long day (LD) stimulus induces secretion of thyroid-stimulating hormone (TSH) from the pars tuberalis (PT) of the pituitary gland. PT-derived TSH locally activates thyroid hormone (TH) in the hypothalamus, which induces gonadotropin-releasing hormone (GnRH) and hence gonadotropin secretion. However, during winter, low temperatures increase serum TH for adaptive thermogenesis, which accelerates germ cell apoptosis by activating the genes involved in metamorphosis. Therefore, TH has a dual role in the regulation of seasonal reproduction. Studies using TSH receptor knockout mice confirmed the involvement of PT-derived TSH in mammalian seasonal reproduction. In addition, studies in mice revealed that the tissue-specific glycosylation of TSH diversifies its function in the circulation to avoid crosstalk. In contrast to birds and mammals, one of the molecular machineries necessary for the seasonal reproduction of fish are localized in the saccus vasculosus from the photoreceptor to the neuroendocrine output. Thus, comparative analysis is a powerful tool to uncover the universality and diversity of fundamental properties in various organisms. Copyright © 2015 Elsevier Inc. All rights reserved.

Exact Mesonic Eightfold Way From Dynamics and Confinement in Strongly Coupled Lattice QCD

NASA Astrophysics Data System (ADS)

Neto, A. Francisco; O'Carroll, M.; Faria da Veiga, P. A.

2009-01-01

We review our results on the exact determination of the mesonic eightfold way from first principles, directly from the quark-gluon dynamics. For this, we consider an imaginary-time functional integral formulation of 3 + 1 dimensional lattice QCD with Wilson action, three flavors, SU(3) f flavor symmetry and SU(3) c local gauge symmetry. We work in the strong coupling regime: a small hopping parameter κ>0 and a much smaller plaquette coupling β>0. By establishing a Feynman-Kac formula and a spectral representation to the two-meson correlation, we provide a rigorous connection between this correlation and the one-meson energy-momentum spectrum. The particle states can be labeled by the usual SU(3) f quantum numbers of total isospin I and its third-component I3, the quadratic Casimir C2 and, by a partial restoration of the continuous rotational symmetry on the lattice, as well as by the total spin J and its z-component Jz. We show that, up to near the two-meson energy threshold of ≈-4lnκ, the spectrum in the meson sector is given only by isolated dispersion curves of the eightfold way mesons. The mesons have all asymptotic mass of -2lnκ and, by deriving convergent expansions for the masses both in κ and β, we also show a κ mass splitting between the J=0,1 states. The splitting persists for β≠0. Our approach employs the decoupling of hyperplane method to uncover the basic excitations, complex analysis to determine the dispersion curves and a correlation subtraction method to show the curves are isolated. Using the latter and recalling our similar results for baryons, we also show confinement up to near the two-meson threshold.

Effect of Phototherapy on the Reliability of Transcutaneous Bilirubin Devices in Term and Near-Term Infants: A Systematic Review and Meta-Analysis.

PubMed

Nagar, Gaurav; Vandermeer, Ben; Campbell, Sandy; Kumar, Manoj

2016-01-01

Transcutaneous bilirubin (TcB) devices are commonly used for screening of hyperbilirubinemia in term and near-term infants not exposed to phototherapy. However, the accuracy of TcB devices in infants exposed to phototherapy is unclear. To conduct a systematic review of studies comparing TcB devices with total serum bilirubin (TSB) in infants receiving phototherapy or in the postphototherapy phase. MEDLINE, EMBASE, Cochrane Library, CINAHL and Scopus databases (from inception to May 8, 2014) were searched. Additional citations were identified from the bibliography of selected articles and from the abstracts of conference proceedings. The studies were included if they compared TcB results with TSB in term and near-term infants during phototherapy or after discontinuation of phototherapy. Two reviewers independently assessed studies for inclusion, and discrepancies were resolved with consensus. Risk of bias was assessed using the QUADAS-2 tool. Fourteen studies were identified. The pooled estimates of correlation coefficients (r) during phototherapy were: covered sites 0.71 (95% CI 0.64-0.77, 11 studies), uncovered sites 0.65 (95% CI 0.55-0.74), 8 studies), forehead 0.70 (95% CI 0.64-0.75, 12 studies) and sternum 0.64 (95% CI 0.43-0.77, 5 studies). Two studies also provided results as Bland-Altman difference plots (mean TcB-TSB differences -29.2 and 30 µmol/l, respectively). The correlation coefficient improved marginally in the postphototherapy phase (r = 0.72, 95% CI 0.64-0.78, 4 studies). We found a moderate correlation between TcB and TSB during phototherapy with a marginal improvement in the postphototherapy phase. Further research is needed before the use of TcB devices can be recommended for these settings. © 2016 S. Karger AG, Basel.

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key.

PubMed

Haupt, V Joachim; Daminelli, Simone; Schroeder, Michael

2013-01-01

Drug repositioning applies established drugs to new disease indications with increasing success. A pre-requisite for drug repurposing is drug promiscuity (polypharmacology) - a drug's ability to bind to several targets. There is a long standing debate on the reasons for drug promiscuity. Based on large compound screens, hydrophobicity and molecular weight have been suggested as key reasons. However, the results are sometimes contradictory and leave space for further analysis. Protein structures offer a structural dimension to explain promiscuity: Can a drug bind multiple targets because the drug is flexible or because the targets are structurally similar or even share similar binding sites? We present a systematic study of drug promiscuity based on structural data of PDB target proteins with a set of 164 promiscuous drugs. We show that there is no correlation between the degree of promiscuity and ligand properties such as hydrophobicity or molecular weight but a weak correlation to conformational flexibility. However, we do find a correlation between promiscuity and structural similarity as well as binding site similarity of protein targets. In particular, 71% of the drugs have at least two targets with similar binding sites. In order to overcome issues in detection of remotely similar binding sites, we employed a score for binding site similarity: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary structural binding site alignments. Three representative examples, namely the anti-cancer drug methotrexate, the natural product quercetin and the anti-diabetic drug acarbose are discussed in detail. Our findings suggest that global structural and binding site similarity play a more important role to explain the observed drug promiscuity in the PDB than physicochemical drug properties like hydrophobicity or molecular weight. Additionally, we find ligand flexibility to have a minor influence.

Characterizing the (Perceived) Newsworthiness of Health Science Articles: A Data-Driven Approach.

PubMed

Zhang, Ye; Willis, Erin; Paul, Michael J; Elhadad, Noémie; Wallace, Byron C

2016-09-22

Health science findings are primarily disseminated through manuscript publications. Information subsidies are used to communicate newsworthy findings to journalists in an effort to earn mass media coverage and further disseminate health science research to mass audiences. Journal editors and news journalists then select which news stories receive coverage and thus public attention. This study aims to identify attributes of published health science articles that correlate with (1) journal editor issuance of press releases and (2) mainstream media coverage. We constructed four novel datasets to identify factors that correlate with press release issuance and media coverage. These corpora include thousands of published articles, subsets of which received press release or mainstream media coverage. We used statistical machine learning methods to identify correlations between words in the science abstracts and press release issuance and media coverage. Further, we used a topic modeling-based machine learning approach to uncover latent topics predictive of the perceived newsworthiness of science articles. Both press release issuance for, and media coverage of, health science articles are predictable from corresponding journal article content. For the former task, we achieved average areas under the curve (AUCs) of 0.666 (SD 0.019) and 0.882 (SD 0.018) on two separate datasets, comprising 3024 and 10,760 articles, respectively. For the latter task, models realized mean AUCs of 0.591 (SD 0.044) and 0.783 (SD 0.022) on two datasets-in this case containing 422 and 28,910 pairs, respectively. We reported most-predictive words and topics for press release or news coverage. We have presented a novel data-driven characterization of content that renders health science "newsworthy." The analysis provides new insights into the news coverage selection process. For example, it appears epidemiological papers concerning common behaviors (eg, alcohol consumption) tend to receive media attention.

Traditional neuropsychological correlates and reliability of the automated neuropsychological assessment metrics-4 battery for Parkinson's disease.

PubMed

Hawkins, Keith A; Jennings, Danna; Vincent, Andrea S; Gilliland, Kirby; West, Adrienne; Marek, Kenneth

2012-08-01

The automated neuropsychological assessment metrics battery-4 for PD offers the promise of a computerized approach to cognitive assessment. To assess its utility, the ANAM4-PD was administered to 72 PD patients and 24 controls along with a traditional battery. Reliability was assessed by retesting 26 patients. The cognitive efficiency score (CES; a global score) exhibited high reliability (r = 0.86). Constituent variables exhibited lower reliability. The CES correlated strongly with the traditional battery global score, but displayed weaker relationships to UPDRS scores than the traditional score. Multivariate analysis of variance revealed a significant difference between the patient and control groups in ANAM4-PD performance, with three ANAM4-PD tests, math, tower, and pursuit tracking, displaying sizeable differences. In discriminant analyses these variables were as effective as the total ANAM4-PD in classifying cases designated as impaired based on traditional variables. Principal components analyses uncovered fewer factors in the ANAM4-PD relative to the traditional battery. ANAM4-PD variables correlated at higher levels with traditional motor and processing speed variables than with untimed executive, intellectual or memory variables. The ANAM4-PD displays high global reliability, but variable subtest reliability. The battery assesses a narrower range of cognitive functions than traditional tests, and discriminates between patients and controls less effectively. Three ANAM4-PD tests, pursuit tracking, math, and tower performed as well as the total ANAM4-PD in classifying patients as cognitively impaired. These findings could guide the refinement of the ANAM4-PD as an efficient method of screening for mild to moderate cognitive deficits in PD patients. Copyright © 2012 Elsevier Ltd. All rights reserved.

A Comparison of Saudi and Canadian Children's Knowledge of the Causes of Learning Difficulties

ERIC Educational Resources Information Center

Felimban, Huda; Nowicki, Elizabeth A.; Dare, Lynn; Brown, Jason

2016-01-01

In this comparative study, students from inclusive schools in Canada and Saudi Arabia shared their beliefs about factors associated with learning difficulties. Qualitative data were collected through interviews with 36 Canadian and 62 Saudi elementary students in Grades 5 and 6. Thematic analysis uncovered six themes: lack of knowledge,…

Fostering Gender Equity in Schools through Reflective Professional Development: A Critical Analysis of Teacher Perspectives

ERIC Educational Resources Information Center

Towery, Ila Deshmukh

2007-01-01

The continued persistence of sexism and institutional gender bias in schools is well documented. The empirical research in this area has uncovered a host of negative outcomes associated with gender inequity for all children. Research suggests that schools provide an excellent forum in which issues of gender inequities may be examined and…

"The Teacher Is an Octopus": Uncovering Preservice English Language Teachers' Prior Beliefs through Metaphor Analysis

ERIC Educational Resources Information Center

Farrell, Thomas S. C.

2006-01-01

Preservice teachers come to any teacher education course with prior experiences, knowledge and beliefs about learning and teaching. Additionally, the belief systems of preservice teachers often serve as a lens through which they view the content of the teacher education program. Consequently, it is essential that teacher educators take these prior…

L1 to Teach L2: Complexities and Contradictions

ERIC Educational Resources Information Center

Copland, Fiona; Neokleous, Georgios

2011-01-01

This article uncovers the complexities and contradictions inherent in making decisions about L1 use in the English language classroom. Through an analysis of data from classrooms in a Cypriot context and from interviews with Cypriot teachers, a number of functions for L1 use are identified, as are the teachers' rationales for using L1 for…

Root and shoot transcriptome analysis of two ecotypes of Noccaea caerulescens uncovers the role of NcNramp1 in Cd hyperaccumulation

USDA-ARS?s Scientific Manuscript database

The Zn/Cd hyperaccumulator, Noccaea caerulescens, has been studied extensively for its ability to accumulate Zn and Cd in its leaves to extremely high levels. Previous studies have indicated that the Zn and Cd hyperaccumulation trait exhibited by this species involves different transport and toleran...

Applying Physics Concepts--Uncovering the Gender Differences in Assessment of Performance Unit Results.

ERIC Educational Resources Information Center

Bransky, Judith; Qualter, Anne

1993-01-01

Describes the findings of secondary analysis of data from the Assessment of Performance Unit (APU) Science. The most striking feature of the study is the extremely low level of scores obtained for questions which invite a written response. The results also clearly show the consistent negative reaction of girls to the technical context of…

Chronotopes and Timespace Contexts: Academic Identity Work Revealed in Narrative Fiction

ERIC Educational Resources Information Center

Pick, David; Symons, Christine; Teo, Stephen T. T.

2017-01-01

In this paper, academic identity work is explored through an examination of its portrayal in a work of narrative fiction using a conceptual tool from literary studies. It is found that such an approach provides insights that would otherwise be difficult to uncover by more conventional methods. The analysis reveals academic identity work as an…

Synthetic-Creative Intelligence and Psychometric Intelligence: Analysis of the Threshold Theory and Creative Process

ERIC Educational Resources Information Center

Ferrando, Mercedes; Soto, Gloria; Prieto, Lola; Sáinz, Marta; Ferrándiz, Carmen

2016-01-01

There has been an increasing body of research to uncover the relationship between creativity and intelligence. This relationship usually has been examined using traditional measures of intelligence and seldom using new approaches (i.e. Ferrando et al. 2005). In this work, creativity is measured by tools developed based on Sternberg's successful…

What Are They Thinking? Automated Analysis of Student Writing about Acid-Base Chemistry in Introductory Biology

ERIC Educational Resources Information Center

Haudek, Kevin C.; Prevost, Luanna B.; Moscarella, Rosa A.; Merrill, John; Urban-Lurain, Mark

2012-01-01

Students' writing can provide better insight into their thinking than can multiple-choice questions. However, resource constraints often prevent faculty from using writing assessments in large undergraduate science courses. We investigated the use of computer software to analyze student writing and to uncover student ideas about chemistry in an…

The Lived Experiences of Students at Risk of Dropping Out: An Interpretive Phenomenological Analysis

ERIC Educational Resources Information Center

Robinson, Kellie D.

2014-01-01

Of the many important issues facing policy makers, educators, concerned citizens and parents throughout this country, one stands apart: the alarming number of teenagers who choose to drop out of school. While considerable research exists substantiating the statistics for this societal predicament, studies that seek to uncover the individual human…

The Pennsylvania State University Child Sexual Abuse Scandal: An Analysis of Institutional Factors Affecting Response

ERIC Educational Resources Information Center

Holland, Alice R.

2015-01-01

The outcomes of The Pennsylvania State University (Penn State) child sexual abuse scandal have left many scholars and individuals questioning the university's collective identity. The goal of this research was to uncover the dominant themes that describe a problematic institutional response to the child sexual abuse incidents in order to provide…

Go Ask Alice: Uncovering the Role of a University Partner in an Informal Science Curriculum Support Network

ERIC Educational Resources Information Center

Baker-Doyle, Kira J.

2013-01-01

This article describes a study from the Linking Instructors Networks of Knowledge in Science Education project, which aims to examine the informal science curriculum support networks of teachers in a school-university curriculum reform partnership. We used social network analysis and qualitative methods to reveal characteristics of the informal…

Principals' Conceptions of Instructional Leadership and Their Informal Social Networks: An Exploration of the Mechanisms of the Mesolevel

ERIC Educational Resources Information Center

Rigby, Jessica G.

2016-01-01

First-year principals encounter multiple messages about what it means to be instructional leaders; this may matter for how they enact instructional leadership. This cross-case qualitative study uses a qualitative approach of social network analysis to uncover the mechanisms through which first-year principals encountered particular beliefs about…

National Suicide Rates a Century after Durkheim: Do We Know Enough to Estimate Error?

ERIC Educational Resources Information Center

Claassen, Cynthia A.; Yip, Paul S.; Corcoran, Paul; Bossarte, Robert M.; Lawrence, Bruce A.; Currier, Glenn W.

2010-01-01

Durkheim's nineteenth-century analysis of national suicide rates dismissed prior concerns about mortality data fidelity. Over the intervening century, however, evidence documenting various types of error in suicide data has only mounted, and surprising levels of such error continue to be routinely uncovered. Yet the annual suicide rate remains the…

Uncovering Categories of Civically Engaged College Students: A Latent Class Analysis

ERIC Educational Resources Information Center

Weerts, David J.; Cabrera, Alberto F.; Mejias, Paulina Perez

2014-01-01

Various commissions and reports have called on colleges and universities to better prepare students for participation in a democratic society. A limit of such reports is that they often fail to consider how students might be categorized relative to their shared patterns of civic behaviors. Relying on alumni survey data from American College…

What Motivates Biology Instructors to Engage and Persist in Teaching Professional Development?

ERIC Educational Resources Information Center

McCourt, Jill S.; Andrews, Tessa C.; Knight, Jennifer K.; Merrill, John E.; Nehm, Ross H.; Pelletreau, Karen N.; Prevost, Luanna B.; Smith, Michelle K.; Urban-Lurain, Mark; Lemons, Paula P.

2017-01-01

We conducted a study of 19 biology instructors participating in small, local groups at six research-intensive universities connected to the Automated Analysis of Constructed Response (AACR) project (www.msu.edu/~aacr). Our aim was to uncover participants' motivation to persist in a long-term teaching professional development effort, a topic that…

Transcriptome analysis of a Ustilago maydis ust1 deletion mutant uncovers involvement of laccase and polyketide synthase genes in spore development

USDA-ARS?s Scientific Manuscript database

Ustilago maydis, causal agent of corn smut disease, is a dimorphic fungus alternating between a saprobic budding haploid, and an obligate pathogenic filamentous dikaryon. Maize responds to U. maydis colonization by producing tumorous structures, and only within these does the fungus sporulate, produ...

The Relevance of Interlanguage and Pidginization to French Immersion Schooling. Research Report 81-07.

ERIC Educational Resources Information Center

Parkin, Michael

Research on the language development of children in immersion programs has uncovered a certain amount of data. Immersion students have less well developed productive skills than their francophone peers and passive receptive skills which approach those of francophones. Error analysis studies have found that immersion students reach a plateau in…

Commenting to Learn: Evidence of Language and Intercultural Learning in Comments on YouTube Videos

ERIC Educational Resources Information Center

Benson, Phil

2015-01-01

It is often observed that the globalization of social media has opened up new opportunities for informal intercultural communication and foreign language learning. This study aims to go beyond this general observation through a case study that explores how discourse analysis tools might be used to uncover evidence of language and intercultural…

Are Two Minds Better than One? Creativity and Teacher Education

ERIC Educational Resources Information Center

Roberge, Ginette D.; Gagnon, Lissa L.

2012-01-01

When students are directly engaged in group activities, what factors make it more likely that group work will serve as a conduit to creativity? And--since working with groups means working with people--does the concept of "two minds are better than one" lead to greater creativity? An analysis of student teacher narratives uncovered six main,…

A Quantitative Analysis of Organizational Factors That Relate to Data Mining Success

ERIC Educational Resources Information Center

Huebner, Richard A.

2017-01-01

The ubiquity of data in various forms has fueled the need for advanced data-mining techniques within organizations. The advent of data mining methods used to uncover hidden nuggets of information buried within large data sets has also fueled the need for determining how these unique projects can be successful. There are many challenges associated…

Transcriptome analysis and identification of genes associated with omega-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens

USDA-ARS?s Scientific Manuscript database

Background: Perilla (Perilla frutescens (L.) var frutescens) produces high levels of a-linolenic acid (ALA), an omega-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cD...

Life-Metaphors among Colombian Medical Students: Uncovering Core Values and Educational Implications

ERIC Educational Resources Information Center

Hoffman, Edward; Acosta-Orozco, Catalina; Compton, William C.

2015-01-01

The present study utilized metaphor analysis to examine the core values of Colombian medical students. The entire 9th semester medical class of 60 students was invited to respond to a structured questionnaire. It asked participants to state their preferred life-metaphor, whether they had always preferred this metaphor since childhood or…

Whose Immigration Story?: Attending to Hidden Messages of Material in Social Studies

ERIC Educational Resources Information Center

Oikonomidoy, Eleni; Williams, Gwendolyn

2010-01-01

Sometimes materials used in schools with good intentions can have effects opposite from those stated. Through the microscopic analysis of a parent-student immigration interview assignment on a social studies unit on immigration, this article aims to uncover the hidden story that underlies the questions asked. In so doing, it intends not only to…

Proteoglycan concentrations in healthy and diseased articular cartilage by Fourier transform infrared imaging and principal component regression

NASA Astrophysics Data System (ADS)

Yin, Jianhua; Xia, Yang

2014-12-01

Fourier transform infrared imaging (FTIRI) combining with principal component regression (PCR) analysis were used to determine the reduction of proteoglycan (PG) in articular cartilage after the transection of the anterior cruciate ligament (ACL). A number of canine knee cartilage sections were harvested from the meniscus-covered and meniscus-uncovered medial tibial locations from the control joints, the ACL joints at three time points after the surgery, and their contralateral joints. The PG loss in the ACL cartilage was related positively to the durations after the surgery. The PG loss in the contralateral knees was less than that of the ACL knees. The PG loss in the meniscus-covered cartilage was less than that of the meniscus-uncovered tissue in both ACL and contralateral knees. The quantitative mapping of PG loss could monitor the disease progression and repair processes in arthritis.

Use of a three-color chromosome in situ suppression technique for the detection of past radiation exposure

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

Gebhart, E.; Neubauer, S.; Schmitt, G.

1996-01-01

A three-color chromosome in situ suppression technique and classical cytogenetic analysis were compared for the detection of chromosomal aberrations in blood lymphocytes of 27 patients who had undergone radiation therapies from 1 month to 9 years ago. Depending on the respective regimens of therapy, a high variability was found in the aberration data. Aberration rates depended on the interval between exposure and scoring rather than on the locally applied radiation doses, which were rather uniform among most patients. Chromosome in situ suppression was found to be superior to classical cytogenetics with respect not only to the spectrum of detectable aberrationsmore » but also to the uncovering of long-term effects of irradiation. Of particular interest were the relative stability of the frequency of radiation-induced reciprocal translocations and the utility of chromosome in situ suppression to uncover complex rearrangements. 27 refs., 4 figs.« less

Integrative mouse and human mRNA studies using WGCNA nominates novel candidate genes involved in the pathogenesis of major depressive disorder.

PubMed

Malki, Karim; Tosto, Maria Grazia; Jumabhoy, Irfan; Lourdusamy, Anbarasu; Sluyter, Frans; Craig, Ian; Uher, Rudolf; McGuffin, Peter; Schalkwyk, Leonard C

2013-12-01

This study aims to identify novel genes associated with major depressive disorder and pharmacological treatment response using animal and human mRNA studies. Weighted gene coexpression network analysis was used to uncover genes associated with stress factors in mice and to inform mRNA probe set selection in a post-mortem study of depression. A total of 171 genes were found to be differentially regulated in response to both early and late stress protocols in a mouse study. Ten human genes, orthologous to mouse genes differentially expressed by stress, were also found to be dysregulated in depressed cases in a human post-mortem brain study from the Stanley Foundation Brain Collection. Several novel genes associated with depression were uncovered, including NOVA1 and USP9X. Moreover, we found further evidence in support of hippocampal neurogenesis and peripheral inflammation in major depressive disorder.

SBLOCA outside containment at Browns Ferry Unit One: accident sequence analysis. [Small break

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

Condon, W.A.; Harrington, R.M.; Greene, S.R.

1982-11-01

This study describes the predicted response of Unit 1 at the Browns Ferry Nuclear Plant to a postulated small-break loss-of-coolant accident outside of the primary containment. The break has been assumed to occur in the scram discharge volume piping immediately following a reactor scram that cannot be reset. The events before core uncovering are discussed for both the worst-case accident sequence without operator action and for the more likely sequences with operator action. Without operator action, the events after core uncovering would include core meltdown and subsequent containment failure, and this event sequence has been determined through use of themore » MARCH code. An estimate of the magnitude and timing of the concomitant release of the noble gas, cesium, and iodine-based fission products to the environment is provided in Volume 2 of this report.« less

Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map.

PubMed

Yoo, Minjae; Shin, Jimin; Kim, Hyunmin; Kim, Jihye; Kang, Jaewoo; Tan, Aik Choon

2018-04-04

Traditional Chinese Medicine (TCM) has been practiced over thousands of years in China and other Asian countries for treating various symptoms and diseases. However, the underlying molecular mechanisms of TCM are poorly understood, partly due to the "multi-component, multi-target" nature of TCM. To uncover the molecular mechanisms of TCM, we perform comprehensive gene expression analysis using connectivity map. We interrogated gene expression signatures obtained 102 TCM components using the next generation Connectivity Map (CMap) resource. We performed systematic data mining and analysis on the mechanism of action (MoA) of these TCM components based on the CMap results. We clustered the 102 TCM components into four groups based on their MoAs using next generation CMap resource. We performed gene set enrichment analysis on these components to provide additional supports for explaining these molecular mechanisms. We also provided literature evidence to validate the MoAs identified through this bioinformatics analysis. Finally, we developed the Traditional Chinese Medicine Drug Repurposing Hub (TCM Hub) - a connectivity map resource to facilitate the elucidation of TCM MoA for drug repurposing research. TCMHub is freely available in http://tanlab.ucdenver.edu/TCMHub. Molecular mechanisms of TCM could be uncovered by using gene expression signatures and connectivity map. Through this analysis, we identified many of the TCM components possess diverse MoAs, this may explain the applications of TCM in treating various symptoms and diseases. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Systems analysis of apoptotic priming in ovarian cancer identifies vulnerabilities and predictors of drug response.

PubMed

Zervantonakis, Ioannis K; Iavarone, Claudia; Chen, Hsing-Yu; Selfors, Laura M; Palakurthi, Sangeetha; Liu, Joyce F; Drapkin, Ronny; Matulonis, Ursula; Leverson, Joel D; Sampath, Deepak; Mills, Gordon B; Brugge, Joan S

2017-08-28

The lack of effective chemotherapies for high-grade serous ovarian cancers (HGS-OvCa) has motivated a search for alternative treatment strategies. Here, we present an unbiased systems-approach to interrogate a panel of 14 well-annotated HGS-OvCa patient-derived xenografts for sensitivity to PI3K and PI3K/mTOR inhibitors and uncover cell death vulnerabilities. Proteomic analysis reveals that PI3K/mTOR inhibition in HGS-OvCa patient-derived xenografts induces both pro-apoptotic and anti-apoptotic signaling responses that limit cell killing, but also primes cells for inhibitors of anti-apoptotic proteins. In-depth quantitative analysis of BCL-2 family proteins and other apoptotic regulators, together with computational modeling and selective anti-apoptotic protein inhibitors, uncovers new mechanistic details about apoptotic regulators that are predictive of drug sensitivity (BIM, caspase-3, BCL-X L ) and resistance (MCL-1, XIAP). Our systems-approach presents a strategy for systematic analysis of the mechanisms that limit effective tumor cell killing and the identification of apoptotic vulnerabilities to overcome drug resistance in ovarian and other cancers.High-grade serous ovarian cancers (HGS-OvCa) frequently develop chemotherapy resistance. Here, the authors through a systematic analysis of proteomic and drug response data of 14 HGS-OvCa PDXs demonstrate that targeting apoptosis regulators can improve response of these tumors to inhibitors of the PI3K/mTOR pathway.

Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns.

PubMed

Zhou, Hao; Yan, Bing; Chen, Shun; Wang, Mingshu; Jia, Renyong; Cheng, Anchun

2015-10-01

Tembusu virus (TMUV) is a single-stranded, positive-sense RNA virus. As reported, TMUV infection has resulted in significant poultry losses, and the virus may also pose a threat to public health. To characterize TMUV evolutionarily and to understand the factors accounting for codon usage properties, we performed, for the first time, a comprehensive analysis of codon usage bias for the genomes of 60 TMUV strains. The most recently published TMUV strains were found to be widely distributed in coastal cities of southeastern China. Codon preference among TMUV genomes exhibits a low bias (effective number of codons (ENC)=53.287) and is maintained at a stable level. ENC-GC3 plots and the high correlation between composition constraints and principal component factor analysis of codon usage demonstrated that mutation pressure dominates over natural selection pressure in shaping the TMUV coding sequence composition. The high correlation between the major components of the codon usage pattern and hydrophobicity (Gravy) or aromaticity (Aromo) was obvious, indicating that properties of viral proteins also account for the observed variation in TMUV codon usage. Principal component analysis (PCA) showed that CQW1 isolated from Chongqing may have evolved from GX2013H or GX2013G isolated from Guangxi, thus indicating that TMUV likely disseminated from southeastern China to the mainland. Moreover, the preferred codons encoding eight amino acids were consistent with the optimal codons for human cells, indicating that TMUV may pose a threat to public health due to possible cross-species transmission (birds to birds or birds to humans). The results of this study not only have theoretical value for uncovering the characteristics of synonymous codon usage patterns in TMUV genomes but also have significant meaning with regard to the molecular evolutionary tendencies of TMUV. Copyright © 2015 Elsevier B.V. All rights reserved.

Network analysis of surgical innovation: Measuring value and the virality of diffusion in robotic surgery.

PubMed

Garas, George; Cingolani, Isabella; Panzarasa, Pietro; Darzi, Ara; Athanasiou, Thanos

2017-01-01

Existing surgical innovation frameworks suffer from a unifying limitation, their qualitative nature. A rigorous approach to measuring surgical innovation is needed that extends beyond detecting simply publication, citation, and patent counts and instead uncovers an implementation-based value from the structure of the entire adoption cascades produced over time by diffusion processes. Based on the principles of evidence-based medicine and existing surgical regulatory frameworks, the surgical innovation funnel is described. This illustrates the different stages through which innovation in surgery typically progresses. The aim is to propose a novel and quantitative network-based framework that will permit modeling and visualizing innovation diffusion cascades in surgery and measuring virality and value of innovations. Network analysis of constructed citation networks of all articles concerned with robotic surgery (n = 13,240, Scopus®) was performed (1974-2014). The virality of each cascade was measured as was innovation value (measured by the innovation index) derived from the evidence-based stage occupied by the corresponding seed article in the surgical innovation funnel. The network-based surgical innovation metrics were also validated against real world big data (National Inpatient Sample-NIS®). Rankings of surgical innovation across specialties by cascade size and structural virality (structural depth and width) were found to correlate closely with the ranking by innovation value (Spearman's rank correlation coefficient = 0.758 (p = 0.01), 0.782 (p = 0.008), 0.624 (p = 0.05), respectively) which in turn matches the ranking based on real world big data from the NIS® (Spearman's coefficient = 0.673;p = 0.033). Network analysis offers unique new opportunities for understanding, modeling and measuring surgical innovation, and ultimately for assessing and comparing generative value between different specialties. The novel surgical innovation metrics developed may prove valuable especially in guiding policy makers, funding bodies, surgeons, and healthcare providers in the current climate of competing national priorities for investment.

Network analysis of surgical innovation: Measuring value and the virality of diffusion in robotic surgery

PubMed Central

Cingolani, Isabella; Panzarasa, Pietro; Darzi, Ara; Athanasiou, Thanos

2017-01-01

Background Existing surgical innovation frameworks suffer from a unifying limitation, their qualitative nature. A rigorous approach to measuring surgical innovation is needed that extends beyond detecting simply publication, citation, and patent counts and instead uncovers an implementation-based value from the structure of the entire adoption cascades produced over time by diffusion processes. Based on the principles of evidence-based medicine and existing surgical regulatory frameworks, the surgical innovation funnel is described. This illustrates the different stages through which innovation in surgery typically progresses. The aim is to propose a novel and quantitative network-based framework that will permit modeling and visualizing innovation diffusion cascades in surgery and measuring virality and value of innovations. Materials and methods Network analysis of constructed citation networks of all articles concerned with robotic surgery (n = 13,240, Scopus®) was performed (1974–2014). The virality of each cascade was measured as was innovation value (measured by the innovation index) derived from the evidence-based stage occupied by the corresponding seed article in the surgical innovation funnel. The network-based surgical innovation metrics were also validated against real world big data (National Inpatient Sample–NIS®). Results Rankings of surgical innovation across specialties by cascade size and structural virality (structural depth and width) were found to correlate closely with the ranking by innovation value (Spearman’s rank correlation coefficient = 0.758 (p = 0.01), 0.782 (p = 0.008), 0.624 (p = 0.05), respectively) which in turn matches the ranking based on real world big data from the NIS® (Spearman’s coefficient = 0.673;p = 0.033). Conclusion Network analysis offers unique new opportunities for understanding, modeling and measuring surgical innovation, and ultimately for assessing and comparing generative value between different specialties. The novel surgical innovation metrics developed may prove valuable especially in guiding policy makers, funding bodies, surgeons, and healthcare providers in the current climate of competing national priorities for investment. PMID:28841648

Near-infrared spectroscopy during stagnant ischemia estimates central venous oxygen saturation and mixed venous oxygen saturation discrepancy in patients with severe left heart failure and additional sepsis/septic shock.

PubMed

Mozina, Hugo; Podbregar, Matej

2010-01-01

Discrepancies of 5-24% between superior vena cava oxygen saturation (ScvO2) and mixed venous oxygen saturation (SvO2) have been reported in patients with severe heart failure. Thenar muscle tissue oxygenation (StO2) measured with near-infrared spectroscopy (NIRS) during arterial occlusion testing decreases slower in sepsis/septic shock patients (lower StO2 deoxygenation rate). The StO2 deoxygenation rate is influenced by dobutamine. The aim of this study was to determine the relationship between the StO2 deoxygenation rate and the ScvO2-SvO2 discrepancy in patients with severe left heart failure and additional sepsis/septic shock treated with or without dobutamine. Fifty-two patients with severe left heart failure due to primary heart disease with additional severe sepsis/septic shock were included. SvO2 and ScvO2 were compared to the thenar muscle StO2 before and during arterial occlusion. SvO2 correlated significantly with ScvO2 (Pearson correlation 0.659, P = 0.001), however, Bland Altman analysis showed a clinically important difference between both variables (ScvO2-SvO2 mean 72 +/- 8%, ScvO2-SvO2 difference 9.4 +/- 7.5%). The ScvO2-SvO2 difference correlated with plasma lactate (Pearson correlation 0.400, P = 0.003) and the StO2 deoxygenation rate (Pearson correlation 0.651, P = 0.001). In the group of patients treated with dobutamine, the ScvO2-SvO2 difference correlated with plasma lactate (Pearson correlation 0.389, P = 0.011) and the StO2 deoxygenation rate (Pearson correlation 0.777, P = 0.0001). In patients with severe heart failure with additional severe sepsis/septic shock the ScvO2-SvO2 discrepancy presents a clinical problem. In these patients the skeletal muscle StO2 deoxygenation rate is inversely proportional to the difference between ScvO2 and SvO2; dobutamine does not influence this relationship. When using ScvO2 as a treatment goal, the NIRS measurement may prove to be a useful non-invasive diagnostic test to uncover patients with a normal ScvO2 but potentially an abnormally low SvO2. NCT00384644 ClinicalTrials.Gov.

Activity-based protein profiling for biochemical pathway discovery in cancer

PubMed Central

Nomura, Daniel K.; Dix, Melissa M.; Cravatt, Benjamin F.

2011-01-01

Large-scale profiling methods have uncovered numerous gene and protein expression changes that correlate with tumorigenesis. However, determining the relevance of these expression changes and which biochemical pathways they affect has been hindered by our incomplete understanding of the proteome and its myriad functions and modes of regulation. Activity-based profiling platforms enable both the discovery of cancer-relevant enzymes and selective pharmacological probes to perturb and characterize these proteins in tumour cells. When integrated with other large-scale profiling methods, activity-based proteomics can provide insight into the metabolic and signalling pathways that support cancer pathogenesis and illuminate new strategies for disease diagnosis and treatment. PMID:20703252

Numerically exact full counting statistics of the nonequilibrium Anderson impurity model

NASA Astrophysics Data System (ADS)

Ridley, Michael; Singh, Viveka N.; Gull, Emanuel; Cohen, Guy

2018-03-01

The time-dependent full counting statistics of charge transport through an interacting quantum junction is evaluated from its generating function, controllably computed with the inchworm Monte Carlo method. Exact noninteracting results are reproduced; then, we continue to explore the effect of electron-electron interactions on the time-dependent charge cumulants, first-passage time distributions, and n -electron transfer distributions. We observe a crossover in the noise from Coulomb blockade to Kondo-dominated physics as the temperature is decreased. In addition, we uncover long-tailed spin distributions in the Kondo regime and analyze queuing behavior caused by correlations between single-electron transfer events.

Numerically exact full counting statistics of the nonequilibrium Anderson impurity model

DOE PAGES

Ridley, Michael; Singh, Viveka N.; Gull, Emanuel; ...

2018-03-06

The time-dependent full counting statistics of charge transport through an interacting quantum junction is evaluated from its generating function, controllably computed with the inchworm Monte Carlo method. Exact noninteracting results are reproduced; then, we continue to explore the effect of electron-electron interactions on the time-dependent charge cumulants, first-passage time distributions, and n-electron transfer distributions. We observe a crossover in the noise from Coulomb blockade to Kondo-dominated physics as the temperature is decreased. In addition, we uncover long-tailed spin distributions in the Kondo regime and analyze queuing behavior caused by correlations between single-electron transfer events

Medical dosimetry in Hungary

NASA Astrophysics Data System (ADS)

Turák, O.; Osvay, M.; Ballay, L.

2012-09-01

Radiation exposure of medical staff during cardiological and radiological procedures was investigated. The exposure of medical staff is directly connected to patient exposure. The aim of this study was to determine the distribution of doses on uncovered part of body of medical staff using LiF thermoluminescent (TL) dosimeters in seven locations. Individual Kodak film dosimeters (as authorized dosimetry system) were used for the assessment of medical staff's effective dose. Results achieved on dose distribution measurements confirm that wearing only one film badge under the lead apron does not provide enough information on the personal dose. The value of estimated annual doses on eye lens and extremities (fingers) were in good correlation with international publications.

Numerically exact full counting statistics of the nonequilibrium Anderson impurity model

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

Ridley, Michael; Singh, Viveka N.; Gull, Emanuel

The time-dependent full counting statistics of charge transport through an interacting quantum junction is evaluated from its generating function, controllably computed with the inchworm Monte Carlo method. Exact noninteracting results are reproduced; then, we continue to explore the effect of electron-electron interactions on the time-dependent charge cumulants, first-passage time distributions, and n-electron transfer distributions. We observe a crossover in the noise from Coulomb blockade to Kondo-dominated physics as the temperature is decreased. In addition, we uncover long-tailed spin distributions in the Kondo regime and analyze queuing behavior caused by correlations between single-electron transfer events

Personality traits and educational identity formation in late adolescents: longitudinal associations and academic progress.

PubMed

Klimstra, Theo A; Luyckx, Koen; Germeijs, Veerle; Meeus, Wim H J; Goossens, Luc

2012-03-01

Changes in personality traits in late adolescence and young adulthood are believed to co-occur with changes in identity, but little research is available that supports this hypothesis. The present study addressed this relatively understudied area of research by examining longitudinal associations of Big Five personality traits (i.e., Neuroticism, Extraversion, Openness, Agreeableness, and Conscientiousness) with dimensions of identity formation (i.e., identification with commitment and exploration in depth) in the domain of education. For this purpose, we used four annual waves of longitudinal data on 485 Belgian late adolescents (87.4% female; mean age at T1 = 18.6 years) covering a 3-year period. Multivariate growth models revealed that changes in Big Five personality traits were related to changes in identification with commitment and exploration in depth. Cross-lagged panel models uncovered that, except for Openness, all Big Five traits predicted educational identity dimensions. Educational identity dimensions only predicted Neuroticism. In addition, adolescents with higher levels on the personality trait of Conscientiousness faced fewer study delays. In sum, the present study adds to the growing literature that explores the antecedents, correlates, and consequences of personality trait development by uncovering the interplay of personality traits, educational identity dimensions, and academic progress in late adolescents.

A low-pungency S3212 genotype of Capsicum frutescens caused by a mutation in the putative aminotransferase (p-AMT) gene.

PubMed

Park, Young-Jun; Nishikawa, Tomotaro; Minami, Mineo; Nemoto, Kazuhiro; Iwasaki, Tomohiro; Matsushima, Kenichi

2015-12-01

The purpose of this study was to identify the genetic mechanism underlying capsinoid biosynthesis in S3212, a low-pungency genotype of Capsicum frutescens. Screening of C. frutescens accessions for capsaicinoid and capsiate contents by high-performance liquid chromatography revealed that low-pungency S3212 contained high levels of capsiate but no capsaicin. Comparison of DNA coding sequences of pungent (T1 and Bird Eye) and low-pungency (S3212) genotypes uncovered a significant 12-bp deletion mutation in exon 7 of the p-AMT gene of S3212. In addition, p-AMT gene transcript levels in placental tissue were positively correlated with the degree of pungency. S3212, the low-pungency genotype, exhibited no significant p-AMT transcript levels, whereas T1, one of the pungent genotypes, displayed high transcript levels of this gene. We therefore conclude that the deletion mutation in the p-AMT gene is related to the loss of pungency in placental tissue and has given rise to the low-pungency S3212 C. frutescens genotype. C. frutescens S3212 represents a good natural source of capsinoids. Finally, our basic characterization of the uncovered p-AMT gene mutation should contribute to future studies of capsinoid biosynthesis in Capsicum.

Using the Theory of Planned Behavior as a Framework for the Evaluation of a Professional Development Workshop

PubMed Central

PATTERSON, ROBIN R.

2001-01-01

This purpose of this study was to use a theoretical framework based on several decades of attitudinal research to assess the intentions of Microbial Discovery Workshop participants to incorporate the inquiry activities presented at the workshop into their curricula, to evaluate the participants actual use of these activities after the workshop, and to uncover the barriers and enablers the participants faced in doing so. As a framework, the theory of planned behavior was ascertained to be an appropriate means of assessment and it was revealed that participants’ intention to use the workshop activities significantly correlated with their actual use. The participants’ attitudes toward using the activities influenced their use more than the participants’ perceptions of the social pressures that would influence their decision to use the activities or their belief as to how easy or difficult it would be to incorporate a given activity. The participants were found to be highly self-efficacious pertaining to their ability to implement the activities, but perceived self-efficacy was not a significant predictor of the participants’ intentions to incorporate the activities into their teaching-learning repertoire. The study also uncovered other behaviors the participants displayed as a result of attending the workshop consistent with the goals and objectives of the workshop organizers. PMID:23653542

Neuropsychological exploration of alleged mold neurotoxicity.

PubMed

Reinhard, Matthew J; Satz, Paul; Scaglione, Cris A; D'Elia, Louis F; Rassovsky, Yuri; Arita, Anthony A; Hinkin, Charles H; Thrasher, Delaney; Ordog, Gary

2007-05-01

Cognitive and emotional correlates of toxic mold exposure and potential dose-response effects for both outcomes were investigated. Self-reported length of exposure, time since last exposure, and serum immunoglobulin (IgG) levels were assessed. Despite CNS complaints often seen with mold exposed individuals, overall results did not uncover concomitant cognitive deficits suggested in previous studies or a significant reduction in intellectual functioning. Fewer subjects were excluded as result of failing effort/motivation assessment than expected. Correlations of IgG and cognitive function are discussed. A dose-effect for self-reported length of exposure and cognitive outcome was not seen. The sample's overall Minnesota Multiphasic Personality Inventory II (MMPI-2) profile indicated elevations on scales 1, 2, 3, 7 and 8. MMPI-2 clinical scales 1 and 3 were significantly correlated with length of exposure. The MMPI-2 may be sensitive to increasing physical and emotional sequelae as length of exposure increases. A potential subgroup of cognitively impaired outliers within mold exposure litigants is explored. Limitations of self-reported and objective measurements for mold exposure and exploratory statistical methodology are discussed.

Dependence of the correlated-momentum patterns in double ionization on the carrier-envelope phase and intensity of a few-cycle laser pulse

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

Xin, G. G.; Ye, D. F.; Graduate School, China Academy of Engineering Physics, Beijing 100088

2010-12-15

In the present paper, we investigate the correlated electron emission of atoms irradiated by a few-cycle laser pulse, with emphasis on the correlated longitudinal momentum spectra. We find that the spectra show clear v-shaped structures, in analogy to what was observed recently in long-pulse experiments. Moreover, the patterns of the spectra depend sensitively on the carrier-envelope phase as well as the laser intensity. The v-shaped structure is more pronounced at lower and higher intensities and becomes obscure at medium intensity. At a lower intensity, upon change of the phase from 0 to {pi}/2, the v-shaped structure shifts from the firstmore » quadrant to the third quadrant and the ratios between the double ionization yields in the first and third quadrants are found to increase by a few orders of magnitude. The semiclassical rescattering model is exploited in the preceding calculations and the underlying mechanisms are uncovered by analyzing the subcycle dynamics of classical trajectories.« less

Transient and permanent changes in DNA methylation patterns in inorganic arsenic-mediated epithelial-to-mesenchymal transition.

PubMed

Eckstein, Meredith; Rea, Matthew; Fondufe-Mittendorf, Yvonne N

2017-09-15

Chronic low dose inorganic arsenic exposure causes cells to take on an epithelial-to-mesenchymal phenotype, which is a crucial process in carcinogenesis. Inorganic arsenic is not a mutagen and thus epigenetic alterations have been implicated in this process. Indeed, during the epithelial-to-mesenchymal transition, morphologic changes to cells correlate with changes in chromatin structure and gene expression, ultimately driving this process. However, studies on the effects of inorganic arsenic exposure/withdrawal on the epithelial-to-mesenchymal transition and the impact of epigenetic alterations in this process are limited. In this study we used high-resolution microarray analysis to measure the changes in DNA methylation in cells undergoing inorganic arsenic-induced epithelial-to-mesenchymal transition, and on the reversal of this process, after removal of the inorganic arsenic exposure. We found that cells exposed to chronic, low-dose inorganic arsenic exposure showed 30,530 sites were differentially methylated, and with inorganic arsenic withdrawal several differential methylated sites were reversed, albeit not completely. Furthermore, these changes in DNA methylation mainly correlated with changes in gene expression at most sites tested but not at all. This study suggests that DNA methylation changes on gene expression are not clear-cut and provide a platform to begin to uncover the relationship between DNA methylation and gene expression, specifically within the context of inorganic arsenic treatment. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Reward anticipation in the adolescent and aging brain.

PubMed

Lorenz, Robert C; Gleich, Tobias; Beck, Anne; Pöhland, Lydia; Raufelder, Diana; Sommer, Werner; Rapp, Michael A; Kühn, Simone; Gallinat, Jürgen

2014-10-01

Processing of reward is the basis of adaptive behavior of the human being. Neural correlates of reward processing seem to be influenced by developmental changes from adolescence to late adulthood. The aim of this study is to uncover these neural correlates during a slot machine gambling task across the lifespan. Therefore, we used functional magnetic resonance imaging to investigate 102 volunteers in three different age groups: 34 adolescents, 34 younger adults, and 34 older adults. We focused on the core reward areas ventral striatum (VS) and ventromedial prefrontal cortex (VMPFC), the valence processing associated areas, anterior cingulate cortex (ACC) and insula, as well as information integration associated areas, dorsolateral prefrontal cortex (DLPFC), and inferior parietal lobule (IPL). Results showed that VS and VMPFC were characterized by a hyperactivation in adolescents compared with younger adults. Furthermore, the ACC and insula were characterized by a U-shape pattern (hypoactivation in younger adults compared with adolescents and older adults), whereas the DLPFC and IPL were characterized by a J-shaped form (hyperactivation in older adults compared with younger groups). Furthermore, a functional connectivity analysis revealed an elevated negative functional coupling between the inhibition-related area rIFG and VS in younger adults compared with adolescents. Results indicate that lifespan-related changes during reward anticipation are characterized by different trajectories in different reward network modules and support the hypothesis of an imbalance in maturation of striatal and prefrontal cortex in adolescents. Furthermore, these results suggest compensatory age-specific effects in fronto-parietal regions. Copyright © 2014 Wiley Periodicals, Inc.

Content-specific coordination of listeners' to speakers' EEG during communication.

PubMed

Kuhlen, Anna K; Allefeld, Carsten; Haynes, John-Dylan

2012-01-01

Cognitive neuroscience has recently begun to extend its focus from the isolated individual mind to two or more individuals coordinating with each other. In this study we uncover a coordination of neural activity between the ongoing electroencephalogram (EEG) of two people-a person speaking and a person listening. The EEG of one set of twelve participants ("speakers") was recorded while they were narrating short stories. The EEG of another set of twelve participants ("listeners") was recorded while watching audiovisual recordings of these stories. Specifically, listeners watched the superimposed videos of two speakers simultaneously and were instructed to attend either to one or the other speaker. This allowed us to isolate neural coordination due to processing the communicated content from the effects of sensory input. We find several neural signatures of communication: First, the EEG is more similar among listeners attending to the same speaker than among listeners attending to different speakers, indicating that listeners' EEG reflects content-specific information. Secondly, listeners' EEG activity correlates with the attended speakers' EEG, peaking at a time delay of about 12.5 s. This correlation takes place not only between homologous, but also between non-homologous brain areas in speakers and listeners. A semantic analysis of the stories suggests that listeners coordinate with speakers at the level of complex semantic representations, so-called "situation models". With this study we link a coordination of neural activity between individuals directly to verbally communicated information.

Content-specific coordination of listeners' to speakers' EEG during communication

PubMed Central

Kuhlen, Anna K.; Allefeld, Carsten; Haynes, John-Dylan

2012-01-01

Cognitive neuroscience has recently begun to extend its focus from the isolated individual mind to two or more individuals coordinating with each other. In this study we uncover a coordination of neural activity between the ongoing electroencephalogram (EEG) of two people—a person speaking and a person listening. The EEG of one set of twelve participants (“speakers”) was recorded while they were narrating short stories. The EEG of another set of twelve participants (“listeners”) was recorded while watching audiovisual recordings of these stories. Specifically, listeners watched the superimposed videos of two speakers simultaneously and were instructed to attend either to one or the other speaker. This allowed us to isolate neural coordination due to processing the communicated content from the effects of sensory input. We find several neural signatures of communication: First, the EEG is more similar among listeners attending to the same speaker than among listeners attending to different speakers, indicating that listeners' EEG reflects content-specific information. Secondly, listeners' EEG activity correlates with the attended speakers' EEG, peaking at a time delay of about 12.5 s. This correlation takes place not only between homologous, but also between non-homologous brain areas in speakers and listeners. A semantic analysis of the stories suggests that listeners coordinate with speakers at the level of complex semantic representations, so-called “situation models”. With this study we link a coordination of neural activity between individuals directly to verbally communicated information. PMID:23060770

Self-spinning nanoparticle laden microdroplets for sensing and energy harvesting.

PubMed

Bhattacharjee, Mitradip; Pasumarthi, Viswanath; Chaudhuri, Joydip; Singh, Amit Kumar; Nemade, Harshal; Bandyopadhyay, Dipankar

2016-03-21

Exposure of a volatile organic vapour could set in powerful rotational motion a microdroplet composed of an aqueous salt solution loaded with metal nanoparticles. The solutal Marangoni motion on the surface originating from the sharp difference in the surface tension of water and organic vapour stimulated the strong vortices inside the droplet. The vapour sources of methanol, ethanol, diethyl ether, toluene, and chloroform stimulated motions of different magnitudes could easily be correlated to the surface tension gradient on the drop surface. Interestingly, when the nanoparticle laden droplet of aqueous salt solution was connected to an external electric circuit through a pair of electrodes, an ∼85-95% reduction in the electrical resistance was observed across the spinning droplet. The extent of reduction in the resistance was found to have a correlation with the difference in the surface tension of the vapour source and the water droplet, which could be employed to distinguish the vapour sources. Remarkably, the power density of the same prototype was estimated to be around 7 μW cm(-2), which indicated the potential of the phenomenon in converting surface energy into electrical in a non-destructive manner and under ambient conditions. Theoretical analysis uncovered that the difference in the ζ-potential near the electrodes was the major reason for the voltage generation. The prototype could also detect the repeated exposure and withdrawal of vapour sources, which helped in the development of a proof-of-concept detector to sense alcohol issuing out of the human breathing system.

Comparison of Covered Versus Uncovered Stents for Benign Superior Vena Cava (SVC) Obstruction.

PubMed

Haddad, Mustafa M; Simmons, Benjamin; McPhail, Ian R; Kalra, Manju; Neisen, Melissa J; Johnson, Matthew P; Stockland, Andrew H; Andrews, James C; Misra, Sanjay; Bjarnason, Haraldur

2018-05-01

To identify whether long-term symptom relief and stent patency vary with the use of covered versus uncovered stents for the treatment of benign SVC obstruction. We retrospectively identified all patients with benign SVC syndrome treated to stent placement between January 2003 and December 2015 (n = 59). Only cases with both clinical and imaging follow-up were included (n = 47). In 33 (70%) of the patients, the obstruction was due to a central line or pacemaker wires, and in 14 (30%), the cause was fibrosing mediastinitis. Covered stents were placed in 17 (36%) of the patients, and 30 (64%) patients had an uncovered stent. Clinical and treatment outcomes, complications, and the percent stenosis of each stent were evaluated. Technical success was achieved in all cases at first attempt. Average clinical and imaging follow-up in years was 2.7 (range 0.1-11.1) (covered) and 1.7 (range 0.2-10.5) (uncovered), respectively. There was a significant difference (p = 0.044) in the number of patients who reported a return of symptoms between the covered (5/17 or 29.4%) and uncovered (18/30 or 60%) groups. There was also a significant difference (p = < 0.001) in the mean percent stenosis after stent placement between the covered [17.9% (range 0-100) ± 26.2] and uncovered [48.3% (range 6.8-100) ± 33.5] groups. No significant difference (p = 0.227) was found in the time (days) between the date of the procedure and the date of clinical follow-up where a return of symptoms was reported [covered: 426.6 (range 28-1554) ± 633.9 and uncovered 778.1 (range 23-3851) ± 1066.8]. One patient in the uncovered group had non-endovascular surgical intervention (innominate to right atrial bypass), while none in the covered group required surgical intervention. One major complication (SIR grade C) occurred that consisted of a pericardial hemorrhagic effusion after angioplasty that required covered stent placement. There were no procedure-related deaths. Both covered and uncovered stents can be used for treating benign SVC syndrome. Covered stents, however, may be a more effective option at providing symptom relief and maintaining stent patency if validated by further studies.

Co-creation of market expansion in point-of-care testing in the United States: Industry leadership perspectives on the community pharmacy segment.

PubMed

Hohmeier, Kenneth C; McDonough, Sharon L K; Wang, Junling

Point-of-care testing (POCT) is a specialty of laboratory medicine that occurs at the bedside or near the patient when receiving health services. Despite its established clinical utility and consumer demand in the community pharmacy, the implementation of POCT within this setting has remained modest for a variety of reasons. One possible solution to this problem is the concept of co-creation - the partnership between consumer and manufacturer in the development of value for a service or device. Using the theoretical underpinning of co-creation, this study aimed to investigate perceptions of point-of-care-testing (POCT) industry leadership on the community pharmacy market in the United States to uncover reasons for limited implementation within community pharmacies. Participants were recruited for this study through the use of snowball sampling. A series of semi-structured interviews were conducted with the participants via telephone. Interviews were recorded, transcribed, and entered into a qualitative analysis software program to summarize the data. Five key themes were uncovered: gaps in understanding, areas of positive impact, barriers to implementation, facilitators of implementation, and community pharmacy - a potential major player. Through uncovering gaps in perceptions, it may be possible to leverage the U.S. pharmacy industry's size, potential for scalability, and ease of patient access to further patient care. Copyright © 2016 Elsevier Inc. All rights reserved.

Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules.

PubMed

Curtis, Ross E; Kim, Seyoung; Woolford, John L; Xu, Wenjie; Xing, Eric P

2013-03-21

Association analysis using genome-wide expression quantitative trait locus (eQTL) data investigates the effect that genetic variation has on cellular pathways and leads to the discovery of candidate regulators. Traditional analysis of eQTL data via pairwise statistical significance tests or linear regression does not leverage the availability of the structural information of the transcriptome, such as presence of gene networks that reveal correlation and potentially regulatory relationships among the study genes. We employ a new eQTL mapping algorithm, GFlasso, which we have previously developed for sparse structured regression, to reanalyze a genome-wide yeast dataset. GFlasso fully takes into account the dependencies among expression traits to suppress false positives and to enhance the signal/noise ratio. Thus, GFlasso leverages the gene-interaction network to discover the pleiotropic effects of genetic loci that perturb the expression level of multiple (rather than individual) genes, which enables us to gain more power in detecting previously neglected signals that are marginally weak but pleiotropically significant. While eQTL hotspots in yeast have been reported previously as genomic regions controlling multiple genes, our analysis reveals additional novel eQTL hotspots and, more interestingly, uncovers groups of multiple contributing eQTL hotspots that affect the expression level of functional gene modules. To our knowledge, our study is the first to report this type of gene regulation stemming from multiple eQTL hotspots. Additionally, we report the results from in-depth bioinformatics analysis for three groups of these eQTL hotspots: ribosome biogenesis, telomere silencing, and retrotransposon biology. We suggest candidate regulators for the functional gene modules that map to each group of hotspots. Not only do we find that many of these candidate regulators contain mutations in the promoter and coding regions of the genes, in the case of the Ribi group, we provide experimental evidence suggesting that the identified candidates do regulate the target genes predicted by GFlasso. Thus, this structured association analysis of a yeast eQTL dataset via GFlasso, coupled with extensive bioinformatics analysis, discovers a novel regulation pattern between multiple eQTL hotspots and functional gene modules. Furthermore, this analysis demonstrates the potential of GFlasso as a powerful computational tool for eQTL studies that exploit the rich structural information among expression traits due to correlation, regulation, or other forms of biological dependencies.

A prospective randomized study for efficacy of an uncovered double bare metal stent compared to a single bare metal stent in malignant biliary obstruction.

PubMed

Lee, Hyun Jik; Chung, Moon Jae; Park, Jeong Yup; Park, Seung Woo; Nam, Chung Mo; Song, Si Young; Bang, Seungmin

2017-08-01

A biliary self-expandable metal stent (SEMS) is commonly used to relieve malignant biliary obstruction. The aim of this study was to compare the efficacy of a conventional uncovered SEMS with that of a newly developed uncovered double bare metal stent in reducing the risk of stent occlusion caused by tumor ingrowth. We performed a prospective, open-labeled, randomized trial in 71 patients at Severance Hospital, Yonsei University College of Medicine from June 2013 to June 2014. Patients with inoperable malignant biliary obstruction were included and randomized to receive an uncovered single bare metal stent (SBSs; S&G Biotech Inc.), an uncovered single bare metal stent (SBSt; Taewoong Medical), or an uncovered double bare metal stent (DBS; S&G Biotech Inc.). The mean age was 66.6 years (range, 35-83), and 42 (59.2%) were male. The mean duration of stent patency was 212 days (±152) in the DBS group (n = 24) compared with 124 days (±98) in the SBSs group (n = 23; P = 0.022 for noninferiority) and 116 days (±79) in the SBSt group (n = 24; P = 0.010 for noninferiority). There were no differences in the incidences of early and delayed complications or migration. The newly developed DBS is noninferior to the conventional uncovered SEMSs on duration of stent patency and tumor ingrowth occurred less frequently in the DBS group. This might decrease the need for reintervention and offer a better quality of life. The trial is registered with Clinicaltrials.gov no: NCT01869894.

Chemometric evaluation of concentrations of trace elements in intervertebral disc tissue in patient with degenerative disc disease.

PubMed

Kubaszewski, Łukasz; Zioła-Frankowska, Anetta; Gasik, Zuzanna; Frankowski, Marcin; Dąbrowski, Mikołaj; Molisak, Bartłomiej; Kaczmarczyk, Jacek; Gasik, Robert

2017-12-23

The work is designed to uncover the pattern of mutual relation among trace elements and epidemiological data in the degenerated intervertebral disk tissue in humans. Hitherto the reason of the degenerative process is not fully understood. Trace elements are the basic components of the biological compound related both its metabolism as well as environmental exposure. The relation pattern among elements occurs gives new perspective in solving the cause of the disease. We have analysed trace elements content in the 30 intervertebral disc from 22 patients with degenerative disc disease. The concentrations of Al, Cu, Cd, Mo, Ni and Pb were determined with Atomic Absorption Spectrometry. To analyse the multidimentional relation between trace element concentration and epidemiological data the chemometric analysis was applied. The similarity have been shown in occurrence of following pairs: Cd-Mo as well as Mg-Zn. The second pair was correlated with Pb concentration. Pb levels are observed to be competitive to Cu concentration. Cd concentration was related to Zn and Mg deficiency. No single but rather cluster of epidemiological data show observable influence on the TE tissue variance. Zn and Cu was related to the male sex. Operation with orthopedic implants were related to combined Al, Mo and Zn concentration. This is the first chemometric analysis of trace elements in disk tissue. It shows multidimentional relations that are missed by the classical statistic. The analysis shows significant relation. The nature of the relations is the basis for further metabolic and environmental research.

An alternative assessment of second-order closure models in turbulent shear flows

NASA Technical Reports Server (NTRS)

Speziale, Charles G.; Gatski, Thomas B.

1994-01-01

The performance of three recently proposed second-order closure models is tested in benchmark turbulent shear flows. Both homogeneous shear flow and the log-layer of an equilibrium turbulent boundary layer are considered for this purpose. An objective analysis of the results leads to an assessment of these models that stands in contrast to that recently published by other authors. A variety of pitfalls in the formulation and testing of second-order closure models are uncovered by this analysis.

Development, Vibration, and Thermal Characterization of a Steady Operating Pulsed Power System for FRC Thrusters

DTIC Science & Technology

2015-04-01

to successfully operate after being exposed to the harsh launch vibration environment. 2. Uncover workmanship flaws such as loose fasteners or weak...uncover any workmanship errors in spite of exposing the PPUs to vibration levels in excess of what is expected for flight on any of the launchers ...successfully operate after being exposed to the harsh launch vibration environment. 2. Uncover workmanship flaws such as loose fasteners or weak

Genome analysis of a clinical isolate of Shewanella sp. uncovered an active hybrid integrative and conjugative element carrying an integron platform inserted in a novel genomic locus.

PubMed

Parmeciano Di Noto, Gisela; Jara, Eugenio; Iriarte, Andrés; Centrón, Daniela; Quiroga, Cecilia

2016-08-01

Shewanella spp. are currently considered to be emerging pathogens that can code for a blaOXA carbapenemase in their chromosome. Complete genome analysis of the clinical isolate Shewanella sp. Sh95 revealed that this strain is a novel species, which shares a lineage with marine isolates. Characterization of its resistome showed that it codes for genes drfA15, qacH and blaOXA-48. We propose that Shewanella sp. Sh95 acts as reservoir of blaOXA-48. Moreover, analysis of mobilome showed that it contains a novel integrative and conjugative element (ICE), named ICESh95. Comparative analysis between the close relatives ICESpuPO1 from Shewanella sp. W3-18-1 and ICE SXTMO10 from Vibrio cholerae showed that ICESh95 encompassed two new regions, a type III restriction modification system and a multidrug resistance integron. The integron platform contained a novel arrangement formed by gene cassettes drfA15 and qacH, and a class C-attC group II intron. Furthermore, insertion of ICESh95 occurred at a unique target site, which correlated with the presence of a different xis/int module. Mobility of ICESh95 was assessed and demonstrated its ability to self-transfer with high efficiency to different species of bacteria. Our results show that ICESh95 is a self-transmissible, mobile element, which can contribute to the dissemination of antimicrobial resistance; this is clearly a threat when natural bacteria from water ecosystems, such as Shewanella, act as vectors in its propagation.

Quality Group Home Care for Adults with Developmental Disabilities and/or Mental Health Disorders: Yearning for Understanding, Security and Freedom

ERIC Educational Resources Information Center

Shipton, Leah; Lashewicz, Bonnie M.

2017-01-01

Background: The purpose of this study was to uncover and understand factors influencing quality of care received by adults with developmental disabilities and/or mental health disorders living in group homes. Methods: The present authors conducted a secondary analysis of data from nine focus group discussions with adults with developmental…

An Empirical Analysis of Social Capital and Economic Growth in Europe (1980-2000)

ERIC Educational Resources Information Center

Neira, Isabel; Vazquez, Emilia; Portela, Marta

2009-01-01

It is of paramount concern for economists to uncover the factors that determine economic growth and social development. In recent years a new field of investigation has come to the fore in which social capital is analysed in order to determine its effect on economic growth. Along these lines the work presented here examines the relationships that…

Mining the bitter melon (momordica charantia l.) seed transcriptome by 454 analysis of non-normalized and normalized cDNA populations for conjugated fatty acid metabolism-related genes

USDA-ARS?s Scientific Manuscript database

Seeds of Momordica charantia (bitter melon) produce high levels of eleostearic acid, an unusual conjugated fatty acid with industrial value. Deep sequencing of non-normalized and normalized cDNAs from developing bitter melon seeds was conducted to uncover key genes required for biotechnological tran...

Language and the Medial Temporal Lobe: Evidence from H. M.'s Spontaneous Discourse

ERIC Educational Resources Information Center

Skotko, Brian G.; Andrews, Edna; Einstein, Gillian

2005-01-01

Previous researchers have found it challenging to disentangle the memory and language capabilities of the famous amnesic patient H. M. Here, we present an original linguistic analysis of H. M. based on empirical data drawing upon novel spoken discourse with him. The results did not uncover the language deficits noted previously. Instead, H. M.'s…

Mistake of Criminal Law and Its Influence on the Classification of Crime

ERIC Educational Resources Information Center

Veresha, Roman V.

2016-01-01

The paper examines the characteristics of a mistake of the commitment of crime as an optional feature of the mental state of the crime. The analysis conducted offers an opportunity to state that in international criminal law, a mistake of law, although taken into account, does not generally affect the classification of crime. We uncovered and…

"What about People Our Age?" Applying Qualitative and Quantitative Methods to Uncover How Political Ads Alienate College Students

ERIC Educational Resources Information Center

Parmelee, John H.; Perkins, Stephynie C.; Sayre, Judith J.

2007-01-01

This study uses a sequential transformative mixed methods research design to explain how political advertising fails to engage college students. Qualitative focus groups examined how college students interpret the value of political advertising to them, and a quantitative manifest content analysis concerning ad framing of more than 100 ads from…

What Lies beneath Seemingly Positive Campus Climate Results: Institutional Sexism, Racism, and Male Hostility toward Equity Initiatives and Liberal Bias

ERIC Educational Resources Information Center

Vaccaro, Annemarie

2010-01-01

This article presents qualitative results from a campus climate study at one predominately white university. Data analysis uncovered "what lies beneath" a seemingly positive campus climate. Gender differences in survey responses suggest that men and women experienced the climate in vastly different ways. Additionally, lack of deep diversity…

Infusing and Sustaining Aging Content in Social Work Education: Findings from GeroRich Projects

ERIC Educational Resources Information Center

Hash, Kristina M.; Gottlieb, Jody; Harper-Dorton, Karen V.; Crawley-Woods, Geraldine; Shelek-Furbee, Katherine; Smith, John David; Brown, Rita

2007-01-01

This article presents findings from experiences of 67 projects involved in GeroRich, an initiative funded by the John A. Hartford Foundation designed to infuse, enrich and sustain aging content in BSW and MSW curricula. Thematic qualitative analysis was used to uncover themes in answers to open-ended questions contained in End-of-Year 2 project…

Collective Digital Storytelling: An Activity-Theoretical Analysis of Second Language Learning and Teaching

ERIC Educational Resources Information Center

Kalyaniwala-Thapliyal, Carmenne

2016-01-01

This paper describes the collective activity of a group of four students who created a digital story as a teaching resource that was to be used for teaching English as a foreign language. It uncovers and analyzes the actual processes underlining the activity as it unfolds from one stage to another. Four processes, viz., sociocognitive…

Generic penetration in the retail antidepressant market.

PubMed

Ventimiglia, Jeffrey; Kalali, Amir H

2010-06-01

In this article, we explore the accelerated penetration of generic antidepressants in the United States market following the availability of generic citalopram and sertraline. Analysis suggests that overall, generic penetration into the antidepressant market has grown from approximately 41 percent in January 2004 to over 73 percent in January 2010. Similar trends are uncovered when branded and generic prescriptions are analyzed by specialty.

Uncovering a Hidden Professional Agenda for Teacher Educators: A Mixed Method Study on Flemish Teacher Educators and Their Professional Development

ERIC Educational Resources Information Center

Tack, Hanne; Valcke, Martin; Rots, Isabel; Struyven, Katrien; Vanderlinde, Ruben

2018-01-01

Taking into account the pressing need to understand more about what teacher educators' professional development characterises, this article adopts a mixed method approach to explore Flemish (Dutch-speaking part of Belgium) teacher educators' professional development needs and opportunities. Analysis results of a large-scale survey study with 611…

Uncovering Procedural Knowledge in Craft, Design, and Technology Education: A Case of Hands-On Activities in Electronics

ERIC Educational Resources Information Center

Pirttimaa, Matti; Husu, Jukka; Metsärinne, Mika

2017-01-01

Different knowledge types have their own specific features and tasks in the learning process. Procedural knowledge is used in craft and technology education when students solve problems individually and share their working knowledge with others. This study presents a detailed analysis of a one student's learning process in technology education and…

Perspectives on Academic Staff Involvement in the Acquisition and Implementation of Educational Technologies

ERIC Educational Resources Information Center

Habib, Laurence; Johannesen, Monica

2014-01-01

This article presents the results of a study using both quantitative and qualitative data to uncover the extent and nature of the involvement of academic staff in the processes of acquisition and implementation of educational technologies. Actor-network theory (ANT) is used to inform the design of the study and the analysis of the data. Three main…

Calculation of strained BaTiO3 with different exchange correlation functionals examined with criterion by Ginzburg-Landau theory, uncovering expressions by crystallographic parameters

NASA Astrophysics Data System (ADS)

Watanabe, Yukio

2018-05-01

In the calculations of tetragonal BaTiO3, some exchange-correlation (XC) energy functionals such as local density approximation (LDA) have shown good agreement with experiments at room temperature (RT), e.g., spontaneous polarization (PS), and superiority compared with other XC functionals. This is due to the error compensation of the RT effect and, hence, will be ineffective in the heavily strained case such as domain boundaries. Here, ferroelectrics under large strain at RT are approximated as those at 0 K because the strain effect surpasses the RT effects. To find effective XC energy functionals for strained BaTiO3, we propose a new comparison, i.e., a criterion. This criterion is the properties at 0 K given by the Ginzburg-Landau (GL) theory because GL theory is a thermodynamic description of experiments working under the same symmetry-constraints as ab initio calculations. With this criterion, we examine LDA, generalized gradient approximations (GGA), meta-GGA, meta-GGA + local correlation potential (U), and hybrid functionals, which reveals the high accuracy of some XC functionals superior to XC functionals that have been regarded as accurate. This result is examined directly by the calculations of homogenously strained tetragonal BaTiO3, confirming the validity of the new criterion. In addition, the data points of theoretical PS vs. certain crystallographic parameters calculated with different XC functionals are found to lie on a single curve, despite their wide variations. Regarding these theoretical data points as corresponding to the experimental results, analytical expressions of the local PS using crystallographic parameters are uncovered. These expressions show the primary origin of BaTiO3 ferroelectricity as oxygen displacements. Elastic compliance and electrostrictive coefficients are estimated. For the comparison of strained results, we show that the effective critical temperature TC under strain <-0.01 is >1000 K from an approximate method combining ab initio results with GL theory. In addition, in a definite manner, the present results show much more enhanced ferroelectricity at large strain than the previous reports.

Analyzing Language in Suicide Notes and Legacy Tokens.

PubMed

Egnoto, Michael J; Griffin, Darrin J

2016-03-01

Identifying precursors that will aid in the discovery of individuals who may harm themselves or others has long been a focus of scholarly research. This work set out to determine if it is possible to use the legacy tokens of active shooters and notes left from individuals who completed suicide to uncover signals that foreshadow their behavior. A total of 25 suicide notes and 21 legacy tokens were compared with a sample of over 20,000 student writings for a preliminary computer-assisted text analysis to determine what differences can be coded with existing computer software to better identify students who may commit self-harm or harm to others. The results support that text analysis techniques with the Linguistic Inquiry and Word Count (LIWC) tool are effective for identifying suicidal or homicidal writings as distinct from each other and from a variety of student writings in an automated fashion. Findings indicate support for automated identification of writings that were associated with harm to self, harm to others, and various other student writing products. This work begins to uncover the viability or larger scale, low cost methods of automatic detection for individuals suffering from harmful ideation.

Inequality in Experiences of Physics Education: Secondary School Girls' and Boys' Perceptions of their Physics Education and Intentions to Continue with Physics After the Age of 16

NASA Astrophysics Data System (ADS)

Mujtaba, Tamjid; Reiss, Michael J.

2013-07-01

This paper explores the factors that are associated in England with 15-year-old students' intentions to study physics after the age of 16, when it is no longer compulsory. Survey responses were collated from 5,034 year 10 students as learners of physics during the academic year 2008-2009 from 137 England secondary schools. Our analysis uses individual items from the survey rather than constructs (aggregates of items) to explore what it is about physics teachers, physics lessons and physics itself that is most correlated with intended participation in physics after the age of 16. Our findings indicate that extrinsic material gain motivation in physics was the most important factor associated with intended participation. In addition, an item-level analysis helped to uncover issues around gender inequality in physics educational experiences which were masked by the use of construct-based analyses. Girls' perceptions of their physics teachers were similar to those of boys on many fronts. However, despite the encouragement individual students receive from their teachers being a key factor associated with aspirations to continue with physics, girls were statistically significantly less likely to receive such encouragement. We also found that girls had less positive experiences of their physics lessons and physics education than did boys.

SNHG16/miR-216-5p/ZEB1 signal pathway contributes to the tumorigenesis of cervical cancer cells.

PubMed

Zhu, Hong; Zeng, Yan; Zhou, Chen-Chen; Ye, Weiping

2018-01-01

Long non-coding RNAs (lncRNAs) have been confirmed as crucial regulators in tumorgenesis. Small nucleolar RNA host gene 16 (SNHG16) has been recently uncovered to be a potential oncogene in several types of cancers. However, its expression level and potential role in cervical cancer remain uncertain. In our research, we assessed the expression level of SNHG16 in clinical cervical cancer tissues and cells. We made use of functional assays to determine the biological effects of SNHG16 on cell proliferation and migration of cervical cancer. By employing the bioinformatics analysis tools, we revealed that miR-216-5p could interact with SNHG16 and there existed a negative correlation between the expression levels of miR-216-5p and SNHG16 in cervical cancer specimens. Furthermore, RIP assay, RNA pulldown system and dual luciferase reporter assays confirmed that SNHG16 directly targeted miR-216-5p by harboring the binding sites of microRNA in the SNHG16 sequence. Additionally, bioinformatics analysis provided an evidence that ZEB1 was a potential target of miR-216-5p. Collectively, it was suggested that SNHG16 could serve as an oncogene that promoted tumor progression by acting as an endogenous 'sponge' to regulate miR-216A-5p/ZEB1. Copyright © 2017 Elsevier Inc. All rights reserved.

Pioneer farming in southeast Europe during the early sixth millennium BC: Climate-related adaptations in the exploitation of plants and animals

PubMed Central

De Cupere, Bea; Ethier, Jonathan; Marinova, Elena

2018-01-01

The Old World farming system arose in the semi-arid Mediterranean environments of southwest Asia. Pioneer farmers settling the interior of the Balkans by the early sixth millennium BC were among the first to introduce southwest Asian-style cultivation and herding into areas with increasingly continental temperate conditions. Previous research has shown that the bioarchaeological assemblages from early farming sites in southeast Europe vary in their proportions of plant and animal taxa, but the relationship between taxonomic variation and climate has remained poorly understood. To uncover associations between multiple species and environmental factors simultaneously, we explored a dataset including altitude, five bioclimatic and 30 bioarchaeological variables (plant and animal taxa) for 57 of the earliest farming sites in southeast Europe using Canonical Correspondence Analysis (CCA). An extension of correspondence analysis, CCA is widely used in applied ecology to answer similar questions of species-environment relationships, but has not been previously applied in prehistoric archaeology to explore taxonomic and climatic variables in conjunction. The analyses reveal that the changes in plant and animal exploitation which occurred with the northward dispersal of farmers, crops and livestock correlate with south-north climate gradients, and emphasize the importance of adaptations in the animal domain for the initial establishment of farming beyond the Mediterranean areas. PMID:29775469

Uncovering microRNA-mediated response to SO2 stress in Arabidopsis thaliana by deep sequencing.

PubMed

Li, Lihong; Xue, Meizhao; Yi, Huilan

2016-10-05

Sulfur dioxide (SO2) is a major air pollutant and has significant impacts on plants. MicroRNAs (miRNAs) are a class of gene expression regulators that play important roles in response to environmental stresses. In this study, deep sequencing was used for genome-wide identification of miRNAs and their expression profiles in response to SO2 stress in Arabidopsis thaliana shoots. A total of 27 conserved miRNAs and 5 novel miRNAs were found to be differentially expressed under SO2 stress. qRT-PCR analysis showed mostly negative correlation between miRNA accumulation and target gene mRNA abundance, suggesting regulatory roles of these miRNAs during SO2 exposure. The target genes of SO2-responsive miRNAs encode transcription factors and proteins that regulate auxin signaling and stress response, and the miRNAs-mediated suppression of these genes could improve plant resistance to SO2 stress. Promoter sequence analysis of genes encoding SO2-responsive miRNAs showed that stress-responsive and phytohormone-related cis-regulatory elements occurred frequently, providing additional evidence of the involvement of miRNAs in adaption to SO2 stress. This study represents a comprehensive expression profiling of SO2-responsive miRNAs in Arabidopsis and broads our perspective on the ubiquitous regulatory roles of miRNAs under stress conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

3,3′-Diindolylmethane Ameliorates Staphylococcal Enterotoxin B–Induced Acute Lung Injury through Alterations in the Expression of MicroRNA that Target Apoptosis and Cell-Cycle Arrest in Activated T Cells

PubMed Central

Elliott, David M.; Nagarkatti, Mitzi

2016-01-01

3,3′-Diindolylmethane (DIM), a natural indole found in cruciferous vegetables, has significant anti-cancer and anti-inflammatory properties. In this current study, we investigated the effects of DIM on acute lung injury (ALI) induced by exposure to staphylococcal enterotoxin B (SEB). We found that pretreatment of mice with DIM led to attenuation of SEB-induced inflammation in the lungs, vascular leak, and IFN-γ secretion. Additionally, DIM could induce cell-cycle arrest and cell death in SEB-activated T cells in a concentration-dependent manner. Interestingly, microRNA (miRNA) microarray analysis uncovered an altered miRNA profile in lung-infiltrating mononuclear cells after DIM treatment of SEB-exposed mice. Moreover, computational analysis of miRNA gene targets and regulation networks indicated that DIM alters miRNA in the cell death and cell-cycle progression pathways. Specifically, DIM treatment significantly downregulated several miRNA and a correlative increase associated gene targets. Furthermore, overexpression and inhibition studies demonstrated that DIM-induced cell death, at least in part, used miR-222. Collectively, these studies demonstrate for the first time that DIM treatment attenuates SEB-induced ALI and may do so through the induction of microRNAs that promote apoptosis and cell-cycle arrest in SEB-activated T cells. PMID:26818958

Gut microbial functional maturation and succession during human early life.

PubMed

Cerdó, Tomás; Ruiz, Alicia; Acuña, Inmaculada; Jáuregui, Ruy; Jehmlich, Nico; Haange, Sven-Bastian; von Bergen, Martin; Suárez, Antonio; Campoy, Cristina

2018-04-24

The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional diversity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and fermentation strategies from milk and mucin-derived monosaccharide catabolism feeding acetate/propanoate synthesis to complex food-derived hexoses fuelling butanoate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

NOTCH3 Is a Prognostic Factor That Promotes Glioma Cell Proliferation, Migration and Invasion via Activation of CCND1 and EGFR

PubMed Central

Alqudah, Mohammad A. Y.; Agarwal, Supreet; Al-Keilani, Maha S.; Sibenaller, Zita A.; Ryken, Timothy C.; Assem, Mahfoud

2013-01-01

Using a GWA analysis of a comprehensive glioma specimen population, we identified whole gain of chromosome 19 as one of the major chromosomal aberrations that correlates to patients’ outcomes. Our analysis of significant loci revealed for the first time NOTCH3 as one of the most significant amplification. NOTCH3 amplification is associated with worse outcome compared to tumors with non-amplified locus. NOTCH receptors (NOTCH1-4) are key positive regulators of cell-cell interactions, angiogenesis, cell adhesion and stem cell niche development which have been shown to play critical roles in several human cancers. Our objective is to determine the molecular roles of NOTCH3 in glioma pathogenesis and aggressiveness. Here we show for the first time that NOTCH3 plays a major role in glioma cell proliferation, cell migration, invasion and apoptosis. Therefore, our study uncovers the prognostic value and the oncogenic function of NOTCH3 in gliomagenesis and supports NOTCH3 as a promising target of therapy in high grade glioma. Our studies allowed the identification of a subset of population that may benefit from GSI- or anti-NOTCH3- based therapies. This may lead to the design of novel strategies to improve therapeutic outcome of patients with glioma by establishing medical and scientific basis for personalized chemotherapies. PMID:24143218

An Amino Acid Code to Define a Protein’s Tertiary Packing Surface

PubMed Central

Fraga, Keith J.; Joo, Hyun; Tsai, Jerry

2015-01-01

One difficult aspect of the protein-folding problem is characterizing the non-specific interactions that define packing in protein tertiary structure. To better understand tertiary structure, this work extends the knob-socket model by classifying the interactions of a single knob residue packed into a set of contiguous sockets, or a pocket made up of 4 or more residues. The knob-socket construct allows for a symbolic two-dimensional mapping of pockets. The two-dimensional mapping of pockets provides a simple method to investigate the variety of pocket shapes in order to understand the geometry of protein tertiary surfaces. The diversity of pocket geometries can be organized into groups of pockets that share a common core, which suggests that some interactions in pockets are ancillary to packing. Further analysis of pocket geometries displays a preferred configuration that is right-handed in α-helices and left-handed in β-sheets. The amino acid composition of pockets illustrates the importance of non-polar amino acids in packing as well as position specificity. As expected, all pocket shapes prefer to pack with hydrophobic knobs; however, knobs are not selective for the pockets they pack. Investigating side-chain rotamer preferences for certain pocket shapes uncovers no strong correlations. These findings allow a simple vocabulary based on knobs and sockets to describe protein tertiary packing that supports improved analysis, design and prediction of protein structure. PMID:26575337

Examining the relationship of ethnicity, gender and social cognitive factors with the academic achievement of first-year engineering students

NASA Astrophysics Data System (ADS)

Carr, Bruce Henry

The purpose of the study was to examine the relationships of social cognitive factors and their influence on the academic performance of first-year engineering students. The nine social cognitive variables identified were under the groupings of personal support, occupational self-efficacy, academic self-efficacy, vocational interests, coping, encouragement, discouragement, outcome expectations, and perceived stress. The primary student participants in this study were first-year engineering students from underrepresented groups which include African American, Hispanic American students and women. With this in mind, the researcher sought to examine the interactive influence of race/ethnicity and gender based on the aforementioned social cognitive factors. Differences in academic performance (university GPA of first-year undergraduate engineering students) were analyzed by ethnicity and gender. There was a main effect for ethnicity only. Gender was found not to be significant. Hispanics were not found to be significantly different in their GPAs than Whites but Blacks were found to have lower GPAs than Whites. Also, Pearson correlation coefficients were used to examine the relationship between and among the nine identified social cognitive variables. The data from the analysis uncovered ten significant correlations which were as follows: occupational self-efficacy and academic self-efficacy, occupational self-efficacy and vocational interest, occupational self-efficacy and perceived stress, academic self-efficacy and encouragement, academic self-efficacy and outcome expectations, academic self-efficacy and perceived stress, vocational interest and outcome expectations, discouragement and encouragement, coping and perceived stress, outcome expectations and perceived stress. Next, a Pearson correlation coefficient was utilized to examine the relationship between academic performance (college GPA) of first-year undergraduate engineering students and the nine identified social cognitive variables. The data analysis revealed three significant correlations which were as follows academic performance and occupational self-efficacy, academic performance and academic self-efficacy, and academic performance and encouragement. Finally, a Pearson correlation coefficient was used to examine the relationship between high school GPA and the nine identified social cognitive variables. The Pearson correlational coefficient indicated that there was one statistically significant correlation which was high school GPA and academic self-efficacy. Recommendations for further study included (a) future research involving investigations that compare a variety of institutions in different regions of the country; (b) further investigations utilizing open-ended responses from engineering students based on interviews; (c) a replicated study in 5 to 10 years to evaluate whether differences emerged relating to ethnicity and gender due to possible societal or cultural changes; and (d) a study involving a pretest and posttest of students' self-efficacy beliefs. Finally, the researcher recommends a qualitative study specifically involving interview questions aimed at students with moderate level grades and SAT scores who exhibited above average academic performance. (Abstract shortened by UMI.).

TUSC2(FUS1)-erlotinib Induced Vulnerabilities in Epidermal Growth Factor Receptor(EGFR) Wildtype Non-small Cell Lung Cancer(NSCLC) Targeted by the Repurposed Drug Auranofin.

PubMed

Xiaobo, Cao; Majidi, Mourad; Feng, Meng; Shao, Ruping; Wang, Jing; Zhao, Yang; Baladandayuthapani, Veerabhadran; Song, Juhee; Fang, Bingliang; Ji, Lin; Mehran, Reza; Roth, Jack A

2016-11-15

Expression of the TUSC2/FUS1 tumor suppressor gene in TUSC2 deficient EGFR wildtype lung cancer cells increased sensitivity to erlotinib. Microarray mRNA expression analysis of TUSC2 inducible lung cancer cells treated with erlotinib uncovered defects in the response to oxidative stress suggesting that increasing reactive oxygen species (ROS) would enhance therapeutic efficacy. Addition of the thioredoxin reductase 1 inhibitor (TXNRD1) auranofin (AF) to NSCLC cells treated with combination of TUSC2 forced expression with erlotinib increased tumor cell apoptosis and inhibited colony formation. TXNRD1 overexpression rescued tumors from AF-TUSC2-erlotinib induced apoptosis. Neutralizing ROS with nordihydroguaiaretic acid (NDGA) abrogated cell death induced by AF-TUSC2-erlotinib, indicating a regulatory role for ROS in the efficacy of the three drug combination. Isobologram-based statistical analysis of this combination demonstrated superior synergism, compared with each individual treatment at lower concentrations. In NSCLC tumor xenografts, tumor growth was markedly inhibited and animal survival was prolonged over controls by AF-TUSC2-erlotinib. Microarray mRNA expression analysis uncovered oxidative stress and DNA damage gene signatures significantly upregulated by AF-TUSC2-erlotinib compared to TUSC2-erlotinib. Pathway analysis showed the highest positive z-score for the NRF2-mediated oxidative stress response. Taken together these findings show that the combination of TUSC2-erlotinib induces additional novel vulnerabilities that can be targeted with AF.

Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity

PubMed Central

Heermann, Ralf; Fuchs, Thilo M

2008-01-01

Background Photorhabdus luminescens and Yersinia enterocolitica are both enteric bacteria which are associated with insects. P. luminescens lives in symbiosis with soil nematodes and is highly pathogenic towards insects but not to humans. In contrast, Y. enterocolitica is widely found in the environment and mainly known to cause gastroenteritis in men, but has only recently been shown to be also toxic for insects. It is expected that both pathogens share an overlap of genetic determinants that play a role within the insect host. Results A selective genome comparison was applied. Proteins belonging to the class of two-component regulatory systems, quorum sensing, universal stress proteins, and c-di-GMP signalling have been analysed. The interorganismic synopsis of selected regulatory systems uncovered common and distinct signalling mechanisms of both pathogens used for perception of signals within the insect host. Particularly, a new class of LuxR-like regulators was identified, which might be involved in detecting insect-specific molecules. In addition, the genetic overlap unravelled a two-component system that is unique for the genera Photorhabdus and Yersinia and is therefore suggested to play a major role in the pathogen-insect relationship. Our analysis also highlights factors of both pathogens that are expressed at low temperatures as encountered in insects in contrast to higher (body) temperature, providing evidence that temperature is a yet under-investigated environmental signal for bacterial adaptation to various hosts. Common degradative metabolic pathways are described that might be used to explore nutrients within the insect gut or hemolymph, thus enabling the proliferation of P. luminescens and Y. enterocolitica in their invertebrate hosts. A strikingly higher number of genes encoding insecticidal toxins and other virulence factors in P. luminescens compared to Y. enterocolitica correlates with the higher virulence of P. luminescens towards insects, and suggests a putative broader insect host spectrum of this pathogen. Conclusion A set of factors shared by the two pathogens was identified including those that are involved in the host infection process, in persistence within the insect, or in host exploitation. Some of them might have been selected during the association with insects and then adapted to pathogenesis in mammalian hosts. PMID:18221513

Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.).

PubMed

Huang, You-Jun; Liu, Li-Li; Huang, Jian-Qin; Wang, Zheng-Jia; Chen, Fang-Fang; Zhang, Qi-Xiang; Zheng, Bing-Song; Chen, Ming

2013-10-10

Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary model of gene regulations for seasonal pistillate flowering in hickory (Carya cathayensis) was proposed. The genome-wide dynamic transcriptome was characterized via the joint-approach of RNA sequencing and microarray analysis. Differential transcript abundance analysis uncovered the dynamic transcript abundance patterns of flowering correlated genes and their major functions based on Gene Ontology (GO) analysis. To explore pistillate flowering mechanism in hickory, a comprehensive flowering gene regulatory network based on Arabidopsis thaliana was constructed by additional literature mining. A total of 114 putative flowering or floral genes including 31 with differential transcript abundance were identified in hickory. The locations, functions and dynamic transcript abundances were analyzed in the gene regulatory networks. A genome-wide co-expression network for the putative flowering or floral genes shows three flowering regulatory modules corresponding to response to light abiotic stimulus, cold stress, and reproductive development process, respectively. Totally 27 potential flowering or floral genes were recruited which are meaningful to understand the hickory specific seasonal flowering mechanism better. Flowering event of pistillate flower bud in hickory is triggered by several pathways synchronously including the photoperiod, autonomous, vernalization, gibberellin, and sucrose pathway. Totally 27 potential flowering or floral genes were recruited from the genome-wide co-expression network function module analysis. Moreover, the analysis provides a potential FLC-like gene based vernalization pathway and an 'AC' model for pistillate flower development in hickory. This work provides an available framework for pistillate flower development in hickory, which is significant for insight into regulation of flowering and floral development of woody plants.

Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.)

PubMed Central

2013-01-01

Background Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary model of gene regulations for seasonal pistillate flowering in hickory (Carya cathayensis) was proposed. The genome-wide dynamic transcriptome was characterized via the joint-approach of RNA sequencing and microarray analysis. Results Differential transcript abundance analysis uncovered the dynamic transcript abundance patterns of flowering correlated genes and their major functions based on Gene Ontology (GO) analysis. To explore pistillate flowering mechanism in hickory, a comprehensive flowering gene regulatory network based on Arabidopsis thaliana was constructed by additional literature mining. A total of 114 putative flowering or floral genes including 31 with differential transcript abundance were identified in hickory. The locations, functions and dynamic transcript abundances were analyzed in the gene regulatory networks. A genome-wide co-expression network for the putative flowering or floral genes shows three flowering regulatory modules corresponding to response to light abiotic stimulus, cold stress, and reproductive development process, respectively. Totally 27 potential flowering or floral genes were recruited which are meaningful to understand the hickory specific seasonal flowering mechanism better. Conclusions Flowering event of pistillate flower bud in hickory is triggered by several pathways synchronously including the photoperiod, autonomous, vernalization, gibberellin, and sucrose pathway. Totally 27 potential flowering or floral genes were recruited from the genome-wide co-expression network function module analysis. Moreover, the analysis provides a potential FLC-like gene based vernalization pathway and an 'AC’ model for pistillate flower development in hickory. This work provides an available framework for pistillate flower development in hickory, which is significant for insight into regulation of flowering and floral development of woody plants. PMID:24106755

Genetic control of postnatal human brain growth

PubMed Central

van Dyck, Laura I.; Morrow, Eric M.

2017-01-01

Purpose of review Studies investigating postnatal brain growth disorders inform the biology underlying the development of human brain circuitry. This research is becoming increasingly important for the diagnosis and treatment of childhood neurodevelopmental disorders, including autism and related disorders. Here we review recent research on typical and abnormal postnatal brain growth and examine potential biological mechanisms. Recent findings Clinically, brain growth disorders are heralded by diverging head size for a given age and sex, but are more precisely characterized by brain imaging, postmortem analysis, and animal model studies. Recent neuroimaging and molecular biological studies on postnatal brain growth disorders have broadened our view of both typical and pathological postnatal neurodevelopment. Correlating gene and protein function with brain growth trajectories uncovers postnatal biological mechanisms, including neuronal arborization, synaptogenesis and pruning, and gliogenesis and myelination. Recent investigations of childhood neurodevelopmental and neurodegenerative disorders highlight the underlying genetic programming and experience-dependent remodeling of neural circuitry. Summary In order to understand typical and abnormal postnatal brain development, clinicians and researchers should characterize brain growth trajectories in the context of neurogenetic syndromes. Understanding mechanisms and trajectories of postnatal brain growth will aid in differentiating, diagnosing, and potentially treating neurodevelopmental disorders. PMID:27898583

Premature aging and cancer in nucleotide excision repair-disorders

PubMed Central

Diderich, K.; Alanazi, M.; Hoeijmakers, J.H.J.

2014-01-01

During past decades the major impact of DNA damage on cancer as ‘disease of the genes’ has become abundantly apparent. In addition to cancer recent years have also uncovered a very strong association of DNA damage with many features of (premature) aging. The notion that DNA repair systems not only protect against cancer but equally against too fast aging has become evident from a systematic, integral analysis of a variety of mouse mutants carrying defects in e.g. transcription-coupled repair with or without an additional impairment of global genome nucleotide excision repair and the corresponding segmental premature aging syndromes in man. A striking correlation between the degree of the DNA repair deficiency and the acceleration of specific progeroid symptoms has been discovered for those repair systems that primarily protect from the cytotoxic and cytostatic effects of DNA damage. These observations are explained from the perspective of nucleotide excision repair mouse mutant and human syndromes. However, similar principles likely apply to other DNA repair pathways including interstrand crosslink repair and double strand break repair and genome maintenance systems in general, supporting the notion that DNA damage constitutes an important intermediate in the process of aging. PMID:21680258

Identifying and Investigating Unexpected Response to Treatment: A Diabetes Case Study.

PubMed

Ozery-Flato, Michal; Ein-Dor, Liat; Parush-Shear-Yashuv, Naama; Aharonov, Ranit; Neuvirth, Hani; Kohn, Martin S; Hu, Jianying

2016-09-01

The availability of electronic health records creates fertile ground for developing computational models of various medical conditions. We present a new approach for detecting and analyzing patients with unexpected responses to treatment, building on machine learning and statistical methodology. Given a specific patient, we compute a statistical score for the deviation of the patient's response from responses observed in other patients having similar characteristics and medication regimens. These scores are used to define cohorts of patients showing deviant responses. Statistical tests are then applied to identify clinical features that correlate with these cohorts. We implement this methodology in a tool that is designed to assist researchers in the pharmaceutical field to uncover new features associated with reduced response to a treatment. It can also aid physicians by flagging patients who are not responding to treatment as expected and hence deserve more attention. The tool provides comprehensive visualizations of the analysis results and the supporting data, both at the cohort level and at the level of individual patients. We demonstrate the utility of our methodology and tool in a population of type II diabetic patients, treated with antidiabetic drugs, and monitored by the HbA1C test.

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems.

PubMed

Grunert, Oliver; Hernandez-Sanabria, Emma; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar H; Perneel, Maaike; Van Labeke, Marie-Christine; Reheul, Dirk; Boon, Nico

2016-01-05

The choice of soilless growing medium for plant nutrition, growth and support is crucial for improving the eco-sustainability of the production in horticultural systems. As our current understanding of the functional microbial communities inhabiting this ecosystem is still limited, we examined the microbial community development of the two most important growing media (organic and mineral) used in open soilless horticultural systems. We aimed to identify factors that influence community composition over time, and to compare the distribution of individual taxa across growing media, and their potential functionality. High throughput sequencing analysis revealed a distinctive and stable microbial community in the organic growing medium. Humidity, pH, nitrate-N, ammonium-N and conductivity were uncovered as the main factors associated with the resident bacterial communities. Ammonium-N was correlated with Rhizobiaceae abundance, while potential competitive interactions among both Methylophilaceae and Actinobacteridae with Rhizobiaceae were suggested. Our results revealed that soilless growing media are unique niches for diverse bacterial communities with temporal functional stability, which may possibly impact the resistance to external forces. These differences in communities can be used to develop strategies to move towards a sustainable horticulture with increased productivity and quality.

Structure of human POFUT2: insights into thrombospondin type 1 repeat fold and O-fucosylation

PubMed Central

Chen, Chun-I; Keusch, Jeremy J; Klein, Dominique; Hess, Daniel; Hofsteenge, Jan; Gut, Heinz

2012-01-01

Protein O-fucosylation is a post-translational modification found on serine/threonine residues of thrombospondin type 1 repeats (TSR). The fucose transfer is catalysed by the enzyme protein O-fucosyltransferase 2 (POFUT2) and >40 human proteins contain the TSR consensus sequence for POFUT2-dependent fucosylation. To better understand O-fucosylation on TSR, we carried out a structural and functional analysis of human POFUT2 and its TSR substrate. Crystal structures of POFUT2 reveal a variation of the classical GT-B fold and identify sugar donor and TSR acceptor binding sites. Structural findings are correlated with steady-state kinetic measurements of wild-type and mutant POFUT2 and TSR and give insight into the catalytic mechanism and substrate specificity. By using an artificial mini-TSR substrate, we show that specificity is not primarily encoded in the TSR protein sequence but rather in the unusual 3D structure of a small part of the TSR. Our findings uncover that recognition of distinct conserved 3D fold motifs can be used as a mechanism to achieve substrate specificity by enzymes modifying completely folded proteins of very wide sequence diversity and biological function. PMID:22588082

In the shadow: The emerging role of long non-coding RNAs in the immune response of Atlantic salmon.

PubMed

Tarifeño-Saldivia, E; Valenzuela-Miranda, D; Gallardo-Escárate, C

2017-08-01

The genomic era has increased the research effort to uncover how the genome of an organism, and specifically the transcriptome, is modulated after interplaying with pathogenic microorganisms and ectoparasites. However, the ever-increasing accessibility of sequencing technology has also evidenced regulatory roles of long non-coding RNAs (lncRNAs) related to several biological processes including immune response. This study reports a high-confidence annotation and a comparative transcriptome analysis of lncRNAs from several tissues of Salmo salar infected with the most prevalent pathogens in the Chilean salmon aquaculture such as the infectious salmon anemia (ISA) virus, the intracellular bacterium Piscirickettsia salmonis and the ectoparasite copepod Caligus rogercresseyi. Our analyses showed that lncRNAs are widely modulated during infection. However, this modulation is pathogen-specific and highly correlated with immuno-related genes associated with innate immune response. These findings represent the first discovery for the widespread differential expression of lncRNAs in response to infections with different types of pathogens in Atlantic salmon, suggesting that lncRNAs are pivotal player during the fish immune response. Copyright © 2017 Elsevier Ltd. All rights reserved.

Differential Connectivity in Colorectal Cancer Gene Expression Network

PubMed

Izadi, Fereshteh

2018-05-30

Colorectal cancer (CRC) is one of the challenging types of cancers; thus, exploring effective biomarkers related to colorectal could lead to significant progresses toward the treatment of this disease. In the present study, CRC gene expression datasets have been reanalyzed. Mutual differentially expressed genes across 294 normal mucosa and adjacent tumoral samples were then utilized in order to build two independent transcriptional regulatory networks. By analyzing the networks topologically, genes with differential global connectivity related to cancer state were determined for which the potential transcriptional regulators including transcription factors were identified. The majority of differentially connected genes (DCGs) were up-regulated in colorectal transcriptome experiments. Moreover, a number of these genes have been experimentally validated as cancer or CRC-associated genes. The DCGs, including GART, TGFB1, ITGA2, SLC16A5, SOX9, and MMP7, were investigated across 12 cancer types. Functional enrichment analysis followed by detailed data mining exhibited that these candidate genes could be related to CRC by mediating in metastatic cascade in addition to shared pathways with 12 cancer types by triggering the inflammatory events Our study uncovered correlated alterations in gene expression related to CRC susceptibility and progression that the potent candidate biomarkers could provide a link to disease.

Hidden Structural Codes in Protein Intrinsic Disorder.

PubMed

Borkosky, Silvia S; Camporeale, Gabriela; Chemes, Lucía B; Risso, Marikena; Noval, María Gabriela; Sánchez, Ignacio E; Alonso, Leonardo G; de Prat Gay, Gonzalo

2017-10-17

Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.

Use of Statistical Analysis of Acoustic Emission Data on Carbon-Epoxy COPV Materials-of-Construction for Enhanced Felicity Ratio Onset Determination

NASA Technical Reports Server (NTRS)

Abraham, Arick Reed A.; Johnson, Kenneth L.; Nichols, Charles T.; Saulsberry, Regor L.; Waller, Jess M.

2012-01-01

Broadband modal acoustic emission (AE) data were acquired during intermittent load hold tensile test profiles on Toray T1000G carbon fiber-reinforced epoxy (C/Ep) single tow specimens. A novel trend seeking statistical method to determine the onset of significant AE was developed, resulting in more linear decreases in the Felicity ratio (FR) with load, potentially leading to more accurate failure prediction. The method developed uses an exponentially weighted moving average (EWMA) control chart. Comparison of the EWMA with previously used FR onset methods, namely the discrete (n), mean (n (raised bar)), normalized (n%) and normalized mean (n(raised bar)%) methods, revealed the EWMA method yields more consistently linear FR versus load relationships between specimens. Other findings include a correlation between AE data richness and FR linearity based on the FR methods discussed in this paper, and evidence of premature failure at lower than expected loads. Application of the EWMA method should be extended to other composite materials and, eventually, composite components such as composite overwrapped pressure vessels. Furthermore, future experiments should attempt to uncover the factors responsible for infant mortality in C/Ep strands.

DCE-MRI-Derived Volume Transfer Constant (Ktrans) and DWI Apparent Diffusion Coefficient as Predictive Markers of Short- and Long-Term Efficacy of Chemoradiotherapy in Patients With Esophageal Cancer.

PubMed

Ye, Zhi-Min; Dai, Shu-Jun; Yan, Feng-Qin; Wang, Lei; Fang, Jun; Fu, Zhen-Fu; Wang, Yue-Zhen

2018-01-01

This study aimed to evaluate both the short- and long-term efficacies of chemoradiotherapy in relation to the treatment of esophageal cancer . This was achieved through the use of dynamic contrast-enhanced magnetic resonance imaging-derived volume transfer constant and diffusion weighted imaging-derived apparent diffusion coefficient . Patients with esophageal cancer were assigned into the sensitive and resistant groups based on respective efficacies in chemoradiotherapy. Dynamic contrast-enhanced magnetic resonance imaging and diffusion weighted imaging were used to measure volume transfer constant and apparent diffusion coefficient, while computed tomography was used to calculate tumor size reduction rate. Pearson correlation analyses were conducted to analyze correlation between volume transfer constant, apparent diffusion coefficient, and the tumor size reduction rate. Receiver operating characteristic curve was constructed to analyze the short-term efficacy of volume transfer constant and apparent diffusion coefficient, while Kaplan-Meier curve was employed for survival rate analysis. Cox proportional hazard model was used for the risk factors for prognosis of patients with esophageal cancer. Our results indicated reduced levels of volume transfer constant, while increased levels were observed in ADC min , ADC mean , and ADC max following chemoradiotherapy. A negative correlation was determined between ADC min , ADC mean , and ADC max , as well as in the tumor size reduction rate prior to chemoradiotherapy, whereas a positive correlation was uncovered postchemoradiotherapy. Volume transfer constant was positively correlated with tumor size reduction rate both before and after chemoradiotherapy. The 5-year survival rate of patients with esophageal cancer having high ADC min , ADC mean , and ADC max and volume transfer constant before chemoradiotherapy was greater than those with respectively lower values. According to the Cox proportional hazard model, ADC mean , clinical stage, degree of differentiation, and tumor stage were all confirmed as being independent risk factors in regard to the prognosis of patients with EC. The findings of this study provide evidence suggesting that volume transfer constant and apparent diffusion coefficient as being tools allowing for the evaluation of both the short- and long-term efficacies of chemoradiotherapy esophageal cancer treatment.

Massive sequencing of 70 genes reveals a myriad of missing genes or mechanisms to be uncovered in hereditary spastic paraplegias

PubMed Central

Morais, Sara; Raymond, Laure; Mairey, Mathilde; Coutinho, Paula; Brandão, Eva; Ribeiro, Paula; Loureiro, José Leal; Sequeiros, Jorge; Brice, Alexis; Alonso, Isabel; Stevanin, Giovanni

2017-01-01

Hereditary spastic paraplegias (HSP) are neurodegenerative disorders characterized by lower limb spasticity and weakness that can be complicated by other neurological or non-neurological signs. Despite a high genetic heterogeneity (>60 causative genes), 40–70% of the families remain without a molecular diagnosis. Analysis of one of the pioneer cohorts of 193 HSP families generated in the early 1990s in Portugal highlighted that SPAST and SPG11 are the most frequent diagnoses. We have now explored 98 unsolved families from this series using custom next generation sequencing panels analyzing up to 70 candidate HSP genes. We identified the likely disease-causing variant in 20 of the 98 families with KIF5A being the most frequently mutated gene. We also found 52 variants of unknown significance (VUS) in 38% of the cases. These new diagnoses resulted in 42% of solved cases in the full Portuguese cohort (81/193). Segregation of the variants was not always compatible with the presumed inheritance, indicating that the analysis of all HSP genes regardless of the inheritance mode can help to explain some cases. Our results show that there is still a large set of unknown genes responsible for HSP and most likely novel mechanisms or inheritance modes leading to the disease to be uncovered, but this will require international collaborative efforts, particularly for the analysis of VUS. PMID:28832565

Covariance, correlation matrix, and the multiscale community structure of networks.

PubMed

Shen, Hua-Wei; Cheng, Xue-Qi; Fang, Bin-Xing

2010-07-01

Empirical studies show that real world networks often exhibit multiple scales of topological descriptions. However, it is still an open problem how to identify the intrinsic multiple scales of networks. In this paper, we consider detecting the multiscale community structure of network from the perspective of dimension reduction. According to this perspective, a covariance matrix of network is defined to uncover the multiscale community structure through the translation and rotation transformations. It is proved that the covariance matrix is the unbiased version of the well-known modularity matrix. We then point out that the translation and rotation transformations fail to deal with the heterogeneous network, which is very common in nature and society. To address this problem, a correlation matrix is proposed through introducing the rescaling transformation into the covariance matrix. Extensive tests on real world and artificial networks demonstrate that the correlation matrix significantly outperforms the covariance matrix, identically the modularity matrix, as regards identifying the multiscale community structure of network. This work provides a novel perspective to the identification of community structure and thus various dimension reduction methods might be used for the identification of community structure. Through introducing the correlation matrix, we further conclude that the rescaling transformation is crucial to identify the multiscale community structure of network, as well as the translation and rotation transformations.

Positioning Teachers: A Discourse Analysis of Russian and American Teacher Identities in the Context of Changing National Assessment Mandates

ERIC Educational Resources Information Center

Ignatieva, Raisa P.

2011-01-01

The purpose of the study was to uncover the cultural beliefs and values that underlie American and Russian teachers' representations of their professional identities and their understanding of power in education in the context of globally disseminated education reforms and current educational mandates--the No Child Left Behind Act of 2001 (NCLB)…

Translating Answers to Open-Ended Survey Questions in Cross-Cultural Research: A Case Study on the Interplay between Translation, Coding, and Analysis

ERIC Educational Resources Information Center

Behr, Dorothée

2015-01-01

Open-ended probing questions in cross-cultural surveys help uncover equivalence problems in cross-cultural survey research. For languages that a project team does not understand, probe answers need to be translated into a common project language. This article presents a case study on translating open-ended, that is, narrative answers. It describes…

Functional Analysis of Somatic Mutations in Lung Cancer

DTIC Science & Technology

2015-10-01

antibody cetuximab [11]. Finally, we have developed novel single cell sequencing approaches to uncover EGFR mutational variants in glioblastoma and their...assessed which mutations are epistatic to EGFR or capable of initiating xenograft tumor formation in vivo. Using eVIP, we identified 69% of mutations...analyzed as impactful whereas 31% appear functionally neutral. A subset of the impactful mutations induce xenograft tumor formation in mice and/or

What Indicates Competency in Systems Based Practice? An Analysis of Perspective Consistency among Healthcare Team Members

ERIC Educational Resources Information Center

Graham, Mark J.; Naqvi, Zoon; Encandela, John A.; Bylund, Carma L.; Dean, Randa; Calero-Breckheimer, Ayxa; Schmidt, Hilary J.

2009-01-01

In many parts of the world the practice of medicine and medical education increasingly focus on providing patient care within context of the larger healthcare system. Our purpose is to solicit perceptions of all professional stakeholders (e.g. nurses) of the system regarding the U.S. ACGME competency Systems Based Practice to uncover the extent to…

On the Analysis of Fraction Subtraction Data: The DINA Model, Classification, Latent Class Sizes, and the Q-Matrix

ERIC Educational Resources Information Center

DeCarlo, Lawrence T.

2011-01-01

Cognitive diagnostic models (CDMs) attempt to uncover latent skills or attributes that examinees must possess in order to answer test items correctly. The DINA (deterministic input, noisy "and") model is a popular CDM that has been widely used. It is shown here that a logistic version of the model can easily be fit with standard software for…