Protein Poly(ADP-ribosyl)ation Regulates Arabidopsis Immune Gene Expression and Defense Responses

PubMed Central

Feng, Baomin; Liu, Chenglong; de Oliveira, Marcos V. V.; Intorne, Aline C.; Li, Bo; Babilonia, Kevin; de Souza Filho, Gonçalo A.; Shan, Libo; He, Ping

2015-01-01

Perception of microbe-associated molecular patterns (MAMPs) elicits transcriptional reprogramming in hosts and activates defense to pathogen attacks. The molecular mechanisms underlying plant pattern-triggered immunity remain elusive. A genetic screen identified Arabidopsis poly(ADP-ribose) glycohydrolase 1 (atparg1) mutant with elevated immune gene expression upon multiple MAMP and pathogen treatments. Poly(ADP-ribose) glycohydrolase (PARG) is predicted to remove poly(ADP-ribose) polymers on acceptor proteins modified by poly(ADP-ribose) polymerases (PARPs) with three PARPs and two PARGs in Arabidopsis genome. AtPARP1 and AtPARP2 possess poly(ADP-ribose) polymerase activity, and the activity of AtPARP2 was enhanced by MAMP treatment. AtPARG1, but not AtPARG2, carries glycohydrolase activity in vivo and in vitro. Importantly, mutation (G450R) in atparg1 blocks its activity and the corresponding residue is highly conserved and essential for human HsPARG activity. Consistently, mutant atparp1atparp2 plants exhibited compromised immune gene activation and enhanced susceptibility to pathogen infections. Our study indicates that protein poly(ADP-ribosyl)ation plays critical roles in plant immune gene expression and defense to pathogen attacks. PMID:25569773

DAMPs, MAMPs, and NAMPs in plant innate immunity.

PubMed

Choi, Hyong Woo; Klessig, Daniel F

2016-10-26

Multicellular organisms have evolved systems/mechanisms to detect various forms of danger, including attack by microbial pathogens and a variety of pests, as well as tissue and cellular damage. Detection via cell-surface receptors activates an ancient and evolutionarily conserved innate immune system. Potentially harmful microorganisms are recognized by the presence of molecules or parts of molecules that have structures or chemical patterns unique to microbes and thus are perceived as non-self/foreign. They are referred to as Microbe-Associated Molecular Patterns (MAMPs). Recently, a class of small molecules that is made only by nematodes, and that functions as pheromones in these organisms, was shown to be recognized by a wide range of plants. In the presence of these molecules, termed Nematode-Associated Molecular Patterns (NAMPs), plants activate innate immune responses and display enhanced resistance to a broad spectrum of microbial and nematode pathogens. In addition to pathogen attack, the relocation of various endogenous molecules or parts of molecules, generally to the extracellular milieu, as a result of tissue or cellular damage is perceived as a danger signal, and it leads to the induction of innate immune responses. These relocated endogenous inducers are called Damage-Associated Molecular Patterns (DAMPs). This mini-review is focused on plant DAMPs, including the recently discovered Arabidopsis HMGB3, which is the counterpart of the prototypic animal DAMP HMGB1. The plant DAMPs will be presented in the context of plant MAMPs and NAMPs, as well as animal DAMPs.

Illicit Heroin and Methamphetamine Use among Methadone Maintenance Treatment Patients in Dehong Prefecture of Yunnan Province, China.

PubMed

Wang, Rongrong; Ding, Yingying; Bai, Hongling; Duan, Song; Ye, Runhua; Yang, Yuecheng; Wang, Jibao; Tang, Renhai; Gao, Meiyang; He, Na

2015-01-01

Methadone maintenance treatment (MMT) was introduced to China in 2004 to reduce the harm of injecting drug users (IDUs). However, little is known about continued drug use, especially methamphetamine (MAMP), among MMT patients. A survey was conducted among patients attending five major MMT clinics in Dehong Prefecture in 2014 to investigate the heroin and MAMP use and their associated risk factors. Participants were administered with face-to-face interviews, and urine tests for morphine and MAMP. A total of 2,121 were eligible and participated in the study. Among them, 220 (10.4%) were only positive for morphine, 12.9% were only positive for MAMP, and 196 (9.2%) were positive for both morphine and MAMP. Compared with neither use of heroin nor MAMP during MMT, heroin use (not using MAMP) was associated with ethnicity, shorter duration of MMT, lower dose of methadone, and having had no more than two sex partners in the past year; MAMP use (not using heroin) was associated with ethnicity, longer duration of MMT, higher dose of methadone and being aged <30 years (vs. ≥50 years); use of both heroin and MAMP was associated with being Dai minority (vs. Han), a marital status of divorced or widowed, having used drugs for ≥10 years and shorter duration of MMT. These findings indicate the complexity in the treatment of heroin users and underscore the importance in prescribing appropriate methadone dosages in order to reduce both heroin and MAMP use.

Directed evolution of FLS2 towards novel flagellin peptide recognition

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

Helft, Laura; Thompson, Mikayla; Bent, Andrew F.

Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wildtype Arabidopsis FLS2 confers little or no response. A targeted approachmore » generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. Furthermore, these studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.« less

Directed evolution of FLS2 towards novel flagellin peptide recognition

DOE PAGES

Helft, Laura; Thompson, Mikayla; Bent, Andrew F.

2016-06-06

Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wildtype Arabidopsis FLS2 confers little or no response. A targeted approachmore » generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. Furthermore, these studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.« less

β-glucans and eicosapolyenoic acids as MAMPs in plant–oomycete interactions: past and present

PubMed Central

Robinson, Sara M.; Bostock, Richard M.

2015-01-01

Branched β-1,3-glucans and the eicosapolyenoic acids (EP) are among the best characterized oomycete elicitors that trigger innate immune responses in plants. These elicitors were identified over three decades ago, and they were useful in the study of the sequence of physiological, biochemical and molecular events that induce resistance in plants. However, in spite of the cross-kingdom parallels where these molecules are well-characterized as immune system modulators in animals, their perception and modes of action in plants remains obscure. Oomycetes are among the most important plant pathogens, responsible for diseases that devastate crops, ornamentals, and tree species worldwide. With the recent interest and advances in our understanding of innate immunity in plants, and the redefining of many of the classical elicitors as microbe-associated molecular patterns (MAMPs), it seems timely and important to reexamine β-glucans and EP using contemporary approaches. In this review, we highlight early studies of β-glucans and EP, discuss their roles as evolutionarily conserved signals, and consider their action in relation to current models of MAMP-triggered immunity. PMID:25628639

Functionally Redundant RXLR Effectors from Phytophthora infestans Act at Different Steps to Suppress Early flg22-Triggered Immunity

PubMed Central

Fraiture, Malou; Liu, Xiaoyu; Boevink, Petra C.; Gilroy, Eleanor M.; Chen, Ying; Kandel, Kabindra; Sessa, Guido; Birch, Paul R. J.; Brunner, Frédéric

2014-01-01

Genome sequences of several economically important phytopathogenic oomycetes have revealed the presence of large families of so-called RXLR effectors. Functional screens have identified RXLR effector repertoires that either compromise or induce plant defense responses. However, limited information is available about the molecular mechanisms underlying the modes of action of these effectors in planta. The perception of highly conserved pathogen- or microbe-associated molecular patterns (PAMPs/MAMPs), such as flg22, triggers converging signaling pathways recruiting MAP kinase cascades and inducing transcriptional re-programming, yielding a generic anti-microbial response. We used a highly synchronizable, pathogen-free protoplast-based assay to identify a set of RXLR effectors from Phytophthora infestans (PiRXLRs), the causal agent of potato and tomato light blight that manipulate early stages of flg22-triggered signaling. Of thirty-three tested PiRXLR effector candidates, eight, called Suppressor of early Flg22-induced Immune response (SFI), significantly suppressed flg22-dependent activation of a reporter gene under control of a typical MAMP-inducible promoter (pFRK1-Luc) in tomato protoplasts. We extended our analysis to Arabidopsis thaliana, a non-host plant species of P. infestans. From the aforementioned eight SFI effectors, three appeared to share similar functions in both Arabidopsis and tomato by suppressing transcriptional activation of flg22-induced marker genes downstream of post-translational MAP kinase activation. A further three effectors interfere with MAMP signaling at, or upstream of, the MAP kinase cascade in tomato, but not in Arabidopsis. Transient expression of the SFI effectors in Nicotiana benthamiana enhances susceptibility to P. infestans and, for the most potent effector, SFI1, nuclear localization is required for both suppression of MAMP signaling and virulence function. The present study provides a framework to decipher the molecular mechanisms underlying the manipulation of host MAMP-triggered immunity (MTI) by P. infestans and to understand the basis of host versus non-host resistance in plants towards P. infestans. PMID:24763622

Incorporation of methamphetamine and amphetamine in human hair following controlled oral methamphetamine administration

PubMed Central

Polettini, Aldo; Cone, Edward J.; Gorelick, David A.; Huestis, Marilyn A.

2012-01-01

Background Although hair testing is well established for the assessment of past drug exposure, uncertainties persist about mechanisms of drug incorporation into hair and interpretation of results. The aim of this study was to administer methamphetamine (MAMP) under controlled conditions as a model drug to investigate drug incorporation into human hair. Material and Methods Seven volunteers with a history of stimulant use received 4×10 mg (low) doses of sustained release S-(+)-MAMP HCl within one week, with weekly head hair samples collected by shaving. 3 weeks later, 4 of them received 4×20 mg (high) doses. After extensive isopropanol/phosphate buffer washing of the hair, MAMP and its metabolite amphetamine (AMP) concentrations were determined in all weekly hair samples by LC-MS-MS in selected reaction monitoring mode with the undeca- and deca-deuterated drugs, respectively, as internal standards (LLOQ, 0.005 ng/mg). Results MAMP Tmax occurred from 1 to 2 weeks after both doses, with Cmax ranging from 0.6–3.5 ng/mg after the low and 1.2–5.3 ng/mg after the high MAMP doses. AMP Cmax in hair was 0.1–0.3 ng/mg and 0.2–0.5 ng/mg, respectively, for low and high doses. Highly dose–related concentrations within subjects, but large variability between subjects were observed. MAMP concentrations were above the 0.2 ng/mg cutoff for at least two weeks following administration of both low and high doses. The overall AMP/MAMP ratio ranged from 0.07 to 0.37 with a mean value of 0.15±0.07, and a median of 0.13. The percentage of MAMP and AMP removed with the washing procedure decreased with time after administration. A strong correlation was found between area under the curve of MAMP (r2=0.90, p=0.00) and AMP (r2=0.94, p=0.00) concentrations calculated for the 3-week period following administration and the total melanin concentration in hair. Significant correlations were observed also between Cmax and melanin. Conclusions This study demonstrated that despite large inter-individual differences, the incorporation of MAMP and AMP into hair is dose-related with much of the observed scatter of MAMP and AMP concentrations explained by melanin concentration in hair. PMID:22541011

The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns

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

Henty-Ridilla, Jessica L.; Shimono, Masaki; Li, Jiejie

2013-04-04

Plants are constantly exposed to a large and diverse array of microbes; however, most plants are immune to the majority of potential invaders and susceptible to only a small subset of pathogens. The cytoskeleton comprises a dynamic intracellular framework that responds rapidly to biotic stresses and supports numerous fundamental cellular processes including vesicle trafficking, endocytosis and the spatial distribution of organelles and protein complexes. For years, the actin cytoskeleton has been assumed to play a role in plant innate immunity against fungi and oomycetes, based largely on static images and pharmacological studies. To date, however, there is little evidence thatmore » the host-cell actin cytoskeleton participates in responses to phytopathogenic bacteria. Here, we quantified the spatiotemporal changes in host-cell cytoskeletal architecture during the immune response to pathogenic and non-pathogenic strains of Pseudomonas syringae pv. tomato DC3000. Two distinct changes to host cytoskeletal arrays were observed that correspond to distinct phases of plant-bacterial interactions i.e. the perception of microbe-associated molecular patterns (MAMPs) during pattern-triggered immunity (PTI) and perturbations by effector proteins during effector-triggered susceptibility (ETS). We demonstrate that an immediate increase in actin filament abundance is a conserved and novel component of PTI. Notably, treatment of leaves with a MAMP peptide mimic was sufficient to elicit a rapid change in actin organization in epidermal cells, and this actin response required the host-cell MAMP receptor kinase complex, including FLS2, BAK1 and BIK1. Finally, we found that actin polymerization is necessary for the increase in actin filament density and that blocking this increase with the actin-disrupting drug latrunculin B leads to enhanced susceptibility of host plants to pathogenic and non-pathogenic bacteria.« less

Tomato Prenylated RAB Acceptor Protein 1 Modulates Trafficking and Degradation of the Pattern Recognition Receptor LeEIX2, Affecting the Innate Immune Response

PubMed Central

Pizarro, Lorena; Leibman-Markus, Meirav; Schuster, Silvia; Bar, Maya; Meltz, Tal; Avni, Adi

2018-01-01

Plants recognize microbial/pathogen associated molecular patterns (MAMP/PAMP) through pattern recognition receptors (PRRs) triggering an immune response against pathogen progression. MAMP/PAMP triggered immune response requires PRR endocytosis and trafficking for proper deployment. LeEIX2 is a well-known Solanum lycopersicum RLP-PRR, able to recognize and respond to the fungal MAMP/PAMP ethylene-inducing xylanase (EIX), and its function is highly dependent on intracellular trafficking. Identifying protein machinery components regulating LeEIX2 intracellular trafficking is crucial to our understanding of LeEIX2 mediated immune responses. In this work, we identified a novel trafficking protein, SlPRA1A, a predicted regulator of RAB, as an interactor of LeEIX2. Overexpression of SlPRA1A strongly decreases LeEIX2 endosomal localization, as well as LeEIX2 protein levels. Accordingly, the innate immune responses to EIX are markedly reduced by SlPRA1A overexpression, presumably due to a decreased LeEIX2 availability. Studies into the role of SlPRA1A in LeEIX2 trafficking revealed that LeEIX2 localization in multivesicular bodies/late endosomes is augmented by SlPRA1A. Furthermore, inhibiting vacuolar function prevents the LeEIX2 protein level reduction mediated by SlPRA1A, suggesting that SlPRA1A may redirect LeEIX2 trafficking to the vacuole for degradation. Interestingly, SlPRA1A overexpression reduces the amount of several RLP-PRRs, but does not affect the protein level of receptor-like kinase PRRs, suggesting a specific role of SlPRA1A in RLP-PRR trafficking and degradation. PMID:29545816

Interplay Between Innate Immunity and the Plant Microbiota.

PubMed

Hacquard, Stéphane; Spaepen, Stijn; Garrido-Oter, Ruben; Schulze-Lefert, Paul

2017-08-04

The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.

Identification of quantitative trait loci controlling gene expression during the innate immunity response of soybean

USDA-ARS?s Scientific Manuscript database

Microbe associated molecular pattern (MAMP)-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. However, most of our knowledge of MTI comes from studies of model systems with relatively little work done with crop plants. In this work, we re...

m6A RNA Degradation Products are Catabolized by an Evolutionarily Conserved N6-methyl-AMP Deaminase in Plant and Mammalian Cells.

PubMed

Chen, Mingjia; Urs, Mounashree J; Sánchez-González, Ismael; Olayioye, Monilola A; Herde, Marco; Witte, Claus-Peter

2018-06-08

N6-methylated adenine (m6A) is the most frequent posttranscriptional modification in eukaryotic mRNA. Turnover of RNA generates N6-methylated AMP (N6-mAMP), which has an unclear metabolic fate. We show that Arabidopsis thaliana and human cells require an N6-mAMP deaminase (ADAL, renamed MAPDA) to catabolize N6-mAMP to inosine monophosphate (IMP) in vivo by hydrolytically removing the aminomethyl group. A phylogenetic, structural, and biochemical analysis revealed that many fungi partially or fully lack MAPDA, which coincides with a minor role of N6A-RNA methylation in these organisms. MAPDA likely protects RNA from m6A mis-incorporation. This is required because eukaryotic RNA polymerase can use N6-mATP as a substrate. Upon abrogation of MAPDA, root growth is slightly reduced, and the N6-methyladenosine, N6-mAMP, and N6-mATP concentrations are increased in Arabidopsis. Although this will potentially lead to m6A mis-incorporation into RNA, we show that the frequency is too low to be reliably detected in vivo. Since N6-mAMP was several fold more abundant than N6-mATP in MAPDA mutants, we speculate that additional molecular filters suppress the generation of N6-mATP. Enzyme kinetic data indicate that adenylate kinases represent such filters being highly selective for AMP versus N6-mAMP phosphorylation. We conclude that a multilayer molecular protection system is in place preventing N6-mAMP accumulation and salvage. © 2018 American Society of Plant Biologists. All rights reserved.

Identification of prenatal amphetamines exposure by maternal interview and meconium toxicology in the Infant Development, Environment and Lifestyle (IDEAL) study.

PubMed

Gray, Teresa R; LaGasse, Linda L; Smith, Lynne M; Derauf, Chris; Grant, Penny; Shah, Rizwan; Arria, Amelia M; Della Grotta, Sheri A; Strauss, Arthur; Haning, William F; Lester, Barry M; Huestis, Marilyn A

2009-12-01

The Infant Development Environment and Lifestyle study is investigating the effects of prenatal methamphetamine (MAMP) exposure on infant and child development; potential concurrent exposure to cannabis and tobacco also are evaluated. Maternal self-reported drug use and/or meconium toxicology results defined drug exposure status. It is unclear how the frequency, duration, and magnitude of maternal MAMP exposure affect qualitative and quantitative meconium results. Interviews regarding maternal drug use were collected shortly after birth; meconium specimens were screened for amphetamines, cannabis, and cotinine by immunoassay and confirmed by gas chromatography mass spectrometry. The majority of MAMP- and cannabis-exposed infants were identified by maternal interview alone. Meconium tests were more likely to be positive if the mother reported MAMP and cannabis use, particularly in the third trimester. Less than half of immunoassay-positive amphetamines (31.0%) and cannabis (17.9%) meconium results were confirmed by gas chromatography mass spectrometry. Tobacco exposure was equally detected by immunoassay cotinine screening and maternal report. Meconium concentrations did not correlate with maternal self-report status or trimester of use or frequency or route of MAMP use. Maternal self-report was more sensitive than meconium testing for identifying MAMP and cannabis-exposed neonates; however, the timing of drug exposure may influence meconium toxicology results. Most women stopped MAMP and cannabis use before the third trimester. In the first trimester, meconium has not yet formed, and based on our recent results for opiates and cocaine, drug use in the second trimester appears to be poorly reflected in meconium. Low confirmation rates in meconium reinforce the need for confirmatory testing following positive screening results and additional research to identify alternative biomarkers.

Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000[OPEN

PubMed Central

Lewis, Laura A.; Polanski, Krzysztof; de Torres-Zabala, Marta; Bowden, Laura; Jenkins, Dafyd J.; Hill, Claire; Baxter, Laura; Truman, William; Prusinska, Justyna; Hickman, Richard; Wild, David L.; Ott, Sascha; Buchanan-Wollaston, Vicky; Beynon, Jim

2015-01-01

Transcriptional reprogramming is integral to effective plant defense. Pathogen effectors act transcriptionally and posttranscriptionally to suppress defense responses. A major challenge to understanding disease and defense responses is discriminating between transcriptional reprogramming associated with microbial-associated molecular pattern (MAMP)-triggered immunity (MTI) and that orchestrated by effectors. A high-resolution time course of genome-wide expression changes following challenge with Pseudomonas syringae pv tomato DC3000 and the nonpathogenic mutant strain DC3000hrpA- allowed us to establish causal links between the activities of pathogen effectors and suppression of MTI and infer with high confidence a range of processes specifically targeted by effectors. Analysis of this information-rich data set with a range of computational tools provided insights into the earliest transcriptional events triggered by effector delivery, regulatory mechanisms recruited, and biological processes targeted. We show that the majority of genes contributing to disease or defense are induced within 6 h postinfection, significantly before pathogen multiplication. Suppression of chloroplast-associated genes is a rapid MAMP-triggered defense response, and suppression of genes involved in chromatin assembly and induction of ubiquitin-related genes coincide with pathogen-induced abscisic acid accumulation. Specific combinations of promoter motifs are engaged in fine-tuning the MTI response and active transcriptional suppression at specific promoter configurations by P. syringae. PMID:26566919

Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000.

PubMed

Lewis, Laura A; Polanski, Krzysztof; de Torres-Zabala, Marta; Jayaraman, Siddharth; Bowden, Laura; Moore, Jonathan; Penfold, Christopher A; Jenkins, Dafyd J; Hill, Claire; Baxter, Laura; Kulasekaran, Satish; Truman, William; Littlejohn, George; Prusinska, Justyna; Mead, Andrew; Steinbrenner, Jens; Hickman, Richard; Rand, David; Wild, David L; Ott, Sascha; Buchanan-Wollaston, Vicky; Smirnoff, Nick; Beynon, Jim; Denby, Katherine; Grant, Murray

2015-11-01

Transcriptional reprogramming is integral to effective plant defense. Pathogen effectors act transcriptionally and posttranscriptionally to suppress defense responses. A major challenge to understanding disease and defense responses is discriminating between transcriptional reprogramming associated with microbial-associated molecular pattern (MAMP)-triggered immunity (MTI) and that orchestrated by effectors. A high-resolution time course of genome-wide expression changes following challenge with Pseudomonas syringae pv tomato DC3000 and the nonpathogenic mutant strain DC3000hrpA- allowed us to establish causal links between the activities of pathogen effectors and suppression of MTI and infer with high confidence a range of processes specifically targeted by effectors. Analysis of this information-rich data set with a range of computational tools provided insights into the earliest transcriptional events triggered by effector delivery, regulatory mechanisms recruited, and biological processes targeted. We show that the majority of genes contributing to disease or defense are induced within 6 h postinfection, significantly before pathogen multiplication. Suppression of chloroplast-associated genes is a rapid MAMP-triggered defense response, and suppression of genes involved in chromatin assembly and induction of ubiquitin-related genes coincide with pathogen-induced abscisic acid accumulation. Specific combinations of promoter motifs are engaged in fine-tuning the MTI response and active transcriptional suppression at specific promoter configurations by P. syringae. © 2015 American Society of Plant Biologists. All rights reserved.

Acyloxyacyl hydrolase promotes the resolution of lipopolysaccharide-induced acute lung injury

PubMed Central

Tang, Zihui; Yang, Qian; Qian, Guojun; Qian, Jing; Zeng, Wenjiao; Gu, Jie; Chu, Tianqing; Zhu, Ning; Zhang, Wenhong; Yan, Dapeng; He, Rui; Chu, Yiwei

2017-01-01

Pulmonary infection is the most common risk factor for acute lung injury (ALI). Innate immune responses induced by Microbe-Associated Molecular Pattern (MAMP) molecules are essential for lung defense but can lead to tissue injury. Little is known about how MAMP molecules are degraded in the lung or how MAMP degradation/inactivation helps prevent or ameliorate the harmful inflammation that produces ALI. Acyloxyacyl hydrolase (AOAH) is a host lipase that inactivates Gram-negative bacterial endotoxin (lipopolysaccharide, or LPS). We report here that alveolar macrophages increase AOAH expression upon exposure to LPS and that Aoah+/+ mice recover more rapidly than do Aoah-/- mice from ALI induced by nasally instilled LPS or Klebsiella pneumoniae. Aoah-/- mouse lungs had more prolonged leukocyte infiltration, greater pro- and anti-inflammatory cytokine expression, and longer-lasting alveolar barrier damage. We also describe evidence that the persistently bioactive LPS in Aoah-/- alveoli can stimulate alveolar macrophages directly and epithelial cells indirectly to produce chemoattractants that recruit neutrophils to the lung and may prevent their clearance. Distinct from the prolonged tolerance observed in LPS-exposed Aoah-/- peritoneal macrophages, alveolar macrophages that lacked AOAH maintained or increased their responses to bioactive LPS and sustained inflammation. Inactivation of LPS by AOAH is a previously unappreciated mechanism for promoting resolution of pulmonary inflammation/injury induced by Gram-negative bacterial infection. PMID:28622363

Getting to PTI of bacterial RNAs: Triggering plant innate immunity by extracellular RNAs from bacteria.

PubMed

Park, Yong-Soon; Lee, Boyoung; Ryu, Choong-Min

2016-07-02

Defense against diverse biotic and abiotic stresses requires the plant to distinguish between self and non-self signaling molecules. Pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) are pivotal for triggering innate immunity in plants. Unlike in animals and humans, the precise roles of nucleic acids in plant innate immunity are unclear. We therefore investigated the effects of infiltration of total Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) RNAs into Arabidopsis plants. The pathogen population was 10-fold lower in bacterial RNAs pre-treated Arabidopsis plants than in the control. Bacterial RNAs purity was confirmed by physical (sonication) and chemical (RNase A and proteinase K digestion) methods. The perception of bacterial RNAs, especially rRNAs, positively regulated mitogen-activated protein kinase (MAPK) and induced a reactive oxygen species burst, callose deposition, salicylic acid (SA) and jasmonic acid (JA) signaling, and defense-related genes. Therefore, bacterial RNAs function as a new MAMP that activates plant innate immunity, providing a new paradigm for plant-microbe interactions.

Self/nonself perception in plants in innate immunity and defense

PubMed Central

Sanabria, Natasha M; Huang, Ju-Chi

2010-01-01

The ability to distinguish ‘self’ from ‘nonself’ is the most fundamental aspect of any immune system. The evolutionary solution in plants to the problems of perceiving and responding to pathogens involves surveillance of nonself, damaged-self and altered-self as danger signals. This is reflected in basal resistance or non-host resistance, which is the innate immune response that protects plants against the majority of pathogens. In the case of surveillance of nonself, plants utilize receptor-like proteins or -kinases (RLP/Ks) as pattern recognition receptors (PRRs), which can detect conserved pathogen/microbe-associated molecular pattern (P/MAMP) molecules. P/MAMP detection serves as an early warning system for the presence of a wide range of potential pathogens and the timely activation of plant defense mechanisms. However, adapted microbes express a suite of effector proteins that often interfere or act as suppressors of these defenses. In response, plants have evolved a second line of defense that includes intracellular nucleotide binding leucine-rich repeat (NB-LRR)-containing resistance proteins, which recognize isolate-specific pathogen effectors once the cell wall has been compromised. This host-immunity acts within the species level and is controlled by polymorphic host genes, where resistance protein-mediated activation of defense is based on an ‘altered-self’ recognition mechanism. PMID:21559176

The intestinal complement system in inflammatory bowel disease: Shaping intestinal barrier function.

PubMed

Sina, Christian; Kemper, Claudia; Derer, Stefanie

2018-06-01

The complement system is part of innate sensor and effector systems such as the Toll-like receptors (TLRs). It recognizes and quickly systemically and/or locally respond to microbial-associated molecular patterns (MAMPs) with a tailored defense reaction. MAMP recognition by intestinal epithelial cells (IECs) and appropriate immune responses are of major importance for the maintenance of intestinal barrier function. Enterocytes highly express various complement components that are suggested to be pivotal for proper IEC function. Appropriate activation of the intestinal complement system seems to play an important role in the resolution of chronic intestinal inflammation, while over-activation and/or dysregulation may worsen intestinal inflammation. Mice deficient for single complement components suffer from enhanced intestinal inflammation mimicking the phenotype of patients with chronic inflammatory bowel disease (IBD) such as Crohn's disease (CD) or ulcerative colitis (UC). However, the mechanisms leading to complement expression in IECs seem to differ markedly between UC and CD patients. Hence, how IECs, intestinal bacteria and epithelial cell expressed complement components interact in the course of IBD still remains to be mostly elucidated to define potential unique patterns contributing to the distinct subtypes of intestinal inflammation observed in CD and UC. Copyright © 2018 Elsevier Ltd. All rights reserved.

The role of isoflavone metabolism in plant protection depends on the rhizobacterial MAMP that triggers systemic resistance against Xanthomonas axonopodis pv. glycines in Glycine max (L.) Merr. cv. Osumi.

PubMed

Algar, Elena; Gutierrez-Mañero, F Javier; Garcia-Villaraco, Ana; García-Seco, Daniel; Lucas, J Antonio; Ramos-Solano, Beatriz

2014-09-01

Glycine max (L.) Merr. plays a crucial role in both the field of food and the pharmaceutical industry due to their input as plant protein and to the benefits of isoflavones (IF) for health. In addition, IF play a key role in nodulation and plant defense and therefore, an increase in IF would be desirable for better field performance. IF are secondary metabolites and therefore, inducible, so finding effective agents to increase IF contents is interesting. Among these agents, plant growth promoting rhizobacteria (PGPR) have been used to trigger systemic induction of plant's secondary metabolism through their microbe associated molecular patterns (MAMPs) that fit in the plant's receptors to start a systemic response. The aim of this study was to evaluate the ability of 4 PGPR that had a contrasted effect on IF metabolism, to protect plants against biotic stress and to establish the relation between IF profile and the systemic response triggered by the bacteria. Apparently, the response involves a lower sensitivity to ethylene and despite the decrease in effective photosynthesis, growth is only compromised in the case of M84, the most effective in protection. All strains protected soybean against Xanthomonas axonopodis pv. glycines (M84 > N5.18 > Aur9>N21.4) and only M84 and N5.18 involved IF. N5.18 stimulated accumulation of IF before pathogen challenge. M84 caused a significant increase on IF only after pathogen challenge and N21.4 caused a significant increase on IF content irrespective of pathogen challenge. Aur9 did not affect IF. These results point out that all 4 strains have MAMPs that trigger defensive metabolism in soybean. Protection induced by N21.4 and Aur9 involves other metabolites different to IF and the role of IF in defence depends on the previous metabolic status of the plant and on the bacterial MAMP. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Inflammatory mediators in mastitis and lactation insufficiency.

PubMed

Ingman, Wendy V; Glynn, Danielle J; Hutchinson, Mark R

2014-07-01

Mastitis is a common inflammatory disease during lactation that causes reduced milk supply. A growing body of evidence challenges the central role of pathogenic bacteria in mastitis, with disease severity associated with markers of inflammation rather than infection. Inflammation in the mammary gland may be triggered by microbe-associated molecular patterns (MAMPs) as well as danger-associated molecular patterns (DAMPs) binding to pattern recognition receptors such as the toll-like receptors (TLRs) on the surface of mammary epithelial cells and local immune cell populations. Activation of the TLR4 signalling pathway and downstream nuclear factor kappa B (NFkB) is critical to mediating local mammary gland inflammation and systemic immune responses in mouse models of mastitis. However, activation of NFkB also induces epithelial cell apoptosis and reduced milk protein synthesis, suggesting that inflammatory mediators activated during mastitis promote partial involution. Perturbed milk flow, maternal stress and genetic predisposition are significant risk factors for mastitis, and could lead to a heightened TLR4-mediated inflammatory response, resulting in increased susceptibility and severity of mastitis disease in the context of low MAMP abundance. Therefore, heightened host inflammatory signalling may act in concert with pathogenic or commensal bacterial species to cause both the inflammation associated with mastitis and lactation insufficiency. Here, we present an alternate paradigm to the widely held notion that breast inflammation is driven principally by infectious bacterial pathogens, and suggest there may be other therapeutic strategies, apart from the currently utilised antimicrobial agents, that could be employed to prevent and treat mastitis in women.

Draft Genome Sequence of Methylobacterium radiotolerans Strain MAMP 4754, a Bacterial Endophyte Isolated from Combretum erythrophyllum in South Africa

PubMed Central

Photolo, Mampolelo M.; Mavumengwana, Vuyo; Serepa-Dlamini, Mahloro H.

2017-01-01

ABSTRACT We announce here the draft genome sequence of Methylobacterium radiotolerans strain MAMP 4754, isolated from the roots of the medicinal plant Combretum erythrophyllum. M. radiotolerans has a genome size of 7,389,282 bp with 7,166 genes and a G+C content of 70.5%. PMID:28982992

Lysin Motif–Containing Proteins LYP4 and LYP6 Play Dual Roles in Peptidoglycan and Chitin Perception in Rice Innate Immunity[W][OA

PubMed Central

Liu, Bing; Li, Jian-Feng; Ao, Ying; Qu, Jinwang; Li, Zhangqun; Su, Jianbin; Zhang, Yang; Liu, Jun; Feng, Dongru; Qi, Kangbiao; He, Yanming; Wang, Jinfa; Wang, Hong-Bin

2012-01-01

Plant innate immunity relies on successful detection of microbe-associated molecular patterns (MAMPs) of invading microbes via pattern recognition receptors (PRRs) at the plant cell surface. Here, we report two homologous rice (Oryza sativa) lysin motif–containing proteins, LYP4 and LYP6, as dual functional PRRs sensing bacterial peptidoglycan (PGN) and fungal chitin. Live cell imaging and microsomal fractionation consistently revealed the plasma membrane localization of these proteins in rice cells. Transcription of these two genes could be induced rapidly upon exposure to bacterial pathogens or diverse MAMPs. Both proteins selectively bound PGN and chitin but not lipopolysaccharide (LPS) in vitro. Accordingly, silencing of either LYP specifically impaired PGN- or chitin- but not LPS-induced defense responses in rice, including reactive oxygen species generation, defense gene activation, and callose deposition, leading to compromised resistance against bacterial pathogen Xanthomonas oryzae and fungal pathogen Magnaporthe oryzae. Interestingly, pretreatment with excess PGN dramatically attenuated the alkalinization response of rice cells to chitin but not to flagellin; vice versa, pretreatment with chitin attenuated the response to PGN, suggesting that PGN and chitin engage overlapping perception components in rice. Collectively, our data support the notion that LYP4 and LYP6 are promiscuous PRRs for PGN and chitin in rice innate immunity. PMID:22872757

Molecularly imprinted-solid phase extraction combined with simultaneous derivatization and dispersive liquid-liquid microextraction for selective extraction and preconcentration of methamphetamine and ecstasy from urine samples followed by gas chromatography.

PubMed

Djozan, Djavanshir; Farajzadeh, Mir Ali; Sorouraddin, Saeed Mohammad; Baheri, Tahmineh

2012-07-27

In this study, a developed technique was reported for extraction and pre-concentration of methamphetamine (MAMP) and 3,4-methylenedioxymethamphetamine (MDMA, ecstasy) from urine samples using molecularly imprinted-solid phase extraction (MISPE) along with simultaneous derivatization and dispersive liquid-liquid microextraction (DLLME). Molecularly imprinted microspheres as sorbent in solid phase extraction (SPE) procedure were synthesized using precipitation polymerization with MAMP as the template. Aqueous solution of the target analytes was passed through MAMP-MIP cartridge and the adsorbed analytes were then eluted with methanol. The collected eluate was mixed with butylchloroformate which served as the derivatization reagent as well as the extraction solvent. The mixture was immediately injected into deionized water. After centrifugation, 1 μL of the settled organic phase was injected into gas chromatography-flame ionization detection (GC-FID) or gas chromatography-mass spectrometry (GC-MS). Various experimental parameters affecting the performance of both of the steps (MISPE and DLLME) were thoroughly investigated. The calibration graphs were linear in the ranges of 10-1500 ng mL(-1) (MAMP) and 50-1500 ng mL(-1) (MDMA), and the detection limits (LODs) were 2 and 18 ng mL(-1), respectively. The relative standard deviations (%RSDs) obtained for six repeated experiments (100 ng mL(-1) of each drug) were 5.1% and 6.8% for MAMP and MDMA, respectively. The relative recoveries obtained for the analytes in human urine samples, spiked with different levels of each drug, were within the range of 80-88%. Copyright © 2012 Elsevier B.V. All rights reserved.

Genetic and biochemical investigations of the role of MamP in redox control of iron biomineralization in Magnetospirillum magneticum.

PubMed

Jones, Stephanie R; Wilson, Tiffany D; Brown, Margaret E; Rahn-Lee, Lilah; Yu, Yi; Fredriksen, Laura L; Ozyamak, Ertan; Komeili, Arash; Chang, Michelle C Y

2015-03-31

Magnetotactic bacteria have evolved complex subcellular machinery to construct linear chains of magnetite nanocrystals that allow the host cell to sense direction. Each mixed-valent iron nanoparticle is mineralized from soluble iron within a membrane-encapsulated vesicle termed the magnetosome, which serves as a specialized compartment that regulates the iron, redox, and pH environment of the growing mineral. To dissect the biological components that control this process, we have carried out a genetic and biochemical study of proteins proposed to function in iron mineralization. In this study, we show that the redox sites of c-type cytochromes of the Magnetospirillum magneticum AMB-1 magnetosome island, MamP and MamT, are essential to their physiological function and that ablation of one or both heme motifs leads to loss of function, suggesting that their ability to carry out redox chemistry in vivo is important. We also develop a method to heterologously express fully heme-loaded MamP from AMB-1 for in vitro biochemical studies, which show that its Fe(III)-Fe(II) redox couple is set at an unusual potential (-89 ± 11 mV) compared with other related cytochromes involved in iron reduction or oxidation. Despite its low reduction potential, it remains competent to oxidize Fe(II) to Fe(III) and mineralize iron to produce mixed-valent iron oxides. Finally, in vitro mineralization experiments suggest that Mms mineral-templating peptides from AMB-1 can modulate the iron redox chemistry of MamP.

Phenylpropanoid Defences in Nicotiana tabacum Cells: Overlapping Metabolomes Indicate Common Aspects to Priming Responses Induced by Lipopolysaccharides, Chitosan and Flagellin-22

PubMed Central

Mhlongo, Msizi I.; Piater, Lizelle A.; Madala, Ntakadzeni E.; Steenkamp, Paul A.; Dubery, Ian A.

2016-01-01

Plants have evolved both constitutive and inducible defence strategies to cope with different biotic stimuli and stresses. Exposure of a plant to a challenging stress can lead to a primed state that allows it to launch a more rapid and stronger defence. Here we applied a metabolomic approach to study and compare the responses induced in Nicotiana tabacum cells by microbe-associated molecular pattern (MAMP) molecules, namely lipopolysaccharides (LPS), chitosan (CHT) and flagellin-22 (FLG22). Early response metabolites, extracted with methanol, were analysed by UHPLC-MS/MS. Using multivariate statistical tools the metabolic profiles induced by these elicitors were analysed. In the metabolic fingerprint of these agents a total of 19 cinnamic acid derivatives conjugated to quinic acids (chlorogenic acids), shikimic acid, tyramine, polyamines or glucose were found as discriminant biomarkers. In addition, treatment with the phytohormones salicylic acid (SA), methyljasmonic acid (MJ) and abscisic acid (ABA) resulted in differentially-induced phenylpropanoid pathway metabolites. The results indicate that the phenylpropanoid pathway is activated by these elicitors while hydroxycinnamic acid derivatives are commonly associated with the metabolic response to the MAMPs, and that the activated responses are modulated by both SA and MJ, with ABA not playing a role. PMID:26978774

Microbe associated molecular patterns from rhizosphere bacteria trigger germination and Papaver somniferum metabolism under greenhouse conditions.

PubMed

Bonilla, A; Sarria, A L F; Algar, E; Muñoz Ledesma, F J; Ramos Solano, B; Fernandes, J B; Gutierrez Mañero, F J

2014-01-01

Ten PGPR from different backgrounds were assayed on Papaver somniferum var. Madrigal to evaluate their potential as biotic elicitors to increase alkaloid content under the rationale that some microbe associated molecular patterns (MAMPs) are able to trigger plant metabolism. First, the 10 strains and their culture media at two different concentrations were tested for their ability to trigger seed germination. Then, the best three strains were tested for their ability to increase seedling growth and alkaloid levels under greenhouse conditions. Only three strains and their culture media enhanced germination. Then, germination enhancing capacity of these best three strains, N5.18 Stenotrophomonas maltophilia, Aur9 Chryseobacterium balustinum and N21.4 Pseudomonas fluorescens was evaluated in soil. Finally, the three strains were applied on seedlings at two time points, by soil drench or by foliar spray. Photosynthesis was measured, plant height was recorded, capsules were weighted and alkaloids analyzed by HPLC. Only N5.18 delivered by foliar spray significantly increased plant height coupled to an increase in total alkaloids and a significant increase in opium poppy straw dry weight; these increases were supported by a better photosynthetic efficiency. The relative contents of morphine, thebaine, codeine and oripavine were affected by this treatment causing a significant increase in morphine coupled to a decrease in thebaine, demonstrating the effectivity of MAMPs from N5.18 in this plant species. Considering the increase in capsule biomass and alkaloids together with the acceleration of germination, strain N5.18 appears as a good candidate to elicit plant metabolism and consequently, to increase productivity of Papaver somniferum. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Nonredundant functions of Arabidopsis LecRK-V.2 and LecRK-VII.1 in controlling stomatal immunity and jasmonate-mediated stomatal closure.

PubMed

Yekondi, Shweta; Liang, Fu-Chun; Okuma, Eiji; Radziejwoski, Amandine; Mai, Hsien-Wei; Swain, Swadhin; Singh, Prashant; Gauthier, Mathieu; Chien, Hsiao-Chiao; Murata, Yoshiyuki; Zimmerli, Laurent

2018-04-01

Stomatal immunity restricts bacterial entry to leaves through the recognition of microbe-associated molecular patterns (MAMPs) by pattern-recognition receptors (PRRs) and downstream abscisic acid and salicylic acid signaling. Through a reverse genetics approach, we characterized the function of the L-type lectin receptor kinase-V.2 (LecRK-V.2) and -VII.1 (LecRK-VII.1). Analyses of interactions with the PRR FLAGELLIN SENSING2 (FLS2) were performed by co-immunoprecipitation and bimolecular fluorescence complementation and whole-cell patch-clamp analyses were used to evaluate guard cell Ca 2+ -permeable cation channels. The Arabidopsis thaliana LecRK-V.2 and LecRK-VII.1 and notably their kinase activities were required for full activation of stomatal immunity. Knockout lecrk-V.2 and lecrk-VII.1 mutants were hyper-susceptible to Pseudomonas syringae infection and showed defective stomatal closure in response to bacteria or to the MAMPs flagellin and EF-Tu. By contrast, Arabidopsis over-expressing LecRK-V.2 or LecRK-VII.1 demonstrated a potentiated stomatal immunity. LecRK-V.2 and LecRK-VII.1 are shown to be part of the FLS2 PRR complex. In addition, LecRK-V.2 and LecRK-VII.1 were critical for methyl jasmonate (MeJA)-mediated stomatal closure, notably for MeJA-induced activation of guard cell Ca 2+ -permeable cation channels. This study highlights the role of LecRK-V.2 and LecRK-VII.1 in stomatal immunity at the FLS2 PRR complex and in MeJA-mediated stomatal closure. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

ETHYLENE INSENSITIVE3 and ETHYLENE INSENSITIVE3-LIKE1 repress SALICYLIC ACID INDUCTION DEFICIENT2 expression to negatively regulate plant innate immunity in Arabidopsis.

PubMed

Chen, Huamin; Xue, Li; Chintamanani, Satya; Germain, Hugo; Lin, Huiqiong; Cui, Haitao; Cai, Run; Zuo, Jianru; Tang, Xiaoyan; Li, Xin; Guo, Hongwei; Zhou, Jian-Min

2009-08-01

Pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) trigger plant immunity that forms the first line inducible defenses in plants. The regulatory mechanism of MAMP-triggered immunity, however, is poorly understood. Here, we show that Arabidopsis thaliana transcription factors ETHYLENE INSENSITIVE3 (EIN3) and ETHYLENE INSENSITIVE3-LIKE1 (EIL1), previously known to mediate ethylene signaling, also negatively regulate PAMP-triggered immunity. Plants lacking EIN3 and EIL1 display enhanced PAMP defenses and heightened resistance to Pseudomonas syringae bacteria. Conversely, plants overaccumulating EIN3 are compromised in PAMP defenses and exhibit enhanced disease susceptibility to Pseudomonas syringae. Microarray analysis revealed that EIN3 and EIL1 negatively control PAMP response genes. Further analyses indicated that SALICYLIC ACID INDUCTION DEFICIENT2 (SID2), which encodes isochorismate synthase required for pathogen-induced biosynthesis of salicylic acid (SA), is a key target of EIN3 and EIL1. Consistent with this, the ein3-1 eil1-1 double mutant constitutively accumulates SA in the absence of pathogen attack, and a mutation in SID2 restores normal susceptibility in the ein3 eil1 double mutant. EIN3 can specifically bind SID2 promoter sequence in vitro and in vivo. Taken together, our data provide evidence that EIN3/EIL1 directly target SID2 to downregulate PAMP defenses.

A look at plant immunity through the window of the multitasking coreceptor BAK1.

PubMed

Yasuda, Shigetaka; Okada, Kentaro; Saijo, Yusuke

2017-08-01

Recognition of microbe- and danger-associated molecular patterns (MAMPs and DAMPs, respectively) by pattern recognition receptors (PRRs) is central to innate immunity in both plants and animals. The plant PRRs described to date are all cell surface-localized receptors. According to their ligand-binding ectodomains, each PRR engages a specific coreceptor or adaptor kinase in its signaling complexes to regulate defense signaling. With a focus on the coreceptor RLK BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) and related SOMATIC EMBRYOGENESIS RECEPTOR KINASEs (SERKs), here we review the increasing inventory of BAK1 partners and their functions in plant immunity. We also discuss the significance of autoimmunity triggered by BAK1/SERK4 disintegration in shaping the strategies for attenuation of PRR signaling by infectious microbes and host plants. Copyright © 2017 Elsevier Ltd. All rights reserved.

OsLYP4 and OsLYP6 play critical roles in rice defense signal transduction.

PubMed

Liu, Bing; Li, Jian-Feng; Ao, Ying; Li, Zhangqun; Liu, Jun; Feng, Dongru; Qi, Kangbiao; He, Yanming; Zeng, Liexian; Wang, Jinfa; Wang, Hong-Bin

2013-02-01

Plant innate immunity relies on successful detection of trespassing pathogens through recognizing their microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) at the cell surface. We recently reported two rice lysin motif (LysM)-containing proteins, OsLYP4 and OsLYP6, as dual functional PRRs sensing bacterial peptidoglycan (PGN) and fungal chitin. Here we further demonstrated the important roles of OsLYP4 and OsLYP6 in rice defense signaling, as silencing of either LYP impaired the defense marker gene activation induced by either bacterial pathogen Xanthomonas oryzaecola or fungal pathogen Magnaporthe oryzae. Moreover, we found that OsLYP4 and OsLYP6 could form homo- and hetero-dimers, and could interact with CEBiP, suggesting an unexpected complexity of chitin perception in rice.

Rapid simultaneous determination of amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine, 3,4-methylenedioxymethamphetamine, and 3,4-methylenedioxyethylamphetamine in urine by solid-phase extraction and GC-MS: a method optimized for high-volume laboratories.

PubMed

Stout, Peter R; Horn, Carl K; Klette, Kevin L

2002-01-01

To facilitate analysis of high sample volumes, an extraction, derivatization and gas chromatographic-mass spectrometric analysis method was developed to simultaneously determine amphetamine (AMP), methamphetamine (MAMP), 3,4-methylenedioxyamphetamine (MDA) 3,4-methylenedioxymethamphetamine (MDMA), and 3,4-methylenedioxyethylamphetamine (MDEA) in urine. This method utilized a positive-pressure manifold cation-exchange polymer-based solid-phase extraction followed by elution directly into automated liquid sampler (ALS) vials. Rapid derivatization was accomplished using heptafluorobutyric anhydride (HFBA). Recoveries averaged 90% or greater for each of the compounds. Limits of detection were 62.5 ng/mL (AMP and MDEA), 15.6 ng/mL (MAMP), and 31.3 ng/mL (MDA and MDMA) using a 2-mL sample volume. The method was linear to 5000 ng/mL for all compounds using MDMA-d5 and MAMP-d14 as internal standards. Over 200 human urine samples previously determined to contain the target analytes were analyzed using the method. Excellent agreement was seen with previous quantitations. The method was challenged with 75 potentially interfering compounds and no interferences were seen. These interfering compounds included ephedrine, pseudoephedrine, phenylpropanolamine, and phenethylamine. The method resulted in dramatic reductions in processing time and waste production.

CSS/EMW/SOF (Combat Service Support/Engineering and Mine Warfare/Special Operations Forces) Mission Area Materiel Plan (MAMP) Software.

DTIC Science & Technology

1986-09-01

receive much benefit . [] 2. The MAMP program prioritization algorithm is the responsibility of TRADOC. This study analyzed the perceived deficiencies...C o I 0 w m a 0 0 - 0.. -W >. m a -a ZZ II w u3 c w Ir 0 ccD I j cnC 0 o w a w W a- Im 3 El0 1>1- - < OUU4 0 .0.. 3.0 I * T- ui l. IT w3 >0 . I- *, wWE ...34Related" else if deftpe - 3 then print "Non-Materiel" else if def tqjpe - 4 then print " Health Service’ alse print skip I line printcolum-81

Prebiotics as immunostimulants in aquaculture: a review.

PubMed

Song, Seong Kyu; Beck, Bo Ram; Kim, Daniel; Park, John; Kim, Jungjoon; Kim, Hyun Duk; Ringø, Einar

2014-09-01

Prebiotics are indigestible fibers that increase beneficial gut commensal bacteria resulting in improvements of the host's health. The beneficial effects of prebiotics are due to the byproducts generated from their fermentation by gut commensal bacteria. In this review, the direct effects of prebiotics on the innate immune system of fish are discussed. Prebiotics, such as fructooligosaccharide, mannanoligosaccharide, inulin, or β-glucan, are called immunosaccharides. They directly enhance innate immune responses including: phagocytic activation, neutrophil activation, activation of the alternative complement system, increased lysozyme activity, and more. Immunosaccharides directly activate the innate immune system by interacting with pattern recognition receptors (PRR) expressed on innate immune cells. They can also associate with microbe associated molecular patterns (MAMPs) to activate innate immune cells. However, the underlying mechanisms involved in innate immune cell activation need to be further explored. Many studies have indicated that immunosaccharides are beneficial to both finfish and shellfish. Copyright © 2014 Elsevier Ltd. All rights reserved.

DAMPs as mediators of sterile inflammation in aging-related pathologies.

PubMed

Feldman, Noa; Rotter-Maskowitz, Aviva; Okun, Eitan

2015-11-01

Accumulating evidence indicates that aging is associated with a chronic low-level inflammation, termed sterile-inflammation. Sterile-inflammation is a form of pathogen-free inflammation caused by mechanical trauma, ischemia, stress or environmental conditions such as ultra-violet radiation. These damage-related stimuli induce the secretion of molecular agents collectively termed danger-associated molecular patterns (DAMPs). DAMPs are recognized by virtue of specialized innate immune receptors, such as toll-like receptors (TLRs) and NOD-like receptor family, pyrin domain containing 3 (NLRP3). These receptors initiate signal transduction pathways, which typically drive inflammation in response to microbe-associated molecular patterns (MAMPs) and/or DAMPs. This review summarizes the current knowledge on DAMPs-mediated sterile-inflammation, its associated downstream signaling, and discusses the possibility that DAMPs activating TLRs or NLRP3 complex mediate sterile inflammation during aging and in aging-related pathologies. Copyright © 2015 Elsevier B.V. All rights reserved.

B cell Toll-like receptors and immunoglobulin class-switch DNA recombination

PubMed Central

Pone, Egest J.; Xu, Zhenming; White, Clayton A.; Zan, Hong; Casali, Paolo

2014-01-01

Toll-like receptors (TLRs) are a family of conserved pattern recognition receptors (PRRs). Engagement of TLRs in B cells by microbe-associated molecular patterns (MAMPs) induces T-independent (TI) antibody responses and plays an important role in the early stages of T-dependent (TD) antibody responses before specific T cell help becomes available, in part by facilitating B cell entry into the germinal center reaction. The role of B cell TLRs in the antibody response is magnified by the synergy of B cell receptor (BCR) crosslinking and TLR engagement in promoting B cell proliferation and efficiently inducing immunoglobulin (Ig) class switch DNA recombination (CSR), which crucially diversifies the antibody biological effector functions. Dual engagement of TLRs and BCR can be mediated by complex MAMPs such as lipopolysaccharides (LPS), which engages TLR4 through its lipid A moiety and crosslinks the BCR through its polysaccharidic moiety (O-antigen). Dual BCR/TLR engagement induces CSR to all Ig isotypes, as directed by different cytokines, while engagement of any TLR alone induces only marginal CSR. Integration of BCR and TLR signaling results in activation of the canonical and non-canonical NF-κB pathways, induction of activation-induced cytidine deaminase (AID) and germline transcription of switch (S) regions in the IgH locus. The last two are essential events for CSR to unfold. A critical role of dual BCR/TLR engagement in induction of CSR and generation of neutralizing antibodies is emphasized by the emergence of TLR ligands as integral components of vaccines that greatly boost humoral immunity in a B cell-intrinsic fashion. Further, dual BCR/TLR engagement by complex self-antigens will result in dysregulation of AID expression and CSR in autoreactive B cells, leading to generation of isotype-switched pathogenic autoantibodies. Finally, an important aspect of dual BCR/TLR engagement is the boosting of specific antibody response to tumor antigens, as suggested by high titers of anti-tumor antibodies in response to tumor vaccines that contain TLR agonists. PMID:22652800

Chitin-induced activation of immune signaling by the rice receptor CEBiP relies on a unique sandwich-type dimerization

PubMed Central

Hayafune, Masahiro; Berisio, Rita; Marchetti, Roberta; Silipo, Alba; Kayama, Miyu; Desaki, Yoshitake; Arima, Sakiko; Squeglia, Flavia; Ruggiero, Alessia; Tokuyasu, Ken; Molinaro, Antonio; Kaku, Hanae; Shibuya, Naoto

2014-01-01

Perception of microbe-associated molecular patterns (MAMPs) through pattern recognition receptors (PRRs) triggers various defense responses in plants. This MAMP-triggered immunity plays a major role in the plant resistance against various pathogens. To clarify the molecular basis of the specific recognition of chitin oligosaccharides by the rice PRR, CEBiP (chitin-elicitor binding protein), as well as the formation and activation of the receptor complex, biochemical, NMR spectroscopic, and computational studies were performed. Deletion and domain-swapping experiments showed that the central lysine motif in the ectodomain of CEBiP is essential for the binding of chitin oligosaccharides. Epitope mapping by NMR spectroscopy indicated the preferential binding of longer-chain chitin oligosaccharides, such as heptamer-octamer, to CEBiP, and also the importance of N-acetyl groups for the binding. Molecular modeling/docking studies clarified the molecular interaction between CEBiP and chitin oligosaccharides and indicated the importance of Ile122 in the central lysine motif region for ligand binding, a notion supported by site-directed mutagenesis. Based on these results, it was indicated that two CEBiP molecules simultaneously bind to one chitin oligosaccharide from the opposite side, resulting in the dimerization of CEBiP. The model was further supported by the observations that the addition of (GlcNAc)8 induced dimerization of the ectodomain of CEBiP in vitro, and the dimerization and (GlcNAc)8-induced reactive oxygen generation were also inhibited by a unique oligosaccharide, (GlcNβ1,4GlcNAc)4, which is supposed to have N-acetyl groups only on one side of the molecule. Based on these observations, we proposed a hypothetical model for the ligand-induced activation of a receptor complex, involving both CEBiP and Oryza sativa chitin-elicitor receptor kinase-1. PMID:24395781

Cerato-platanin induces resistance in Arabidopsis leaves through stomatal perception, overexpression of salicylic acid- and ethylene-signalling genes and camalexin biosynthesis.

PubMed

Baccelli, Ivan; Lombardi, Lara; Luti, Simone; Bernardi, Rodolfo; Picciarelli, Piero; Scala, Aniello; Pazzagli, Luigia

2014-01-01

Microbe-associated molecular patterns (MAMPs) lead to the activation of the first line of plant defence. Few fungal molecules are universally qualified as MAMPs, and proteins belonging to the cerato-platanin protein (CPP) family seem to possess these features. Cerato-platanin (CP) is the name-giving protein of the CPP family and is produced by Ceratocystis platani, the causal agent of the canker stain disease of plane trees (Platanus spp.). On plane tree leaves, the biological activity of CP has been widely studied. Once applied on the leaf surface, CP acts as an elicitor of defence responses. The molecular mechanism by which CP elicits leaves is still unknown, and the protective effect of CP against virulent pathogens has not been clearly demonstrated. In the present study, we tried to address these questions in the model plant Arabidopsis thaliana. Our results suggest that stomata rapidly sense CP since they responded to the treatment with ROS signalling and stomatal closure, and that CP triggers salicylic acid (SA)- and ethylene (ET)-signalling pathways, but not the jasmonic acid (JA)-signalling pathway, as revealed by the expression pattern of 20 marker genes. Among these, EDS1, PAD4, NPR1, GRX480, WRKY70, ACS6, ERF1a/b, COI1, MYC2, PDF1.2a and the pathogenesis-related (PR) genes 1-5. CP rapidly induced MAPK phosphorylation and induced the biosynthesis of camalexin within 12 hours following treatment. The induction of localised resistance was shown by a reduced susceptibility of the leaves to the infection with Botrytis cinerea and Pseudomonas syringae pv. tomato. These results contribute to elucidate the key steps of the signalling process underlying the resistance induction in plants by CP and point out the central role played by the stomata in this process.

Upregulation of toll-like receptors in chronic enteropathies in dogs.

PubMed

Burgener, I A; König, A; Allenspach, K; Sauter, S N; Boisclair, J; Doherr, M G; Jungi, T W

2008-01-01

Inflammatory bowel disease (IBD) is thought to result from a dysregulated interaction between the host immune system and commensal microflora. Toll-like receptors (TLRs) recognize microbe-associated molecular patterns (MAMPs), but their role in enteropathies in dogs is unknown. That there is a dysregulation of TLRs recognizing bacterial MAMPs in dogs with IBD. Sixteen healthy beagles and 12 dogs with steroid-treated (ST) and 23 dogs with food-responsive (FR) diarrhea. Prospective, observational study. mRNA expression of canine TLR2, 4, and 9 was evaluated by quantitative real-time RT-PCR in duodenal and colonic biopsies obtained before and after standard therapy. Samples from control dogs were taken at necropsy, with additional biopsies of stomach, jejunum, ileum, and mesenteric lymph node in 6 dogs. There were significant differences (P< or = .017) in expression of TLR2, 4, and 9 between the 6 sampled locations in healthy control dogs (lymph node > small intestine > or = colon). Before therapy, ST expressed more mRNA than control dogs for all 3 receptors (P < .05). There were no significant differences between pretreatment and posttreatment values, even though 32/35 dogs improved clinically. No associations were found when comparing receptor mRNA expression with either histology or clinical activity scores. Bacteria-responsive TLR2, 4, and 9 are upregulated in duodenal and colonic mucosa in IBD. This might lead to increased inflammation through interaction with the commensal flora. The absence of significant changes after therapy despite clinical improvement might point toward the existence of a genetic predisposition to IBD as described in human IBD.

Anion channels: master switches of stress responses.

PubMed

Roelfsema, M Rob G; Hedrich, Rainer; Geiger, Dietmar

2012-04-01

During stress, plant cells activate anion channels and trigger the release of anions across the plasma membrane. Recently, two new gene families have been identified that encode major groups of anion channels. The SLAC/SLAH channels are characterized by slow voltage-dependent activation (S-type), whereas ALMT genes encode rapid-activating channels (R-type). Both S- and R-type channels are stimulated in guard cells by the stress hormone ABA, which leads to stomatal closure. Besides their role in ABA-dependent stomatal movement, anion channels are also activated by biotic stress factors such as microbe-associated molecular patterns (MAMPs). Given that anion channels occur throughout the plant kingdom, they are likely to serve a general function as master switches of stress responses. Copyright © 2012 Elsevier Ltd. All rights reserved.

Untargeted metabolomics analysis reveals dynamic changes in azelaic acid- and salicylic acid derivatives in LPS-treated Nicotiana tabacum cells.

PubMed

Mhlongo, M I; Tugizimana, F; Piater, L A; Steenkamp, P A; Madala, N E; Dubery, I A

2017-01-22

To counteract biotic stress factors, plants employ multilayered defense mechanisms responsive to pathogen-derived elicitor molecules, and regulated by different phytohormones and signaling molecules. Here, lipopolysaccharide (LPS), a microbe-associated molecular pattern (MAMP) molecule, was used to induce defense responses in Nicotiana tabacum cell suspensions. Intracellular metabolites were extracted with methanol and analyzed using a liquid chromatography-mass spectrometry (UHPLC-qTOF-MS/MS) platform. The generated data were processed and examined with multivariate and univariate statistical tools. The results show time-dependent dynamic changes and accumulation of glycosylated signaling molecules, specifically those of azelaic acid, salicylic acid and methyl-salicylate as contributors to the altered metabolomic state in LPS-treated cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Receptor-mediated signalling in plants: molecular patterns and programmes

PubMed Central

Tör, Mahmut; Lotze, Michael T.; Holton, Nicholas

2009-01-01

A highly evolved surveillance system in plants is able to detect a broad range of signals originating from pathogens, damaged tissues, or altered developmental processes, initiating sophisticated molecular mechanisms that result in defence, wound healing, and development. Microbe-associated molecular pattern molecules (MAMPs), damage-associated molecular pattern molecules (DAMPs), virulence factors, secreted proteins, and processed peptides can be recognized directly or indirectly by this surveillance system. Nucleotide binding-leucine rich repeat proteins (NB-LRR) are intracellular receptors and have been targeted by breeders for decades to elicit resistance to crop pathogens in the field. Receptor-like kinases (RLKs) or receptor like proteins (RLPs) are membrane bound signalling molecules with an extracellular receptor domain. They provide an early warning system for the presence of potential pathogens and activate protective immune signalling in plants. In addition, they act as a signal amplifier in the case of tissue damage, establishing symbiotic relationships and effecting developmental processes. The identification of several important ligands for the RLK-type receptors provided an opportunity to understand how plants differentiate, how they distinguish beneficial and detrimental stimuli, and how they co-ordinate the role of various types of receptors under varying environmental conditions. The diverse roles of extra-and intracellular plant receptors are examined here and the recent findings on how they promote defence and development is reviewed. PMID:19628572

Automatic mobile device synchronization and remote control system for high-performance medical applications.

PubMed

Constantinescu, L; Kim, J; Chan, C; Feng, D

2007-01-01

The field of telemedicine is in need of generic solutions that harness the power of small, easily carried computing devices to increase efficiency and decrease the likelihood of medical errors. Our study resolved to build a framework to bridge the gap between handheld and desktop solutions by developing an automated network protocol that wirelessly propagates application data and images prepared by a powerful workstation to handheld clients for storage, display and collaborative manipulation. To this end, we present the Mobile Active Medical Protocol (MAMP), a framework capable of nigh-effortlessly linking medical workstation solutions to corresponding control interfaces on handheld devices for remote storage, control and display. The ease-of-use, encapsulation and applicability of this automated solution is designed to provide significant benefits to the rapid development of telemedical solutions. Our results demonstrate that the design of this system allows an acceptable data transfer rate, a usable framerate for diagnostic solutions and enough flexibility to enable its use in a wide variety of cases. To this end, we also present a large-scale multi-modality image viewer as an example application based on the MAMP.

Machine Learning Through Signature Trees. Applications to Human Speech.

ERIC Educational Resources Information Center

White, George M.

A signature tree is a binary decision tree used to classify unknown patterns. An attempt was made to develop a computer program for manipulating signature trees as a general research tool for exploring machine learning and pattern recognition. The program was applied to the problem of speech recognition to test its effectiveness for a specific…

The receptor-like cytoplasmic kinase BSR1 mediates chitin-induced defense signaling in rice cells.

PubMed

Kanda, Yasukazu; Yokotani, Naoki; Maeda, Satoru; Nishizawa, Yoko; Kamakura, Takashi; Mori, Masaki

2017-08-01

Broad-Spectrum Resistance 1 (BSR1) encodes a rice receptor-like cytoplasmic kinase, and enhances disease resistance when overexpressed. Rice plants overexpressing BSR1 are highly resistant to diverse pathogens, including rice blast fungus. However, the mechanism responsible for this resistance has not been fully characterized. To analyze the BSR1 function, BSR1-knockout (BSR1-KO) plants were generated using a clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system. Experiments using suspension-cultured cells revealed that defense responses including H 2 O 2 production (i.e. oxidative burst) and expression of defense-related genes induced by autoclaved conidia of the rice blast fungus significantly decreased in BSR1-KO cells. Furthermore, a treatment with chitin oligomers which function as microbe-associated molecular patterns (MAMPs) of the rice blast fungus resulted in considerably suppressed defense responses in BSR1-KO cells. These results suggest that BSR1 is important for the rice innate immunity triggered by the perception of chitin.

Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples.

PubMed

Díaz-Gay, Marcos; Vila-Casadesús, Maria; Franch-Expósito, Sebastià; Hernández-Illán, Eva; Lozano, Juan José; Castellví-Bel, Sergi

2018-06-14

Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic packages to address this topic have been developed in different languages/platforms. MutationalPatterns has arisen as the most efficient tool for the comparison with the signatures currently reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. However, the analysis of mutational signatures is nowadays restricted to a small community of bioinformatic experts. In this work we present Mutational Signatures in Cancer (MuSiCa), a new web tool based on MutationalPatterns and built using the Shiny framework in R language. By means of a simple interface suited to non-specialized researchers, it provides a comprehensive analysis of the somatic mutational status of the supplied cancer samples. It permits characterizing the profile and burden of mutations, as well as quantifying COSMIC-reported mutational signatures. It also allows classifying samples according to the above signature contributions. MuSiCa is a helpful web application to characterize mutational signatures in cancer samples. It is accessible online at http://bioinfo.ciberehd.org/GPtoCRC/en/tools.html and source code is freely available at https://github.com/marcos-diazg/musica .

Discriminative Features Mining for Offline Handwritten Signature Verification

NASA Astrophysics Data System (ADS)

Neamah, Karrar; Mohamad, Dzulkifli; Saba, Tanzila; Rehman, Amjad

2014-03-01

Signature verification is an active research area in the field of pattern recognition. It is employed to identify the particular person with the help of his/her signature's characteristics such as pen pressure, loops shape, speed of writing and up down motion of pen, writing speed, pen pressure, shape of loops, etc. in order to identify that person. However, in the entire process, features extraction and selection stage is of prime importance. Since several signatures have similar strokes, characteristics and sizes. Accordingly, this paper presents combination of orientation of the skeleton and gravity centre point to extract accurate pattern features of signature data in offline signature verification system. Promising results have proved the success of the integration of the two methods.

Collective iteration behavior for online social networks

NASA Astrophysics Data System (ADS)

Liu, Jian-Guo; Li, Ren-De; Guo, Qiang; Zhang, Yi-Cheng

2018-06-01

Understanding the patterns of collective behavior in online social network (OSNs) is critical to expanding the knowledge of human behavior and tie relationship. In this paper, we investigate a specific pattern called social signature in Facebook and Wiki users' online communication behaviors, capturing the distribution of frequency of interactions between different alters over time in the ego network. The empirical results show that there are robust social signatures of interactions no matter how friends change over time, which indicates that a stable commutation pattern exists in online communication. By comparing a random null model, we find the that commutation pattern is heterogeneous between ego and alters. Furthermore, in order to regenerate the pattern of the social signature, we present a preferential interaction model, which assumes that new users intend to look for the old users with strong ties while old users have tendency to interact with new friends. The experimental results show that the presented model can reproduce the heterogeneity of social signature by adjusting 2 parameters, the number of communicating targets m and the max number of interactions n, for Facebook users, m = n = 5, for Wiki users, m = 2 and n = 8. This work helps in deeply understanding the regularity of social signature.

matK-QR classifier: a patterns based approach for plant species identification.

PubMed

More, Ravi Prabhakar; Mane, Rupali Chandrashekhar; Purohit, Hemant J

2016-01-01

DNA barcoding is widely used and most efficient approach that facilitates rapid and accurate identification of plant species based on the short standardized segment of the genome. The nucleotide sequences of maturaseK ( matK ) and ribulose-1, 5-bisphosphate carboxylase ( rbcL ) marker loci are commonly used in plant species identification. Here, we present a new and highly efficient approach for identifying a unique set of discriminating nucleotide patterns to generate a signature (i.e. regular expression) for plant species identification. In order to generate molecular signatures, we used matK and rbcL loci datasets, which encompass 125 plant species in 52 genera reported by the CBOL plant working group. Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. Further, we detected Discriminating Patterns (DP) at genus and species level using PSSM for the matK dataset. Combining DP and consecutive pattern distances, we generated molecular signatures for each species. Finally, we performed a comparative assessment of these signatures with the existing methods including BLASTn, Support Vector Machines (SVM), Jrip-RIPPER, J48 (C4.5 algorithm), and the Naïve Bayes (NB) methods against NCBI-GenBank matK dataset. Due to the higher discrimination success obtained with the matK as compared to the rbcL , we selected matK gene for signature generation. We generated signatures for 60 species based on identified discriminating patterns at genus and species level. Our comparative assessment results suggest that a total of 46 out of 60 species could be correctly identified using generated signatures, followed by BLASTn (34 species), SVM (18 species), C4.5 (7 species), NB (4 species) and RIPPER (3 species) methods As a final outcome of this study, we converted signatures into QR codes and developed a software matK -QR Classifier (http://www.neeri.res.in/matk_classifier/index.htm), which search signatures in the query matK gene sequences and predict corresponding plant species. This novel approach of employing pattern-based signatures opens new avenues for the classification of species. In addition to existing methods, we believe that matK -QR Classifier would be a valuable tool for molecular taxonomists enabling precise identification of plant species.

Arabidopsis EF-Tu receptor enhances bacterial disease resistance in transgenic wheat.

PubMed

Schoonbeek, Henk-Jan; Wang, Hsi-Hua; Stefanato, Francesca L; Craze, Melanie; Bowden, Sarah; Wallington, Emma; Zipfel, Cyril; Ridout, Christopher J

2015-04-01

Perception of pathogen (or microbe)-associated molecular patterns (PAMPs/MAMPs) by pattern recognition receptors (PRRs) is a key component of plant innate immunity. The Arabidopsis PRR EF-Tu receptor (EFR) recognizes the bacterial PAMP elongation factor Tu (EF-Tu) and its derived peptide elf18. Previous work revealed that transgenic expression of AtEFR in Solanaceae confers elf18 responsiveness and broad-spectrum bacterial disease resistance. In this study, we developed a set of bioassays to study the activation of PAMP-triggered immunity (PTI) in wheat. We generated transgenic wheat (Triticum aestivum) plants expressing AtEFR driven by the constitutive rice actin promoter and tested their response to elf18. We show that transgenic expression of AtEFR in wheat confers recognition of elf18, as measured by the induction of immune marker genes and callose deposition. When challenged with the cereal bacterial pathogen Pseudomonas syringae pv. oryzae, transgenic EFR wheat lines had reduced lesion size and bacterial multiplication. These results demonstrate that AtEFR can be transferred successfully from dicot to monocot species, further revealing that immune signalling pathways are conserved across these distant phyla. As novel PRRs are identified, their transfer between plant families represents a useful strategy for enhancing resistance to pathogens in crops. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Stress-evoked sterile inflammation, danger associated molecular patterns (DAMPs), microbial associated molecular patterns (MAMPs) and the inflammasome.

PubMed

Fleshner, Monika

2013-01-01

Since the inception of the field of psychoneuroimmunolology research, there has been an appreciation that the physiological response to stressors includes modulation of immune function. Investigators initially focused on the effect of stress on cellular migration and immunosuppression and the resultant decreases in tumor surveillance, anti-viral T cell immunity and antigen-specific antibody responses. More recently, it has become clear that exposure to stressors also potentiate innate immune processes. Stressor exposure, for example, can change the activation status of myeloid lineage cells such as monocytes, macrophages, neutrophils, and microglia, leading to a primed state. In addition, stressor exposure increases the synthesis and release of a vast cadre' of inflammatory proteins both in the blood and within tissues (i.e., spleen, liver, adipose, vasculature and brain). The mechanisms for stress-evoked innate immune 'arousal' remain unknown. The goals of this presidential address are the following: (1) offer a personalized, brief overview of stress and immunity with a focus on 'aroused' innate immunity; (2) describe sterile inflammatory processes and the role of the inflammasome; and (3) suggest that these same processes likely contribute to primed myeloid cells and inflammatory protein responses (systemic and tissue) produced by stress in the absence of pathogens. Copyright © 2012 Elsevier Inc. All rights reserved.

Real-Time Monitoring and Evaluation of a Visual-Based Cervical Cancer Screening Program Using a Decision Support Job Aid.

PubMed

Peterson, Curtis W; Rose, Donny; Mink, Jonah; Levitz, David

2016-05-16

In many developing nations, cervical cancer screening is done by visual inspection with acetic acid (VIA). Monitoring and evaluation (M&E) of such screening programs is challenging. An enhanced visual assessment (EVA) system was developed to augment VIA procedures in low-resource settings. The EVA System consists of a mobile colposcope built around a smartphone, and an online image portal for storing and annotating images. A smartphone app is used to control the mobile colposcope, and upload pictures to the image portal. In this paper, a new app feature that documents clinical decisions using an integrated job aid was deployed in a cervical cancer screening camp in Kenya. Six organizations conducting VIA used the EVA System to screen 824 patients over the course of a week, and providers recorded their diagnoses and treatments in the application. Real-time aggregated statistics were broadcast on a public website. Screening organizations were able to assess the number of patients screened, alongside treatment rates, and the patients who tested positive and required treatment in real time, which allowed them to make adjustments as needed. The real-time M&E enabled by "smart" diagnostic medical devices holds promise for broader use in screening programs in low-resource settings.

Magnetic resonance imaging-based cerebral tissue classification reveals distinct spatiotemporal patterns of changes after stroke in non-human primates.

PubMed

Bouts, Mark J R J; Westmoreland, Susan V; de Crespigny, Alex J; Liu, Yutong; Vangel, Mark; Dijkhuizen, Rick M; Wu, Ona; D'Arceuil, Helen E

2015-12-15

Spatial and temporal changes in brain tissue after acute ischemic stroke are still poorly understood. Aims of this study were three-fold: (1) to determine unique temporal magnetic resonance imaging (MRI) patterns at the acute, subacute and chronic stages after stroke in macaques by combining quantitative T2 and diffusion MRI indices into MRI 'tissue signatures', (2) to evaluate temporal differences in these signatures between transient (n = 2) and permanent (n = 2) middle cerebral artery occlusion, and (3) to correlate histopathology findings in the chronic stroke period to the acute and subacute MRI derived tissue signatures. An improved iterative self-organizing data analysis algorithm was used to combine T2, apparent diffusion coefficient (ADC), and fractional anisotropy (FA) maps across seven successive timepoints (1, 2, 3, 24, 72, 144, 240 h) which revealed five temporal MRI signatures, that were different from the normal tissue pattern (P < 0.001). The distribution of signatures between brains with permanent and transient occlusions varied significantly between groups (P < 0.001). Qualitative comparisons with histopathology revealed that these signatures represented regions with different histopathology. Two signatures identified areas of progressive injury marked by severe necrosis and the presence of gitter cells. Another signature identified less severe but pronounced neuronal and axonal degeneration, while the other signatures depicted tissue remodeling with vascular proliferation and astrogliosis. These exploratory results demonstrate the potential of temporally and spatially combined voxel-based methods to generate tissue signatures that may correlate with distinct histopathological features. The identification of distinct ischemic MRI signatures associated with specific tissue fates may further aid in assessing and monitoring the efficacy of novel pharmaceutical treatments for stroke in a pre-clinical and clinical setting.

Tumor image signatures and habitats: a processing pipeline of multimodality metabolic and physiological images.

PubMed

You, Daekeun; Kim, Michelle M; Aryal, Madhava P; Parmar, Hemant; Piert, Morand; Lawrence, Theodore S; Cao, Yue

2018-01-01

To create tumor "habitats" from the "signatures" discovered from multimodality metabolic and physiological images, we developed a framework of a processing pipeline. The processing pipeline consists of six major steps: (1) creating superpixels as a spatial unit in a tumor volume; (2) forming a data matrix [Formula: see text] containing all multimodality image parameters at superpixels; (3) forming and clustering a covariance or correlation matrix [Formula: see text] of the image parameters to discover major image "signatures;" (4) clustering the superpixels and organizing the parameter order of the [Formula: see text] matrix according to the one found in step 3; (5) creating "habitats" in the image space from the superpixels associated with the "signatures;" and (6) pooling and clustering a matrix consisting of correlation coefficients of each pair of image parameters from all patients to discover subgroup patterns of the tumors. The pipeline was applied to a dataset of multimodality images in glioblastoma (GBM) first, which consisted of 10 image parameters. Three major image "signatures" were identified. The three major "habitats" plus their overlaps were created. To test generalizability of the processing pipeline, a second image dataset from GBM, acquired on the scanners different from the first one, was processed. Also, to demonstrate the clinical association of image-defined "signatures" and "habitats," the patterns of recurrence of the patients were analyzed together with image parameters acquired prechemoradiation therapy. An association of the recurrence patterns with image-defined "signatures" and "habitats" was revealed. These image-defined "signatures" and "habitats" can be used to guide stereotactic tissue biopsy for genetic and mutation status analysis and to analyze for prediction of treatment outcomes, e.g., patterns of failure.

Characterization of geostationary particle signatures based on the 'injection boundary' model

NASA Technical Reports Server (NTRS)

Mauk, B. H.; Meng, C.-I.

1983-01-01

A simplified analytical procedure is used to characterize the details of geostationary particle signatures, in order to lend support to the 'injection boundary' concept. The signatures are generated by the time-of-flight effects evolving from an initial sharply defined, double spiraled boundary configuration. Complex and highly variable dispersion patterns often observed by geostationary satellites are successfully reproduced through the exclusive use of the most fundamental convection configuration characteristics. Many of the details of the patterns have not been previously presented. It is concluded that most of the dynamical dispersion features can be mapped to the double spiral boundary without further ad hoc assumptions, and that predicted and observed dispersion patterns exhibit symmetries distinct from those associated with the quasi-stationary particle convection patterns.

A novel Arabidopsis CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1) mutant with enhanced pathogen-induced cell death and altered receptor processing.

PubMed

Petutschnig, Elena K; Stolze, Marnie; Lipka, Ulrike; Kopischke, Michaela; Horlacher, Juliane; Valerius, Oliver; Rozhon, Wilfried; Gust, Andrea A; Kemmerling, Birgit; Poppenberger, Brigitte; Braus, Gerhard H; Nürnberger, Thorsten; Lipka, Volker

2014-12-01

Plants detect pathogens by sensing microbe-associated molecular patterns (MAMPs) through pattern recognition receptors. Pattern recognition receptor complexes also have roles in cell death control, but the underlying mechanisms are poorly understood. Here, we report isolation of cerk1-4, a novel mutant allele of the Arabidopsis chitin receptor CERK1 with enhanced defense responses. We identified cerk1-4 in a forward genetic screen with barley powdery mildew and consequently characterized it by pathogen assays, mutant crosses and analysis of defense pathways. CERK1 and CERK1-4 proteins were analyzed biochemically. The cerk1-4 mutation causes an amino acid exchange in the CERK1 ectodomain. Mutant plants maintain chitin signaling capacity but exhibit hyper-inducible salicylic acid concentrations and deregulated cell death upon pathogen challenge. In contrast to chitin signaling, the cerk1-4 phenotype does not require kinase activity and is conferred by the N-terminal part of the receptor. CERK1 undergoes ectodomain shedding, a well-known process in animal cell surface proteins. Wild-type plants contain the full-length CERK1 receptor protein as well as a soluble form of the CERK1 ectodomain, whereas cerk1-4 plants lack the N-terminal shedding product. Our work suggests that CERK1 may have a chitin-independent role in cell death control and is the first report of ectodomain shedding in plants. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity

PubMed Central

Birkenbihl, Rainer P.; Kracher, Barbara; Roccaro, Mario

2017-01-01

During microbial-associated molecular pattern-triggered immunity (MTI), molecules derived from microbes are perceived by cell surface receptors and upon signaling to the nucleus initiate a massive transcriptional reprogramming critical to mount an appropriate host defense response. WRKY transcription factors play an important role in regulating these transcriptional processes. Here, we determined on a genome-wide scale the flg22-induced in vivo DNA binding dynamics of three of the most prominent WRKY factors, WRKY18, WRKY40, and WRKY33. The three WRKY factors each bound to more than 1000 gene loci predominantly at W-box elements, the known WRKY binding motif. Binding occurred mainly in the 500-bp promoter regions of these genes. Many of the targeted genes are involved in signal perception and transduction not only during MTI but also upon damage-associated molecular pattern-triggered immunity, providing a mechanistic link between these functionally interconnected basal defense pathways. Among the additional targets were genes involved in the production of indolic secondary metabolites and in modulating distinct plant hormone pathways. Importantly, among the targeted genes were numerous transcription factors, encoding predominantly ethylene response factors, active during early MTI, and WRKY factors, supporting the previously hypothesized existence of a WRKY subregulatory network. Transcriptional analysis revealed that WRKY18 and WRKY40 function redundantly as negative regulators of flg22-induced genes often to prevent exaggerated defense responses. PMID:28011690

Chitin receptor CERK1 links salt stress and chitin-triggered innate immunity in Arabidopsis.

PubMed

Espinoza, Catherine; Liang, Yan; Stacey, Gary

2017-03-01

In nature, plants need to respond to multiple environmental stresses that require the involvement and fine-tuning of different stress signaling pathways. Cross-tolerance, in which plants pre-treated with chitin (a fungal microbe-associated molecular pattern) have improved salt tolerance, was observed in Arabidopsis, but is not well understood. Here, we show a unique link between chitin and salt signaling mediated by the chitin receptor CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1). Transcriptome analysis revealed that salt stress-induced genes are highly correlated with chitin-induced genes, although this was not observed with other microbe-associated molecular patterns (MAMPs) or with other abiotic stresses. The cerk1 mutant was more susceptible to NaCl than was the wild type. cerk1 plants had an irregular increase of cytosolic calcium ([Ca 2+ ] cyt ) after NaCl treatment. Bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation experiments indicated that CERK1 physically interacts with ANNEXIN 1 (ANN1), which was reported to form a calcium-permeable channel that contributes to the NaCl-induced [Ca 2+ ] cyt signal. In turn, ann1 mutants showed elevated chitin-induced rapid responses. In short, molecular components previously shown to function in chitin or salt signaling physically interact and intimately link the downstream responses to fungal attack and salt stress. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Understanding mutagenesis through delineation of mutational signatures in human cancer

DOE PAGES

Petljak, Mia; Alexandrov, Ludmil B.

2016-05-04

Each individual cell within a human body acquires a certain number of somatic mutations during a course of its lifetime. These mutations originate from a wide spectra of both endogenous and exogenous mutational processes that leave distinct patterns of mutations, termed mutational signatures, embedded within the genomes of all cells. In recent years, the vast amount of data produced by sequencing of cancer genomes was coupled with novel mathematical models and computational tools to generate the first comprehensive map of mutational signatures in human cancer. Up to date, >30 distinct mutational signatures have been identified, and etiologies have been proposedmore » for many of them. This paper provides a brief historical background on examination of mutational patterns in human cancer, summarizes the knowledge accumulated since introducing the concept of mutational signatures and discusses their future potential applications and perspectives within the field.« less

High levels of cyclic-di-GMP in plant-associated Pseudomonas correlate with evasion of plant immunity.

PubMed

Pfeilmeier, Sebastian; Saur, Isabel Marie-Luise; Rathjen, John Paul; Zipfel, Cyril; Malone, Jacob George

2016-05-01

The plant innate immune system employs plasma membrane-localized receptors that specifically perceive pathogen/microbe-associated molecular patterns (PAMPs/MAMPs). This induces a defence response called pattern-triggered immunity (PTI) to fend off pathogen attack. Commensal bacteria are also exposed to potential immune recognition and must employ strategies to evade and/or suppress PTI to successfully colonize the plant. During plant infection, the flagellum has an ambiguous role, acting as both a virulence factor and also as a potent immunogen as a result of the recognition of its main building block, flagellin, by the plant pattern recognition receptors (PRRs), including FLAGELLIN SENSING2 (FLS2). Therefore, strict control of flagella synthesis is especially important for plant-associated bacteria. Here, we show that cyclic-di-GMP [bis-(3'-5')-cyclic di-guanosine monophosphate], a central regulator of bacterial lifestyle, is involved in the evasion of PTI. Elevated cyclic-di-GMP levels in the pathogen Pseudomonas syringae pv. tomato (Pto) DC3000, the opportunist P. aeruginosa PAO1 and the commensal P. protegens Pf-5 inhibit flagellin synthesis and help the bacteria to evade FLS2-mediated signalling in Nicotiana benthamiana and Arabidopsis thaliana. Despite this, high cellular cyclic-di-GMP concentrations were shown to drastically reduce the virulence of Pto DC3000 during plant infection. We propose that this is a result of reduced flagellar motility and/or additional pleiotropic effects of cyclic-di-GMP signalling on bacterial behaviour. © 2015 THE AUTHORS MOLECULAR PLANT PATHOLOGY PUBLISHED BY BRITISH SOCIETY FOR PLANT PATHOLOGY AND JOHN WILEY & SONS LTD.

Application of Cellular Automata to Detection of Malicious Network Packets

ERIC Educational Resources Information Center

Brown, Robert L.

2014-01-01

A problem in computer security is identification of attack signatures in network packets. An attack signature is a pattern of bits that characterizes a particular attack. Because there are many kinds of attacks, there are potentially many attack signatures. Furthermore, attackers may seek to avoid detection by altering the attack mechanism so that…

Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection.

PubMed

Rossenkhan, Raabya; MacLeod, Iain J; Brumme, Zabrina L; Magaret, Craig A; Sebunya, Theresa K; Musonda, Rosemary; Gashe, Berhanu A; Edlefsen, Paul T; Novitsky, Vlad; Essex, M

Viral variants that predominate during early infection may exhibit constrained diversity compared with those found during chronic infection and could contain amino acid signature patterns that may enhance transmission, establish productive infection, and influence early events that modulate the infection course. We compared amino acid distributions in 17 patients recently infected with HIV-1C with patients with chronic infection. We found significantly lower entropy in inferred transmitted/founder (t/f) compared with chronic viruses and identified signature patterns in Vif and Vpr from inferred t/f viruses. We investigated sequence evolution longitudinally up to 500 days postseroconversion and compared the impact of selected substitutions on predicted human leukocyte antigen (HLA) binding affinities of published and predicted cytotoxic T-lymphocyte epitopes. Polymorphisms in Vif and Vpr during early infection occurred more frequently at epitope-HLA anchor residues and significantly decreased predicted epitope-HLA binding. Transmission-associated sequence signatures may have implications for novel strategies to prevent HIV-1 transmission.

Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection

PubMed Central

Rossenkhan, Raabya; MacLeod, Iain J.; Brumme, Zabrina L.; Magaret, Craig A.; Sebunya, Theresa K.; Musonda, Rosemary; Gashe, Berhanu A.; Edlefsen, Paul T.; Novitsky, Vlad

2016-01-01

Abstract Viral variants that predominate during early infection may exhibit constrained diversity compared with those found during chronic infection and could contain amino acid signature patterns that may enhance transmission, establish productive infection, and influence early events that modulate the infection course. We compared amino acid distributions in 17 patients recently infected with HIV-1C with patients with chronic infection. We found significantly lower entropy in inferred transmitted/founder (t/f) compared with chronic viruses and identified signature patterns in Vif and Vpr from inferred t/f viruses. We investigated sequence evolution longitudinally up to 500 days postseroconversion and compared the impact of selected substitutions on predicted human leukocyte antigen (HLA) binding affinities of published and predicted cytotoxic T-lymphocyte epitopes. Polymorphisms in Vif and Vpr during early infection occurred more frequently at epitope-HLA anchor residues and significantly decreased predicted epitope-HLA binding. Transmission-associated sequence signatures may have implications for novel strategies to prevent HIV-1 transmission. PMID:27349335

Optical network security using unipolar Walsh code

NASA Astrophysics Data System (ADS)

Sikder, Somali; Sarkar, Madhumita; Ghosh, Shila

2018-04-01

Optical code-division multiple-access (OCDMA) is considered as a good technique to provide optical layer security. Many research works have been published to enhance optical network security by using optical signal processing. The paper, demonstrates the design of the AWG (arrayed waveguide grating) router-based optical network for spectral-amplitude-coding (SAC) OCDMA networks with Walsh Code to design a reconfigurable network codec by changing signature codes to against eavesdropping. In this paper we proposed a code reconfiguration scheme to improve the network access confidentiality changing the signature codes by cyclic rotations, for OCDMA system. Each of the OCDMA network users is assigned a unique signature code to transmit the information and at the receiving end each receiver correlates its own signature pattern a(n) with the receiving pattern s(n). The signal arriving at proper destination leads to s(n)=a(n).

Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE)

PubMed Central

2013-01-01

Background In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand, the role and the type of selection processes shaping the evolution of innate-immunity genes are currently far less clear. In this study we analysed the natural variation and the evolutionary processes acting on two genes involved in the innate-immunity recognition of Microbe-Associated Molecular Patterns (MAMPs). Results We sequenced genes encoding Toll-like receptor 4 (Tlr4) and 7 (Tlr7), two of the key bacterial- and viral-sensing receptors of innate immunity, across 23 species within the subfamily Murinae. Although we have shown that the phylogeny of both Tlr genes is largely congruent with the phylogeny of rodents based on a comparably sized non-immune sequence dataset, we also identified several potentially important discrepancies. The sequence analyses revealed that major parts of both Tlrs are evolving under strong purifying selection, likely due to functional constraints. Yet, also several signatures of positive selection have been found in both genes, with more intense signal in the bacterial-sensing Tlr4 than in the viral-sensing Tlr7. 92% and 100% of sites evolving under positive selection in Tlr4 and Tlr7, respectively, were located in the extracellular domain. Directly in the Ligand-Binding Region (LBR) of TLR4 we identified two rapidly evolving amino acid residues and one site under positive selection, all three likely involved in species-specific recognition of lipopolysaccharide of gram-negative bacteria. In contrast, all putative sites of LBRTLR7 involved in the detection of viral nucleic acids were highly conserved across rodents. Interspecific differences in the predicted 3D-structure of the LBR of both Tlrs were not related to phylogenetic history, while analyses of protein charges clearly discriminated Rattini and Murini clades. Conclusions In consequence of the constraints given by the receptor protein function purifying selection has been a dominant force in evolution of Tlrs. Nevertheless, our results show that episodic diversifying parasite-mediated selection has shaped the present species-specific variability in rodent Tlrs. The intensity of diversifying selection was higher in Tlr4 than in Tlr7, presumably due to structural properties of their ligands. PMID:24028551

Automatic Target Recognition Based on Cross-Plot

PubMed Central

Wong, Kelvin Kian Loong; Abbott, Derek

2011-01-01

Automatic target recognition that relies on rapid feature extraction of real-time target from photo-realistic imaging will enable efficient identification of target patterns. To achieve this objective, Cross-plots of binary patterns are explored as potential signatures for the observed target by high-speed capture of the crucial spatial features using minimal computational resources. Target recognition was implemented based on the proposed pattern recognition concept and tested rigorously for its precision and recall performance. We conclude that Cross-plotting is able to produce a digital fingerprint of a target that correlates efficiently and effectively to signatures of patterns having its identity in a target repository. PMID:21980508

Gene-expression signatures can distinguish gastric cancer grades and stages.

PubMed

Cui, Juan; Li, Fan; Wang, Guoqing; Fang, Xuedong; Puett, J David; Xu, Ying

2011-03-18

Microarray gene-expression data of 54 paired gastric cancer and adjacent noncancerous gastric tissues were analyzed, with the aim to establish gene signatures for cancer grades (well-, moderately-, poorly- or un-differentiated) and stages (I, II, III and IV), which have been determined by pathologists. Our statistical analysis led to the identification of a number of gene combinations whose expression patterns serve well as signatures of different grades and different stages of gastric cancer. A 19-gene signature was found to have discerning power between high- and low-grade gastric cancers in general, with overall classification accuracy at 79.6%. An expanded 198-gene panel allows the stratification of cancers into four grades and control, giving rise to an overall classification agreement of 74.2% between each grade designated by the pathologists and our prediction. Two signatures for cancer staging, consisting of 10 genes and 9 genes, respectively, provide high classification accuracies at 90.0% and 84.0%, among early-, advanced-stage cancer and control. Functional and pathway analyses on these signature genes reveal the significant relevance of the derived signatures to cancer grades and progression. To the best of our knowledge, this represents the first study on identification of genes whose expression patterns can serve as markers for cancer grades and stages.

Uncovering plant-pathogen crosstalk through apoplastic proteomic studies.

PubMed

Delaunois, Bertrand; Jeandet, Philippe; Clément, Christophe; Baillieul, Fabienne; Dorey, Stéphan; Cordelier, Sylvain

2014-01-01

Plant pathogens have evolved by developing different strategies to infect their host, which in turn have elaborated immune responses to counter the pathogen invasion. The apoplast, including the cell wall and extracellular space outside the plasma membrane, is one of the first compartments where pathogen-host interaction occurs. The plant cell wall is composed of a complex network of polysaccharides polymers and glycoproteins and serves as a natural physical barrier against pathogen invasion. The apoplastic fluid, circulating through the cell wall and intercellular spaces, provides a means for delivering molecules and facilitating intercellular communications. Some plant-pathogen interactions lead to plant cell wall degradation allowing pathogens to penetrate into the cells. In turn, the plant immune system recognizes microbial- or damage-associated molecular patterns (MAMPs or DAMPs) and initiates a set of basal immune responses, including the strengthening of the plant cell wall. The establishment of defense requires the regulation of a wide variety of proteins that are involved at different levels, from receptor perception of the pathogen via signaling mechanisms to the strengthening of the cell wall or degradation of the pathogen itself. A fine regulation of apoplastic proteins is therefore essential for rapid and effective pathogen perception and for maintaining cell wall integrity. This review aims to provide insight into analyses using proteomic approaches of the apoplast to highlight the modulation of the apoplastic protein patterns during pathogen infection and to unravel the key players involved in plant-pathogen interaction.

Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity.

PubMed

Birkenbihl, Rainer P; Kracher, Barbara; Somssich, Imre E

2017-01-01

During microbial-associated molecular pattern-triggered immunity (MTI), molecules derived from microbes are perceived by cell surface receptors and upon signaling to the nucleus initiate a massive transcriptional reprogramming critical to mount an appropriate host defense response. WRKY transcription factors play an important role in regulating these transcriptional processes. Here, we determined on a genome-wide scale the flg22-induced in vivo DNA binding dynamics of three of the most prominent WRKY factors, WRKY18, WRKY40, and WRKY33. The three WRKY factors each bound to more than 1000 gene loci predominantly at W-box elements, the known WRKY binding motif. Binding occurred mainly in the 500-bp promoter regions of these genes. Many of the targeted genes are involved in signal perception and transduction not only during MTI but also upon damage-associated molecular pattern-triggered immunity, providing a mechanistic link between these functionally interconnected basal defense pathways. Among the additional targets were genes involved in the production of indolic secondary metabolites and in modulating distinct plant hormone pathways. Importantly, among the targeted genes were numerous transcription factors, encoding predominantly ethylene response factors, active during early MTI, and WRKY factors, supporting the previously hypothesized existence of a WRKY subregulatory network. Transcriptional analysis revealed that WRKY18 and WRKY40 function redundantly as negative regulators of flg22-induced genes often to prevent exaggerated defense responses. © 2016 American Society of Plant Biologists. All rights reserved.

Rotation, scale, and translation invariant pattern recognition using feature extraction

NASA Astrophysics Data System (ADS)

Prevost, Donald; Doucet, Michel; Bergeron, Alain; Veilleux, Luc; Chevrette, Paul C.; Gingras, Denis J.

1997-03-01

A rotation, scale and translation invariant pattern recognition technique is proposed.It is based on Fourier- Mellin Descriptors (FMD). Each FMD is taken as an independent feature of the object, and a set of those features forms a signature. FMDs are naturally rotation invariant. Translation invariance is achieved through pre- processing. A proper normalization of the FMDs gives the scale invariance property. This approach offers the double advantage of providing invariant signatures of the objects, and a dramatic reduction of the amount of data to process. The compressed invariant feature signature is next presented to a multi-layered perceptron neural network. This final step provides some robustness to the classification of the signatures, enabling good recognition behavior under anamorphically scaled distortion. We also present an original feature extraction technique, adapted to optical calculation of the FMDs. A prototype optical set-up was built, and experimental results are presented.

Kinematic signature of a rotating bar near a resonance

NASA Technical Reports Server (NTRS)

Weinberg, Martin D.

1994-01-01

Recent work based on H I, star count and emission data suggests that the Milky Way has rotating bar-like features. In this paper, I show that such features cause distinctive stellar kinematic signatures near Outer Lindblad Resonance (OLR) and Inner Lindblad Resonance (ILR). The effect of these resonances may be observable far from the peak density of the pattern and relatively nearby the solar position. The details of the kinematic signatures depend on the evolutionary history of the 'bar' and therefore velocity data, both systematic and velocity dispersion, may be used to probe the evolutionary history as well as the present state of Galaxy. Kinematic models for a variety of sample scenarios are presented. Models with evolving pattern speeds show significantly stronger dispersion signatures than those with static pattern speeds, suggesting that useful observational constraints are possible. The models are applied to the proposed rotating spheroid and bar models; we find (1) none of these models chosen to represent the proposed large-scale rotating spheroid are consistent with the stellar kinematics and (2) a Galactic bar with semimajor axis of 3 kpc will cause a large increase in velocity dispersion in the vicinity of OLR (approximately 5 kpc) with little change in the net radial motion and such a signature is suggested by K-giant velocity data. Potential future observations and analyses are discussed.

The Signature of Southern Hemisphere Atmospheric Circulation Patterns in Antarctic Precipitation

PubMed Central

Thompson, David W. J.; van den Broeke, Michiel R.

2017-01-01

Abstract We provide the first comprehensive analysis of the relationships between large‐scale patterns of Southern Hemisphere climate variability and the detailed structure of Antarctic precipitation. We examine linkages between the high spatial resolution precipitation from a regional atmospheric model and four patterns of large‐scale Southern Hemisphere climate variability: the southern baroclinic annular mode, the southern annular mode, and the two Pacific‐South American teleconnection patterns. Variations in all four patterns influence the spatial configuration of precipitation over Antarctica, consistent with their signatures in high‐latitude meridional moisture fluxes. They impact not only the mean but also the incidence of extreme precipitation events. Current coupled‐climate models are able to reproduce all four patterns of atmospheric variability but struggle to correctly replicate their regional impacts on Antarctic climate. Thus, linking these patterns directly to Antarctic precipitation variability may allow a better estimate of future changes in precipitation than using model output alone. PMID:29398735

Statistical evaluation of synchronous spike patterns extracted by frequent item set mining

PubMed Central

Torre, Emiliano; Picado-Muiño, David; Denker, Michael; Borgelt, Christian; Grün, Sonja

2013-01-01

We recently proposed frequent itemset mining (FIM) as a method to perform an optimized search for patterns of synchronous spikes (item sets) in massively parallel spike trains. This search outputs the occurrence count (support) of individual patterns that are not trivially explained by the counts of any superset (closed frequent item sets). The number of patterns found by FIM makes direct statistical tests infeasible due to severe multiple testing. To overcome this issue, we proposed to test the significance not of individual patterns, but instead of their signatures, defined as the pairs of pattern size z and support c. Here, we derive in detail a statistical test for the significance of the signatures under the null hypothesis of full independence (pattern spectrum filtering, PSF) by means of surrogate data. As a result, injected spike patterns that mimic assembly activity are well detected, yielding a low false negative rate. However, this approach is prone to additionally classify patterns resulting from chance overlap of real assembly activity and background spiking as significant. These patterns represent false positives with respect to the null hypothesis of having one assembly of given signature embedded in otherwise independent spiking activity. We propose the additional method of pattern set reduction (PSR) to remove these false positives by conditional filtering. By employing stochastic simulations of parallel spike trains with correlated activity in form of injected spike synchrony in subsets of the neurons, we demonstrate for a range of parameter settings that the analysis scheme composed of FIM, PSF and PSR allows to reliably detect active assemblies in massively parallel spike trains. PMID:24167487

Māori identity signatures: A latent profile analysis of the types of Māori identity.

PubMed

Greaves, Lara M; Houkamau, Carla; Sibley, Chris G

2015-10-01

Māori are the indigenous peoples of New Zealand. However, the term 'Māori' can refer to a wide range of people of varying ethnic compositions and cultural identity. We present a statistical model identifying 6 distinct types, or 'Māori Identity Signatures,' and estimate their proportion in the Māori population. The model is tested using a Latent Profile Analysis of a national probability sample of 686 Māori drawn from the New Zealand Attitudes and Values Study. We identify 6 distinct signatures: Traditional Essentialists (22.6%), Traditional Inclusives (16%), High Moderates (31.7%), Low Moderates (18.7%), Spiritually Orientated (4.1%), and Disassociated (6.9%). These distinct Identity Signatures predicted variation in deprivation, age, mixed-ethnic affiliation, and religion. This research presents the first formal statistical model assessing how people's identity as Māori is psychologically structured, documents the relative proportion of these different patterns of structures, and shows that these patterns reliably predict differences in core demographics. We identify a range of patterns of Māori identity far more diverse than has been previously proposed based on qualitative data, and also show that the majority of Māori fit a moderate or traditional identity pattern. The application of our model for studying Māori health and identity development is discussed. (c) 2015 APA, all rights reserved).

Peripheral Blood Signatures of Lead Exposure

PubMed Central

LaBreche, Heather G.; Meadows, Sarah K.; Nevins, Joseph R.; Chute, John P.

2011-01-01

Background Current evidence indicates that even low-level lead (Pb) exposure can have detrimental effects, especially in children. We tested the hypothesis that Pb exposure alters gene expression patterns in peripheral blood cells and that these changes reflect dose-specific alterations in the activity of particular pathways. Methodology/Principal Finding Using Affymetrix Mouse Genome 430 2.0 arrays, we examined gene expression changes in the peripheral blood of female Balb/c mice following exposure to per os lead acetate trihydrate or plain drinking water for two weeks and after a two-week recovery period. Data sets were RMA-normalized and dose-specific signatures were generated using established methods of supervised classification and binary regression. Pathway activity was analyzed using the ScoreSignatures module from GenePattern. Conclusions/Significance The low-level Pb signature was 93% sensitive and 100% specific in classifying samples a leave-one-out crossvalidation. The high-level Pb signature demonstrated 100% sensitivity and specificity in the leave-one-out crossvalidation. These two signatures exhibited dose-specificity in their ability to predict Pb exposure and had little overlap in terms of constituent genes. The signatures also seemed to reflect current levels of Pb exposure rather than past exposure. Finally, the two doses showed differential activation of cellular pathways. Low-level Pb exposure increased activity of the interferon-gamma pathway, whereas high-level Pb exposure increased activity of the E2F1 pathway. PMID:21829687

Age and gender-invariant features of handwritten signatures for verification systems

NASA Astrophysics Data System (ADS)

AbdAli, Sura; Putz-Leszczynska, Joanna

2014-11-01

Handwritten signature is one of the most natural biometrics, the study of human physiological and behavioral patterns. Behavioral biometrics includes signatures that may be different due to its owner gender or age because of intrinsic or extrinsic factors. This paper presents the results of the author's research on age and gender influence on verification factors. The experiments in this research were conducted using a database that contains signatures and their associated metadata. The used algorithm is based on the universal forgery feature idea, where the global classifier is able to classify a signature as a genuine one or, as a forgery, without the actual knowledge of the signature template and its owner. Additionally, the reduction of the dimensionality with the MRMR method is discussed.

On Expression Patterns and Developmental Origin of Human Brain Regions.

PubMed

Kirsch, Lior; Chechik, Gal

2016-08-01

Anatomical substructures of the human brain have characteristic cell-types, connectivity and local circuitry, which are reflected in area-specific transcriptome signatures, but the principles governing area-specific transcription and their relation to brain development are still being studied. In adult rodents, areal transcriptome patterns agree with the embryonic origin of brain regions, but the processes and genes that preserve an embryonic signature in regional expression profiles were not quantified. Furthermore, it is not clear how embryonic-origin signatures of adult-brain expression interplay with changes in expression patterns during development. Here we first quantify which genes have regional expression-patterns related to the developmental origin of brain regions, using genome-wide mRNA expression from post-mortem adult human brains. We find that almost all human genes (92%) exhibit an expression pattern that agrees with developmental brain-region ontology, but that this agreement changes at multiple phases during development. Agreement is particularly strong in neuron-specific genes, but also in genes that are not spatially correlated with neuron-specific or glia-specific markers. Surprisingly, agreement is also stronger in early-evolved genes. We further find that pairs of similar genes having high agreement to developmental region ontology tend to be more strongly correlated or anti-correlated, and that the strength of spatial correlation changes more strongly in gene pairs with stronger embryonic signatures. These results suggest that transcription regulation of most genes in the adult human brain is spatially tuned in a way that changes through life, but in agreement with development-determined brain regions.

On Expression Patterns and Developmental Origin of Human Brain Regions

PubMed Central

Kirsch, Lior; Chechik, Gal

2016-01-01

Anatomical substructures of the human brain have characteristic cell-types, connectivity and local circuitry, which are reflected in area-specific transcriptome signatures, but the principles governing area-specific transcription and their relation to brain development are still being studied. In adult rodents, areal transcriptome patterns agree with the embryonic origin of brain regions, but the processes and genes that preserve an embryonic signature in regional expression profiles were not quantified. Furthermore, it is not clear how embryonic-origin signatures of adult-brain expression interplay with changes in expression patterns during development. Here we first quantify which genes have regional expression-patterns related to the developmental origin of brain regions, using genome-wide mRNA expression from post-mortem adult human brains. We find that almost all human genes (92%) exhibit an expression pattern that agrees with developmental brain-region ontology, but that this agreement changes at multiple phases during development. Agreement is particularly strong in neuron-specific genes, but also in genes that are not spatially correlated with neuron-specific or glia-specific markers. Surprisingly, agreement is also stronger in early-evolved genes. We further find that pairs of similar genes having high agreement to developmental region ontology tend to be more strongly correlated or anti-correlated, and that the strength of spatial correlation changes more strongly in gene pairs with stronger embryonic signatures. These results suggest that transcription regulation of most genes in the adult human brain is spatially tuned in a way that changes through life, but in agreement with development-determined brain regions. PMID:27564987

Stromal signatures in endometrioid endometrial carcinomas.

PubMed

Espinosa, Iñigo; Catasus, Lluis; D' Angelo, Emanuela; Mozos, Ana; Pedrola, Nuria; Bértolo, Cristina; Ferrer, Irene; Zannoni, Gian Franco; West, Robert B; van de Rijn, Matt; Matias-Guiu, Xavier; Prat, Jaime

2014-04-01

The pattern of myometrial invasion in endometrioid endometrial carcinomas varies considerably; ie, from widely scattered glands and cell nests, often associated with a fibromyxoid stromal reaction (desmoplasia) and/or a lymphocytic infiltrate, to invasive glands with little or no stromal response. Recently, two distinct stromal signatures derived from a macrophage response (colony-stimulating factor 1, CSF1) and a fibroblastic response (desmoid-type fibromatosis, DTF) were identified in breast carcinomas and correlated with clinicopathologic features including outcome. In this study, we explored whether these stromal signatures also apply to endometrioid carcinomas and how their expression patterns correlated with morphologic changes. We studied the stromal signatures both by immunohistochemistry and in situ hybridization in 98 primary endometrioid carcinomas with (87 cases) and without (11 cases) myometrial invasion as well as in the corresponding regional lymph nodes metatases of 9 myoinvasive tumors. Desmoplasia correlated positively with the DTF expression signature. Likewise, mononuclear infiltrates were found in the stroma of tumors expressing CSF1. Twenty-four out of eighty-seven (27%) myoinvasive endometrioid carcinomas were positive for the macrophage signature and thirteen out of eighty-seven (15%) expressed the fibroblast signature. Eleven additional cases were positive for both DTF and CSF1 signatures (11/87; 13%). However, over half of the cases (39/87; 45%) and the majority of the non-myoinvasive tumors (8/11; 73%) failed to express any of the two stromal signatures. The macrophage response (CSF1) was associated with higher tumor grade, lymphovascular invasion, and PIK3CA mutations (P<0.05). There was a concordance in the expression of the CSF1 signature in the primary tumors and their corresponding lymph node metastases. This study is the first characterization of stromal signatures in endometrioid carcinomas. Our findings shed new light on the relationship between genetically different endometrioid carcinomas and various stromal responses. Preservation of the CSF1 macrophage stromal response in the metastases leds support to targeting the CSF1 pathway in endometrioid endometrial carcinomas.

A Learning System for Discriminating Variants of Malicious Network Traffic

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

Beaver, Justin M; Symons, Christopher T; Gillen, Rob

Modern computer network defense systems rely primarily on signature-based intrusion detection tools, which generate alerts when patterns that are pre-determined to be malicious are encountered in network data streams. Signatures are created reactively, and only after in-depth manual analysis of a network intrusion. There is little ability for signature-based detectors to identify intrusions that are new or even variants of an existing attack, and little ability to adapt the detectors to the patterns unique to a network environment. Due to these limitations, the need exists for network intrusion detection techniques that can more comprehensively address both known unknown networkbased attacksmore » and can be optimized for the target environment. This work describes a system that leverages machine learning to provide a network intrusion detection capability that analyzes behaviors in channels of communication between individual computers. Using examples of malicious and non-malicious traffic in the target environment, the system can be trained to discriminate between traffic types. The machine learning provides insight that would be difficult for a human to explicitly code as a signature because it evaluates many interdependent metrics simultaneously. With this approach, zero day detection is possible by focusing on similarity to known traffic types rather than mining for specific bit patterns or conditions. This also reduces the burden on organizations to account for all possible attack variant combinations through signatures. The approach is presented along with results from a third-party evaluation of its performance.« less

SIGNATURES OF LONG-LIVED SPIRAL PATTERNS

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

Martinez-Garcia, Eric E.; Gonzalez-Lopezlira, Rosa A., E-mail: ericmartinez@inaoep.mx, E-mail: martinez@astro.unam.mx, E-mail: r.gonzalez@crya.unam.mx

2013-03-10

Azimuthal age/color gradients across spiral arms are a signature of long-lived spirals. From a sample of 19 normal (or weakly barred) spirals where we have previously found azimuthal age/color gradient candidates, 13 objects were further selected if a two-armed grand-design pattern survived in a surface density stellar mass map. Mass maps were obtained from optical and near-infrared imaging, by comparison with a Monte Carlo library of stellar population synthesis models that allowed us to obtain the mass-to-light ratio in the J band, (M/L){sub J}, as a function of (g - i) versus (i - J) color. The selected spirals weremore » analyzed with Fourier methods in search of other signatures of long-lived modes related to the gradients, such as the gradient divergence toward corotation, and the behavior of the phase angle of the two-armed spiral in different wavebands, as expected from theory. The results show additional signatures of long-lived spirals in at least 50% of the objects.« less

Voluntary Enhancement of Neural Signatures of Affiliative Emotion Using fMRI Neurofeedback

PubMed Central

Moll, Jorge; Weingartner, Julie H.; Bado, Patricia; Basilio, Rodrigo; Sato, João R.; Melo, Bruno R.; Bramati, Ivanei E.; de Oliveira-Souza, Ricardo; Zahn, Roland

2014-01-01

In Ridley Scott’s film “Blade Runner”, empathy-detection devices are employed to measure affiliative emotions. Despite recent neurocomputational advances, it is unknown whether brain signatures of affiliative emotions, such as tenderness/affection, can be decoded and voluntarily modulated. Here, we employed multivariate voxel pattern analysis and real-time fMRI to address this question. We found that participants were able to use visual feedback based on decoded fMRI patterns as a neurofeedback signal to increase brain activation characteristic of tenderness/affection relative to pride, an equally complex control emotion. Such improvement was not observed in a control group performing the same fMRI task without neurofeedback. Furthermore, the neurofeedback-driven enhancement of tenderness/affection-related distributed patterns was associated with local fMRI responses in the septohypothalamic area and frontopolar cortex, regions previously implicated in affiliative emotion. This demonstrates that humans can voluntarily enhance brain signatures of tenderness/affection, unlocking new possibilities for promoting prosocial emotions and countering antisocial behavior. PMID:24847819

Influence Of Momentum Excess On The Pattern And Dynamics Of Intermediate-Range Stratified Wakes

DTIC Science & Technology

2016-06-01

excess in order to model the fundamental differences between signatures generated by towed and self- propelled bodies in various ocean states. In cases...which can be used on the operational level for developing and improving algorithms for non- acoustic signature prediction and detection. 14. SUBJECT...order to model the fundamental differences between signatures generated by towed and self- propelled bodies in various ocean states. In cases where

PROSPECT: Profiling of Resistance Patterns Oncogenic Signaling Pathways in Evaluation of Cancers of the Thorax and Therapeutic Target Identification

DTIC Science & Technology

2011-06-01

8w DC in patients treated with erlotinib, but not sorafenib, indicating that it is not merely a prognostic signature; D) Both the 5-gene signature...disease-free, progression-free, and overall survival will vary across prognostically distinct groups. 3. Specific molecular signatures in primary tumors...therapeutic strategies at relapse. Specific Aims: Aim 1: To define characteristic TTF/gene expression profiles of prognostically distinct

Common patterns and disease-related signatures in tuberculosis and sarcoidosis.

PubMed

Maertzdorf, Jeroen; Weiner, January; Mollenkopf, Hans-Joachim; Bauer, Torsten; Prasse, Antje; Müller-Quernheim, Joachim; Kaufmann, Stefan H E

2012-05-15

In light of the marked global health impact of tuberculosis (TB), strong focus has been on identifying biosignatures. Gene expression profiles in blood cells identified so far are indicative of a persistent activation of the immune system and chronic inflammatory pathology in active TB. Definition of a biosignature with unique specificity for TB demands that identified profiles can differentiate diseases with similar pathology, like sarcoidosis (SARC). Here, we present a detailed comparison between pulmonary TB and SARC, including whole-blood gene expression profiling, microRNA expression, and multiplex serum analytes. Our analysis reveals that previously disclosed gene expression signatures in TB show highly similar patterns in SARC, with a common up-regulation of proinflammatory pathways and IFN signaling and close similarity to TB-related signatures. microRNA expression also presented a highly similar pattern in both diseases, whereas cytokines in the serum of TB patients revealed a slightly elevated proinflammatory pattern compared with SARC and controls. Our results indicate several differences in expression between the two diseases, with increased metabolic activity and significantly higher antimicrobial defense responses in TB. However, matrix metallopeptidase 14 was identified as the most distinctive marker of SARC. Described communalities as well as unique signatures in blood profiles of two distinct inflammatory pulmonary diseases not only have considerable implications for the design of TB biosignatures and future diagnosis, but they also provide insights into biological processes underlying chronic inflammatory disease entities of different etiology.

Flow-Signature Analysis of Water Consumption in Nonresidential Building Water Networks Using High-Resolution and Medium-Resolution Smart Meter Data: Two Case Studies

NASA Astrophysics Data System (ADS)

Clifford, Eoghan; Mulligan, Sean; Comer, Joanne; Hannon, Louise

2018-01-01

Real-time monitoring of water consumption activities can be an effective mechanism to achieve efficient water network management. This approach, largely enabled by the advent of smart metering technologies, is gradually being practiced in domestic and industrial contexts. In particular, identifying water consumption habits from flow-signatures, i.e., the specific end-usage patterns, is being investigated as a means for conservation in both the residential and nonresidential context. However, the quality of meter data is bivariate (dependent on number of meters and data temporal resolution) and as a result, planning a smart metering scheme is relatively difficult with no generic design approach available. In this study, a comprehensive medium-resolution to high-resolution smart metering program was implemented at two nonresidential trial sites to evaluate the effect of spatial and temporal data aggregation. It was found that medium-resolution water meter data were capable of exposing regular, continuous, peak use, and diurnal patterns which reflect group wide end-usage characteristics. The high-resolution meter data permitted flow-signature at a personal end-use level. Through this unique opportunity to observe water usage characteristics via flow-signature patterns, newly defined hydraulic-based design coefficients determined from Poisson rectangular pulse were developed to intuitively aid in the process of pattern discovery with implications for automated activity recognition applications. A smart meter classification and siting index was introduced which categorizes meter resolution in terms of their suitable application.

ALD1 Regulates Basal Immune Components and Early Inducible Defense Responses in Arabidopsis.

PubMed

Cecchini, Nicolás M; Jung, Ho Won; Engle, Nancy L; Tschaplinski, Timothy J; Greenberg, Jean T

2015-04-01

Robust immunity requires basal defense machinery to mediate timely responses and feedback cycles to amplify defenses against potentially spreading infections. AGD2-LIKE DEFENSE RESPONSE PROTEIN 1 (ALD1) is needed for the accumulation of the plant defense signal salicylic acid (SA) during the first hours after infection with the pathogen Pseudomonas syringae and is also upregulated by infection and SA. ALD1 is an aminotransferase with multiple substrates and products in vitro. Pipecolic acid (Pip) is an ALD1-dependent bioactive product induced by P. syringae. Here, we addressed roles of ALD1 in mediating defense amplification as well as the levels and responses of basal defense machinery. ALD1 needs immune components PAD4 and ICS1 (an SA synthesis enzyme) to confer disease resistance, possibly through a transcriptional amplification loop between them. Furthermore, ALD1 affects basal defense by controlling microbial-associated molecular pattern (MAMP) receptor levels and responsiveness. Vascular exudates from uninfected ALD1-overexpressing plants confer local immunity to the wild type and ald1 mutants yet are not enriched for Pip. We infer that, in addition to affecting Pip accumulation, ALD1 produces non-Pip metabolites that play roles in immunity. Thus, distinct metabolite signals controlled by the same enzyme affect basal and early defenses versus later defense responses, respectively.

The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1

DOE PAGES

Cao, Yangrong; Liang, Yan; Tanaka, Kiwamu; ...

2014-10-23

Chitin is a fungal microbe-associated molecular pattern (MAMP) that is recognized in Arabidopsis by a lysin motif receptor kinase (LYK), AtCERK1. Previous research suggested that AtCERK1 is the major chitin receptor in plants and mediates chitin-induced signaling through homodimerization and phosphorylation. However, the reported chitin binding affinity of AtCERK1 is quite low, suggesting another receptor with high chitin binding affinity might be present. Here, we propose that AtLYK5 is the primary chitin receptor in Arabidopsis. Mutations in AtLYK5 resulted in a significant reduction in the plant chitin response. However, AtLYK5 shares overlapping function with AtLYK4 and, therefore, only AtLYK4/AtLYK5-2 doublemore » mutants show a complete loss of chitin response. AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. AtLYK5 binds chitin at a much higher affinity than AtCERK1. Furthermore, the data suggest that AtLYK5 is the primary plant receptor for chitin, forming a chitin inducible complex with AtCERK1 to induce plant innate immunity.« less

The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1

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

Cao, Yangrong; Liang, Yan; Tanaka, Kiwamu

Chitin is a fungal microbe-associated molecular pattern (MAMP) that is recognized in Arabidopsis by a lysin motif receptor kinase (LYK), AtCERK1. Previous research suggested that AtCERK1 is the major chitin receptor in plants and mediates chitin-induced signaling through homodimerization and phosphorylation. However, the reported chitin binding affinity of AtCERK1 is quite low, suggesting another receptor with high chitin binding affinity might be present. Here, we propose that AtLYK5 is the primary chitin receptor in Arabidopsis. Mutations in AtLYK5 resulted in a significant reduction in the plant chitin response. However, AtLYK5 shares overlapping function with AtLYK4 and, therefore, only AtLYK4/AtLYK5-2 doublemore » mutants show a complete loss of chitin response. AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. AtLYK5 binds chitin at a much higher affinity than AtCERK1. Furthermore, the data suggest that AtLYK5 is the primary plant receptor for chitin, forming a chitin inducible complex with AtCERK1 to induce plant innate immunity.« less

Cyclic lipopeptides from Bacillus subtilis activate distinct patterns of defence responses in grapevine.

PubMed

Farace, Giovanni; Fernandez, Olivier; Jacquens, Lucile; Coutte, François; Krier, François; Jacques, Philippe; Clément, Christophe; Barka, Essaid Ait; Jacquard, Cédric; Dorey, Stéphan

2015-02-01

Non-self-recognition of microorganisms partly relies on the perception of microbe-associated molecular patterns (MAMPs) and leads to the activation of an innate immune response. Bacillus subtilis produces three main families of cyclic lipopeptides (LPs), namely surfactins, iturins and fengycins. Although LPs are involved in induced systemic resistance (ISR) activation, little is known about defence responses induced by these molecules and their involvement in local resistance to fungi. Here, we showed that purified surfactin, mycosubtilin (iturin family) and plipastatin (fengycin family) are perceived by grapevine plant cells. Although surfactin and mycosubtilin stimulated grapevine innate immune responses, they differentially activated early signalling pathways and defence gene expression. By contrast, plipastatin perception by grapevine cells only resulted in early signalling activation. Gene expression analysis suggested that mycosubtilin activated salicylic acid (SA) and jasmonic acid (JA) signalling pathways, whereas surfactin mainly induced an SA-regulated response. Although mycosubtilin and plipastatin displayed direct antifungal activity, only surfactin and mycosubtilin treatments resulted in a local long-lasting enhanced tolerance to the necrotrophic fungus Botrytis cinerea in grapevine leaves. Moreover, challenge with specific strains overproducing surfactin and mycosubtilin led to a slightly enhanced stimulation of the defence response compared with the LP-non-producing strain of B. subtilis. Altogether, our results provide the first comprehensive view of the involvement of LPs from B. subtilis in grapevine plant defence and local resistance against the necrotrophic pathogen Bo. cinerea. Moreover, this work is the first to highlight the ability of mycosubtilin to trigger an immune response in plants. © 2014 BSPP AND JOHN WILEY & SONS LTD.

A Prototype of Mathematical Treatment of Pen Pressure Data for Signature Verification.

PubMed

Li, Chi-Keung; Wong, Siu-Kay; Chim, Lai-Chu Joyce

2018-01-01

A prototype using simple mathematical treatment of the pen pressure data recorded by a digital pen movement recording device was derived. In this study, a total of 48 sets of signature and initial specimens were collected. Pearson's correlation coefficient was used to compare the data of the pen pressure patterns. From the 820 pair comparisons of the 48 sets of genuine signatures, a high degree of matching was found in which 95.4% (782 pairs) and 80% (656 pairs) had rPA > 0.7 and rPA > 0.8, respectively. In the comparison of the 23 forged signatures with their corresponding control signatures, 20 of them (89.2% of pairs) had rPA values < 0.6, showing a lower degree of matching when compared with the results of the genuine signatures. The prototype could be used as a complementary technique to improve the objectivity of signature examination and also has a good potential to be developed as a tool for automated signature identification. © 2017 American Academy of Forensic Sciences.

The role of nerve monitoring to predict postoperative recurrent laryngeal nerve function in thyroid and parathyroid surgery.

PubMed

Eid, Issam; Miller, Frank R; Rowan, Stephanie; Otto, Randal A

2013-10-01

To determine the role and efficacy of intraoperative recurrent laryngeal nerve (RLN) stimulation in the prediction of early and permanent postoperative nerve function in thyroid and parathyroid surgery. A retrospective review of thyroid and parathyroid surgeries was performed with calculation of sensitivity and specificity of the response of intraoperative stimulation for different pathological groups. Normal electromyography (EMG) response with 0.5 mAmp stimulation was considered a positive stimulation response with postoperative function determined by laryngoscopy. No EMG response at >1-2 mAmps was considered a negative response. The rates of early and permanent paralysis, as well as sensitivity, specificity, and positive and negative predictive values for postoperative nerve function were calculated for separate pathological groups. The number of nerves at risk analyzed was 909. The overall early and permanent paralysis rates were 3.1% and 1.2%, respectively, with the highest rate being for Grave's disease cases. The overall sensitivity was 98.4%. The specificity was lower at 62.5% but acceptable in thyroid carcinoma and Grave's disease patients. The majority of nerves with a positive stimulation result and postoperative paralysis on laryngoscopy recovered function in 3 to 12 weeks, showing positive stimulation to be a good predictor of eventual recovery. Stimulation of the RLN during thyroid and parathyroid surgery is a useful tool in predicting postoperative RLN function. The sensitivity of stimulation is high, showing positive stimulation to be an excellent predictor of normal nerve function. Negative stimulation is more predictive of paralysis in cases of thyroid carcinoma and Grave's disease. 2b. Copyright © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

Neurostimulation of the Lacrimal Nerve for Enhanced Tear Production

PubMed Central

Kossler, Andrea L.; Wang, Jianhua; Feuer, William; Tse, David T.

2014-01-01

Purpose To design a proof-of-concept study to assess the effect of lacrimal nerve stimulation (LNS) with an implantable pulse generator (IPG) to increase aqueous tear production. Methods Experimental animal study design of six Dutch Belted rabbits. Ultra high-resolution optical coherence tomography (UHR-OCT) quantified tear production by measuring the baseline tear volume of each rabbit’s right and left eye. A neurostimulator was implanted adjacent to the right lacrimal nerve. After two minutes of LNS (100 μs, 1.6 mAmp, 20 Hz, 5–8 volts), the tear volumes were measured with UHR-OCT. The change in tear volume was quantified and compared to the non-stimulated left eye. Three rabbits underwent chronic LNS (100 μS, 1.6 mAmp, 10 Hz, 2 volts) and their lacrimal glands were harvested for histopathologic analysis. Results UHR-OCT imaging of the right eyes tear volume showed a 441% average increase in tear production after LNS as a percent of baseline. After stimulation, right eyes had statistically significant greater increase in tear volumes than left eyes (p=0.028, Wilcoxon test). Post-stimulation right eye tear volumes were significantly greater compared to baseline (p=0.028, Wilcoxon test). Histopathologic examination of the lacrimal glands showed no discernible tissue damage from chronic neurostimulation. Additionally, there were no gross adverse effects on the general well-beings of the animals due to chronic stimulation. Conclusions Lacrimal nerve stimulation with an implantable pulse generator appears to increase aqueous tear production. Chronic LNS showed no histopathologic lacrimal gland damage. This study suggests LNS is a promising new treatment strategy to increase aqueous tear production. PMID:25126767

Dynamic surface-enhanced Raman spectroscopy and Chemometric methods for fast detection and intelligent identification of methamphetamine and 3, 4-Methylenedioxy methamphetamine in human urine

NASA Astrophysics Data System (ADS)

Weng, Shizhuang; Dong, Ronglu; Zhu, Zede; Zhang, Dongyan; Zhao, Jinling; Huang, Linsheng; Liang, Dong

2018-01-01

Conventional Surface-Enhanced Raman Spectroscopy (SERS) for fast detection of drugs in urine on the portable Raman spectrometer remains challenges because of low sensitivity and unreliable Raman signal, and spectra process with manual intervention. Here, we develop a novel detection method of drugs in urine using chemometric methods and dynamic SERS (D-SERS) with mPEG-SH coated gold nanorods (GNRs). D-SERS combined with the uniform GNRs can obtain giant enhancement, and the signal is also of high reproducibility. On the basis of the above advantages, we obtained the spectra of urine, urine with methamphetamine (MAMP), urine with 3, 4-Methylenedioxy Methamphetamine (MDMA) using D-SERS. Simultaneously, some chemometric methods were introduced for the intelligent and automatic analysis of spectra. Firstly, the spectra at the critical state were selected through using K-means. Then, the spectra were proposed by random forest (RF) with feature selection and principal component analysis (PCA) to develop the recognition model. And the identification accuracy of model were 100%, 98.7% and 96.7%, respectively. To validate the effect in practical issue further, the drug abusers'urine samples with 0.4, 3, 30 ppm MAMP were detected using D-SERS and identified by the classification model. The high recognition accuracy of > 92.0% can meet the demand of practical application. Additionally, the parameter optimization of RF classification model was simple. Compared with the general laboratory method, the detection process of urine's spectra using D-SERS only need 2 mins and 2 μL samples volume, and the identification of spectra based on chemometric methods can be finish in seconds. It is verified that the proposed approach can provide the accurate, convenient and rapid detection of drugs in urine.

Self-dissimilarity as a High Dimensional Complexity Measure

NASA Technical Reports Server (NTRS)

Wolpert, David H.; Macready, William

2005-01-01

For many systems characterized as "complex" the patterns exhibited on different scales differ markedly from one another. For example the biomass distribution in a human body "looks very different" depending on the scale at which one examines it. Conversely, the patterns at different scales in "simple" systems (e.g., gases, mountains, crystals) vary little from one scale to another. Accordingly, the degrees of self-dissimilarity between the patterns of a system at various scales constitute a complexity "signature" of that system. Here we present a novel quantification of self-dissimilarity. This signature can, if desired, incorporate a novel information-theoretic measure of the distance between probability distributions that we derive here. Whatever distance measure is chosen, our quantification of self-dissimilarity can be measured for many kinds of real-world data. This allows comparisons of the complexity signatures of wholly different kinds of systems (e.g., systems involving information density in a digital computer vs. species densities in a rain-forest vs. capital density in an economy, etc.). Moreover, in contrast to many other suggested complexity measures, evaluating the self-dissimilarity of a system does not require one to already have a model of the system. These facts may allow self-dissimilarity signatures to be used a s the underlying observational variables of an eventual overarching theory relating all complex systems. To illustrate self-dissimilarity we present several numerical experiments. In particular, we show that underlying structure of the logistic map is picked out by the self-dissimilarity signature of time series produced by that map

Waves on Ice

Atmospheric Science Data Center

2013-04-16

article title:  Waves on White: Ice or Clouds?     View Larger ... like a wavy cloud pattern was actually a wavy pattern on the ice surface. One of MISR's cloud classification products, the Angular Signature ...

Winter in the Ouachitas--a severe winter storm signature in Pinus echinata in the Ouachita Mountains of Oklahoma and Arkansas, USA

Treesearch

Douglas J. Stevenson; Thomas B. Lynch; Pradip Saud; Robert Heineman; Randal Holeman; Dennis Wilson; Keith Anderson; Chris Cerny; James M. Guldin

2016-01-01

Each year severe winter storms (≈ice storms) damage trees throughout the southern USA. Arkansas and Oklahoma have a history of severe winter storms. To extend that history back beyond the reach of written records, a distinctive tree ring pattern or signature is needed. Storm-caused breakage, branch loss and bending stress provide that signature. We found a severe storm...

Algorithms for Hyperspectral Endmember Extraction and Signature Classification with Morphological Dendritic Networks

NASA Astrophysics Data System (ADS)

Schmalz, M.; Ritter, G.

Accurate multispectral or hyperspectral signature classification is key to the nonimaging detection and recognition of space objects. Additionally, signature classification accuracy depends on accurate spectral endmember determination [1]. Previous approaches to endmember computation and signature classification were based on linear operators or neural networks (NNs) expressed in terms of the algebra (R, +, x) [1,2]. Unfortunately, class separation in these methods tends to be suboptimal, and the number of signatures that can be accurately classified often depends linearly on the number of NN inputs. This can lead to poor endmember distinction, as well as potentially significant classification errors in the presence of noise or densely interleaved signatures. In contrast to traditional CNNs, autoassociative morphological memories (AMM) are a construct similar to Hopfield autoassociatived memories defined on the (R, +, ?,?) lattice algebra [3]. Unlimited storage and perfect recall of noiseless real valued patterns has been proven for AMMs [4]. However, AMMs suffer from sensitivity to specific noise models, that can be characterized as erosive and dilative noise. On the other hand, the prior definition of a set of endmembers corresponds to material spectra lying on vertices of the minimum convex region covering the image data. These vertices can be characterized as morphologically independent patterns. It has further been shown that AMMs can be based on dendritic computation [3,6]. These techniques yield improved accuracy and class segmentation/separation ability in the presence of highly interleaved signature data. In this paper, we present a procedure for endmember determination based on AMM noise sensitivity, which employs morphological dendritic computation. We show that detected endmembers can be exploited by AMM based classification techniques, to achieve accurate signature classification in the presence of noise, closely spaced or interleaved signatures, and simulated camera optical distortions. In particular, we examine two critical cases: (1) classification of multiple closely spaced signatures that are difficult to separate using distance measures, and (2) classification of materials in simulated hyperspectral images of spaceborne satellites. In each case, test data are derived from a NASA database of space material signatures. Additional analysis pertains to computational complexity and noise sensitivity, which are superior to classical NN based techniques.

Quantifying the lag time to detect barriers in landscape genetics

Treesearch

E. L. Landguth; S. A Cushman; M. K. Schwartz; K. S. McKelvey; M. Murphy; G. Luikart

2010-01-01

Understanding how spatial genetic patterns respond to landscape change is crucial for advancing the emerging field of landscape genetics. We quantified the number of generations for new landscape barrier signatures to become detectable and for old signatures to disappear after barrier removal. We used spatially explicit, individualbased simulations to examine the...

Molecular signatures of selection on reproductive character displacement of flower color in Phlox drummondii.

PubMed

Hopkins, Robin; Levin, Donald A; Rausher, Mark D

2012-02-01

Character displacement, which arises when species diverge in sympatry to decrease competition for resources or reproductive interference, has been observed in a wide variety of plants and animals. A classic example of reproductive character displacement, presumed to be caused by reinforcing selection, is flower-color variation in the native Texas wildflower Phlox drummondii. Here, we use population genetic analyses to investigate molecular signatures of selection on flower-color variation in this species. First, we quantify patterns of neutral genetic variation across the range of P. drummondii to demonstrate that restricted gene flow and genetic drift cannot explain the pattern of flower-color divergence in this species. There is evidence of extensive gene flow across populations with different flower colors, suggesting selection caused flower-color divergence. Second, analysis of sequence variation in the genes underlying this divergence reveals a signature of a selective sweep in one of the two genes, further indicating selection is responsible for divergence in sympatry. The lack of a signature of selection at the second locus does not necessarily indicate a lack of selection on this locus but instead brings attention to the uncertainty in depending on molecular signatures to identify selection. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Neural representations of the concepts in simple sentences: Concept activation prediction and context effects.

PubMed

Just, Marcel Adam; Wang, Jing; Cherkassky, Vladimir L

2017-08-15

Although it has been possible to identify individual concepts from a concept's brain activation pattern, there have been significant obstacles to identifying a proposition from its fMRI signature. Here we demonstrate the ability to decode individual prototype sentences from readers' brain activation patterns, by using theory-driven regions of interest and semantic properties. It is possible to predict the fMRI brain activation patterns evoked by propositions and words which are entirely new to the model with reliably above-chance rank accuracy. The two core components implemented in the model that reflect the theory were the choice of intermediate semantic features and the brain regions associated with the neurosemantic dimensions. This approach also predicts the neural representation of object nouns across participants, studies, and sentence contexts. Moreover, we find that the neural representation of an agent-verb-object proto-sentence is more accurately characterized by the neural signatures of its components as they occur in a similar context than by the neural signatures of these components as they occur in isolation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Signature of dislocations and stacking faults of face-centred cubic nanocrystals in coherent X-ray diffraction patterns: a numerical study.

PubMed

Dupraz, Maxime; Beutier, Guillaume; Rodney, David; Mordehai, Dan; Verdier, Marc

2015-06-01

Crystal defects induce strong distortions in diffraction patterns. A single defect alone can yield strong and fine features that are observed in high-resolution diffraction experiments such as coherent X-ray diffraction. The case of face-centred cubic nanocrystals is studied numerically and the signatures of typical defects close to Bragg positions are identified. Crystals of a few tens of nanometres are modelled with realistic atomic potentials and 'relaxed' after introduction of well defined defects such as pure screw or edge dislocations, or Frank or prismatic loops. Diffraction patterns calculated in the kinematic approximation reveal various signatures of the defects depending on the Miller indices. They are strongly modified by the dissociation of the dislocations. Selection rules on the Miller indices are provided, to observe the maximum effect of given crystal defects in the initial and relaxed configurations. The effect of several physical and geometrical parameters such as stacking fault energy, crystal shape and defect position are discussed. The method is illustrated on a complex structure resulting from the simulated nanoindentation of a gold nanocrystal.

Signature of dislocations and stacking faults of face-centred cubic nanocrystals in coherent X-ray diffraction patterns: a numerical study1

PubMed Central

Dupraz, Maxime; Beutier, Guillaume; Rodney, David; Mordehai, Dan; Verdier, Marc

2015-01-01

Crystal defects induce strong distortions in diffraction patterns. A single defect alone can yield strong and fine features that are observed in high-resolution diffraction experiments such as coherent X-ray diffraction. The case of face-centred cubic nanocrystals is studied numerically and the signatures of typical defects close to Bragg positions are identified. Crystals of a few tens of nanometres are modelled with realistic atomic potentials and ‘relaxed’ after introduction of well defined defects such as pure screw or edge dislocations, or Frank or prismatic loops. Diffraction patterns calculated in the kinematic approximation reveal various signatures of the defects depending on the Miller indices. They are strongly modified by the dissociation of the dislocations. Selection rules on the Miller indices are provided, to observe the maximum effect of given crystal defects in the initial and relaxed configurations. The effect of several physical and geometrical parameters such as stacking fault energy, crystal shape and defect position are discussed. The method is illustrated on a complex structure resulting from the simulated nanoindentation of a gold nanocrystal. PMID:26089755

Analysis of Gene Expression Profiles of Multiple Skin Diseases Identifies a Conserved Signature of Disrupted Homeostasis.

PubMed

Mills, Kevin J; Robinson, Michael K; Sherrill, Joseph D; Schnell, Daniel J; Xu, Jun

2018-05-28

Triggers of skin disease pathogenesis vary, but events associated with the elicitation of a lesion share many features in common. Our objective was to examine gene expression patterns in skin disease to develop a molecular signature of disruption of cutaneous homeostasis. Gene expression data from common inflammatory skin diseases (e.g., psoriasis, atopic dermatitis, seborrheic dermatitis and acne), and a novel statistical algorithm were used to define a unifying molecular signature referred to as the "Unhealthy Skin Signature" (USS). Using a pattern matching algorithm, analysis of public data repositories revealed that the USS is found in diverse epithelial diseases. Studies of milder disruptions of epidermal homeostasis have also shown that these conditions converge, to varying degrees, on the USS and that the degree of convergence is related directly to the severity of homeostatic disruption. The USS contains genes that had no prior published association with skin, but that play important roles in many different disease processes, supporting the importance of the USS to homeostasis. Finally, we show through pattern matching that the USS can be used to discover new potential dermatologic therapeutics. The USS provides a new means to further interrogate epithelial homeostasis and potentially develop novel therapeutics with efficacy across a spectrum of skin conditions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Landscape of supersymmetric particle mass hierarchies and their signature space at the CERN Large Hadron Collider.

PubMed

Feldman, Daniel; Liu, Zuowei; Nath, Pran

2007-12-21

The minimal supersymmetric standard model with soft breaking has a large landscape of supersymmetric particle mass hierarchies. This number is reduced significantly in well-motivated scenarios such as minimal supergravity and alternatives. We carry out an analysis of the landscape for the first four lightest particles and identify at least 16 mass patterns, and provide benchmarks for each. We study the signature space for the patterns at the CERN Large Hadron Collider by analyzing the lepton+ (jet> or =2) + missing P{T} signals with 0, 1, 2, and 3 leptons. Correlations in missing P{T} are also analyzed. It is found that even with 10 fb{-1} of data a significant discrimination among patterns emerges.

A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer.

PubMed

Polak, Paz; Kim, Jaegil; Braunstein, Lior Z; Karlic, Rosa; Haradhavala, Nicholas J; Tiao, Grace; Rosebrock, Daniel; Livitz, Dimitri; Kübler, Kirsten; Mouw, Kent W; Kamburov, Atanas; Maruvka, Yosef E; Leshchiner, Ignaty; Lander, Eric S; Golub, Todd R; Zick, Aviad; Orthwein, Alexandre; Lawrence, Michael S; Batra, Rajbir N; Caldas, Carlos; Haber, Daniel A; Laird, Peter W; Shen, Hui; Ellisen, Leif W; D'Andrea, Alan D; Chanock, Stephen J; Foulkes, William D; Getz, Gad

2017-10-01

Biallelic inactivation of BRCA1 or BRCA2 is associated with a pattern of genome-wide mutations known as signature 3. By analyzing ∼1,000 breast cancer samples, we confirmed this association and established that germline nonsense and frameshift variants in PALB2, but not in ATM or CHEK2, can also give rise to the same signature. We were able to accurately classify missense BRCA1 or BRCA2 variants known to impair homologous recombination (HR) on the basis of this signature. Finally, we show that epigenetic silencing of RAD51C and BRCA1 by promoter methylation is strongly associated with signature 3 and, in our data set, was highly enriched in basal-like breast cancers in young individuals of African descent.

Relationship between Effective Application of Machine Learning and Malware Detection: A Quantitative Study

ERIC Educational Resources Information Center

Enfinger, Kerry Wayne

2016-01-01

The number of malicious files present in the public domain continues to rise at a substantial rate. Current anti-malware software utilizes a signature-based method to detect the presence of malicious software. Generating these pattern signatures is time consuming due to malicious code complexity and the need for expert analysis, however, by making…

Terrain type recognition using ERTS-1 MSS images

NASA Technical Reports Server (NTRS)

Gramenopoulos, N.

1973-01-01

For the automatic recognition of earth resources from ERTS-1 digital tapes, both multispectral and spatial pattern recognition techniques are important. Recognition of terrain types is based on spatial signatures that become evident by processing small portions of an image through selected algorithms. An investigation of spatial signatures that are applicable to ERTS-1 MSS images is described. Artifacts in the spatial signatures seem to be related to the multispectral scanner. A method for suppressing such artifacts is presented. Finally, results of terrain type recognition for one ERTS-1 image are presented.

Weekly Hydrometeorological Signatures - Characterization of Urban-Induced Streamflow and Rainfall Variability

NASA Astrophysics Data System (ADS)

Schnier, S.; Cai, X.; Sivapalan, M.

2014-12-01

About half of all humans alive today live in cities, with that number projected to grow to 70% by 2050. Because most people live in cities, urban streamflow patterns and precipitation events have a large impact on the global population. Urban environments can alter natural streamflow and precipitation patterns in a localized area. This study introduces a novel way to characterize this interference: the weekly hydrometeorological signature. Daily streamflow and precipitation data is collected from USGS gages around three climatically-different major American cities: Chicago, Los Angeles, and Charlotte. The following hypothesis is tested: a persistent weekly pattern (Monday through Sunday) exists in the hydrometeorological data which is unique to each city. All three cities appear to exhibit a persistent weekly pattern which is unique to that city for various climatological, industrial, and topographic reasons. Further study is needed; however these findings have important implications for understanding urban weather and can serve as a unique identifier, or fingerprint, for human interference to local streamflow and precipitation patterns.

Geographic patterns of networks derived from extreme precipitation over the Indian subcontinent

NASA Astrophysics Data System (ADS)

Stolbova, Veronika; Bookhagen, Bodo; Marwan, Norbert; Kurths, Juergen

2014-05-01

Complex networks (CN) and event synchronization (ES) methods have been applied to study a number of climate phenomena such as Indian Summer Monsoon (ISM), South-American Monsoon, and African Monsoon. These methods proved to be powerful tools to infer interdependencies in climate dynamics between geographical sites, spatial structures, and key regions of the considered climate phenomenon. Here, we use these methods to study the spatial temporal variability of the extreme rainfall over the Indian subcontinent, in order to filter the data by coarse-graining the network, and to identify geographic patterns that are signature features (spatial signatures) of the ISM. We find four main geographic patterns of networks derived from extreme precipitation over the Indian subcontinent using up-to-date satellite-derived, and high temporal and spatial resolution rain-gauge interpolated daily rainfall datasets. In order to prove that our results are also relevant for other climatic variables like pressure and temperature, we use re-analysis data provided by the National Center for Environmental Prediction and National Center for Atmospheric Research (NCEP/NCAR). We find that two of the patterns revealed from the CN extreme rainfall analysis coincide with those obtained for the pressure and temperature fields, and all four above mentioned patterns can be explained by topography, winds, and monsoon circulation. CN and ES enable to select the most informative regions for the ISM, providing realistic description of the ISM dynamics with fewer data, and also help to infer geographic pattern that are spatial signatures of the ISM. These patterns deserve a special attention for the meteorologists and can be used as markers of the ISM variability.

Authentication Based on Pole-zero Models of Signature Velocity

PubMed Central

Rashidi, Saeid; Fallah, Ali; Towhidkhah, Farzad

2013-01-01

With the increase of communication and financial transaction through internet, on-line signature verification is an accepted biometric technology for access control and plays a significant role in authenticity and authorization in modernized society. Therefore, fast and precise algorithms for the signature verification are very attractive. The goal of this paper is modeling of velocity signal that pattern and properties is stable for persons. With using pole-zero models based on discrete cosine transform, precise method is proposed for modeling and then features is founded from strokes. With using linear, parzen window and support vector machine classifiers, the signature verification technique was tested with a large number of authentic and forgery signatures and has demonstrated the good potential of this technique. The signatures are collected from three different database include a proprietary database, the SVC2004 and the Sabanci University signature database benchmark databases. Experimental results based on Persian, SVC2004 and SUSIG databases show that our method achieves an equal error rate of 5.91%, 5.62% and 3.91% in the skilled forgeries, respectively. PMID:24696797

Acoustic Signatures of a Model Fan in the NASA-Lewis Anechoic Wind Tunnel

NASA Technical Reports Server (NTRS)

Dietrich, D. A.; Heidmann, M. F.; Abbott, J. M.

1977-01-01

One-third octave band and narrowband spectra and continuous directivity patterns radiated from an inlet are presented over ranges of fan operating conditions, tunnel velocity, and angle of attack. Tunnel flow markedly reduced the unsteadiness and level of the blade passage tone, revealed the cutoff design feature of the blade passage tone, and exposed a lobular directivity pattern for the second harmonic tone. The full effects of tunnel flow are shown to be complete above a tunnel velocity of 20 meters/second. The acoustic signatures are also shown to be strongly affected by fan rotational speed, fan blade loading, and inlet angle of attack.

Repetitive element signature-based visualization, distance computation, and classification of 1766 microbial genomes.

PubMed

Lee, Kang-Hoon; Shin, Kyung-Seop; Lim, Debora; Kim, Woo-Chan; Chung, Byung Chang; Han, Gyu-Bum; Roh, Jeongkyu; Cho, Dong-Ho; Cho, Kiho

2015-07-01

The genomes of living organisms are populated with pleomorphic repetitive elements (REs) of varying densities. Our hypothesis that genomic RE landscapes are species/strain/individual-specific was implemented into the Genome Signature Imaging system to visualize and compute the RE-based signatures of any genome. Following the occurrence profiling of 5-nucleotide REs/words, the information from top-50 frequency words was transformed into a genome-specific signature and visualized as Genome Signature Images (GSIs), using a CMYK scheme. An algorithm for computing distances among GSIs was formulated using the GSIs' variables (word identity, frequency, and frequency order). The utility of the GSI-distance computation system was demonstrated with control genomes. GSI-based computation of genome-relatedness among 1766 microbes (117 archaea and 1649 bacteria) identified their clustering patterns; although the majority paralleled the established classification, some did not. The Genome Signature Imaging system, with its visualization and distance computation functions, enables genome-scale evolutionary studies involving numerous genomes with varying sizes. Copyright © 2015 Elsevier Inc. All rights reserved.

Chlorella Induces Stomatal Closure via NADPH Oxidase-Dependent ROS Production and Its Effects on Instantaneous Water Use Efficiency in Vicia faba

PubMed Central

Li, Yan; Xu, Shan-Shan; Gao, Jing; Pan, Sha; Wang, Gen-Xuan

2014-01-01

Reactive oxygen species (ROS) have been established to participate in stomatal closure induced by live microbes and microbe-associated molecular patterns (MAMPs). Chlorella as a beneficial microorganism can be expected to trigger stomatal closure via ROS production. Here, we reported that Chlorella induced stomatal closure in a dose-and time-dependent manner in epidermal peels of Vicia faba. Using pharmacological methods in this work, we found that the Chlorella-induced stomatal closure was almost completely abolished by a hydrogen peroxide (H2O2) scavenger, catalase (CAT), significantly suppressed by an NADPH oxidase inhibitor, diphenylene iodonium chloride (DPI), and slightly affected by a peroxidase inhibitor, salicylhydroxamic acid (SHAM), suggesting that ROS production involved in Chlorella-induced stomatal closure is mainly mediated by DPI-sensitive NADPH oxidase. Additionally, Exogenous application of optimal concentrations of Chlorella suspension improved instantaneous water use efficiency (WUEi) in Vicia faba via a reduction in leaf transpiration rate (E) without a parallel reduction in net photosynthetic rate (Pn) assessed by gas-exchange measurements. The chlorophyll fluorescence and content analysis further demonstrated that short-term use of Chlorella did not influence plant photosynthetic reactions center. These results preliminarily reveal that Chlorella can trigger stomatal closure via NADPH oxidase-dependent ROS production in epidermal strips and improve WUEi in leave levels. PMID:24687099

Chlorella induces stomatal closure via NADPH oxidase-dependent ROS production and its effects on instantaneous water use efficiency in Vicia faba.

PubMed

Li, Yan; Xu, Shan-Shan; Gao, Jing; Pan, Sha; Wang, Gen-Xuan

2014-01-01

Reactive oxygen species (ROS) have been established to participate in stomatal closure induced by live microbes and microbe-associated molecular patterns (MAMPs). Chlorella as a beneficial microorganism can be expected to trigger stomatal closure via ROS production. Here, we reported that Chlorella induced stomatal closure in a dose-and time-dependent manner in epidermal peels of Vicia faba. Using pharmacological methods in this work, we found that the Chlorella-induced stomatal closure was almost completely abolished by a hydrogen peroxide (H2O2) scavenger, catalase (CAT), significantly suppressed by an NADPH oxidase inhibitor, diphenylene iodonium chloride (DPI), and slightly affected by a peroxidase inhibitor, salicylhydroxamic acid (SHAM), suggesting that ROS production involved in Chlorella-induced stomatal closure is mainly mediated by DPI-sensitive NADPH oxidase. Additionally, Exogenous application of optimal concentrations of Chlorella suspension improved instantaneous water use efficiency (WUEi) in Vicia faba via a reduction in leaf transpiration rate (E) without a parallel reduction in net photosynthetic rate (Pn) assessed by gas-exchange measurements. The chlorophyll fluorescence and content analysis further demonstrated that short-term use of Chlorella did not influence plant photosynthetic reactions center. These results preliminarily reveal that Chlorella can trigger stomatal closure via NADPH oxidase-dependent ROS production in epidermal strips and improve WUEi in leave levels.

Trace-element record in zircons during exhumation from UHP conditions, North-East Greenland Caledonides

USGS Publications Warehouse

McClelland, W.C.; Gilotti, J.A.; Mazdab, F.K.; Wooden, J.L.

2009-01-01

Coesite-bearing zircon formed at ultrahigh-pressure (UHP) conditions share general characteristics of eclogite-facies zircon with trace-element signatures characterized by depleted heavy rare earth elements (HREE), lack of an Eu anomaly, and low Th/ U ratios. Trace-element signatures of zircons from the Caledonian UHP terrane in North-East Greenland were used to examine the possible changes in signature with age during exhumation. Collection and interpretation of age and trace-element analyses of zircon from three samples of quartzofeldspathic gneiss and two leucocratic intrusions were guided by core vs. rim zoning patterns as imaged by cathodoluminesence. Change from igneous to eclogite-facies metamorphic trace-element signature in protolith zircon is characterized by gradual depletion of HREE, whereas newly formed metamorphic rims have flat HREE patterns and REE concentrations that are distinct from the recrystallized inherited cores. The signature associated with eclogite-facies metamorphic zircon is observed in coesite-bearing zircon formed at 358 ?? 4 Ma, metamorphic rims formed at 348 ?? 5 Ma during the initial stages of exhumation, and metamorphic rims formed at 337 ?? 5 Ma. Zircons from a garnet-bearing granite emplaced in the neck of an eclogite boudin and a leucocratic dike that cross-cuts amphibolite-facies structural fabrics have steeply sloping HREE patterns, variably developed negative Eu anomalies, and low Th/U ratios. The granite records initial decompression melting and exhumation at 347 ?? 2 Ma and later zircon rim growth at 329 ?? 5. The leucocratic dike was likely emplaced at amphibolite-facies conditions at 330 ?? 2 Ma, but records additional growth of compositionally similar zircon at 321 ??2 Ma. The difference between the trace-element signature of metamorphic zircon in the gneisses and in part coeval leucocratic intrusions indicates that the zircon signature varies as a function of lithology and context, thus enhancing its ability to aid in the interpretation of U-Pb data and track the exhumation history of UHP terranes. The differences may reflect variation in elemental availability through breakdown reactions in quartzofeldpathic gneiss vs. availability during melt production and/or crystallization. UHP rocks in North-East Greenland began exhumation by 347 ?? 2 Ma, were still at HP eclogite-facies conditions at 337 ?? 5 Ma and were at amphibolite-facies conditions by 330 ?? 2 Ma. ?? 2009 E. Schweizerbart'sche Verlagsbuchhandlung.

Patterns of vegetation in the Owens Valley, California

NASA Technical Reports Server (NTRS)

Ustin, S. L.; Rock, B. N.; Woodward, R. A.

1986-01-01

Spectral characteristics of semi-arid shrub communities were examined using Airborne Imaging Spectrometer (AIS) data collected in the tree mode on 23 May 1985. Mesic sites with relatively high vegetation density and distinct zonation patterns exhibited greater spectral signature variations than sites with more xeric shrub communities. Spectral signature patterns were not directly related to vegetation density or physiognomy, although spatial maps derived from an 8-channel maximum likelihood classification were supported by photo-interpreted surface features. In AIS data, the principal detected effect of shrub vegetation on the alluvial fans is to lower reflectance across the spectrum. These results are similar to those reported during a period of minimal physiological activity in autumn, indicating that shadows cast by vegetation canopies are an important element of soil-vegetation interaction under conditions of relatively low canopy cover.

The metabolic signature associated with the Western dietary pattern: a cross-sectional study.

PubMed

Bouchard-Mercier, Annie; Rudkowska, Iwona; Lemieux, Simone; Couture, Patrick; Vohl, Marie-Claude

2013-12-11

Metabolic profiles have been shown to be associated to obesity status and insulin sensitivity. Dietary intakes influence metabolic pathways and therefore, different dietary patterns may relate to modifications in metabolic signatures. The objective was to verify associations between dietary patterns and metabolic profiles composed of amino acids (AAs) and acylcarnitines (ACs). 210 participants were recruited in the greater Quebec City area between September 2009 and December 2011. Dietary patterns had been previously derived using principal component analysis (PCA). The Prudent dietary pattern was characterised by higher intakes of vegetables, fruits, whole grain products, non-hydrogenated fat and lower intakes of refined grain products, whereas the Western dietary pattern was associated with higher intakes of refined grain products, desserts, sweets and processed meats. Targeted metabolites were quantified in 37 participants with the Biocrates Absolute IDQ p150 (Biocrates Life Sciences AG, Austria) mass spectrometry method (including 14 amino acids and 41 acylcarnitines). PCA analysis with metabolites including AAs and ACs revealed two main components explaining the most variance in overall data (13.8%). PC1 was composed mostly of medium- to long-chain ACs (C16:2, C14:2, C14:2-OH, C16, C14:1-OH, C14:1, C10:2, C5-DC/C6-OH, C12, C18:2, C10, C4:1-DC/C6, C8:1 and C2) whereas PC2 included certain AAs and short-chain ACs (xLeu, Met, Arg, Phe, Pro, Orn, His, C0, C3, C4 and C5). The Western dietary pattern correlated negatively with PC1 and positively with PC2 (r = -0.34, p = 0.05 and r = 0.38, p = 0.03, respectively), independently of age, sex and BMI. These findings suggest that the Western dietary pattern is associated with a specific metabolite signature characterized by increased levels of AAs including branched-chain AAs (BCAAs) and short-chain ACs.

Analysis of passive microwave signatures over snow-covered mountainous area

NASA Astrophysics Data System (ADS)

Kim, R. S.; Durand, M. T.

2015-12-01

Accurate knowledge of snow distribution over mountainous area is critical for climate studies and the passive microwave(PM) measurements have been widely used and invested in order to obtain information about snowpack properties. Understanding and analyzing the signatures for the explicit inversion of the remote sensing data from land surfaces is required for successful using of passive microwave sensors but this task is often ambiguous due to the large variability of physical conditions and object types. In this paper, we discuss the pattern of measured brightness temperatures and emissivities at vertical and horizontal polarization over the frequency range of 10.7 to 89 GHz of land surfaces under various snow and vegetation conditions. The Multiband polarimetric Scanning Radiometer(PSR) imagery is used over NASA Cold Land Processes Field Experiment(CLPX) study area with ground-based measurements of snow depth and snow properties. Classification of snow under various conditions in mountainous area is implemented based on different patterns of microwave signatures.

Profiling of histone H3 lysine 9 trimethylation levels predicts transcription factor activity and survival in acute myeloid leukemia.

PubMed

Müller-Tidow, Carsten; Klein, Hans-Ulrich; Hascher, Antje; Isken, Fabienne; Tickenbrock, Lara; Thoennissen, Nils; Agrawal-Singh, Shuchi; Tschanter, Petra; Disselhoff, Christine; Wang, Yipeng; Becker, Anke; Thiede, Christian; Ehninger, Gerhard; zur Stadt, Udo; Koschmieder, Steffen; Seidl, Matthias; Müller, Frank U; Schmitz, Wilhelm; Schlenke, Peter; McClelland, Michael; Berdel, Wolfgang E; Dugas, Martin; Serve, Hubert

2010-11-04

Acute myeloid leukemia (AML) is commonly associated with alterations in transcription factors because of altered expression or gene mutations. These changes might induce leukemia-specific patterns of histone modifications. We used chromatin-immunoprecipitation on microarray to analyze histone 3 lysine 9 trimethylation (H3K9me3) patterns in primary AML (n = 108), acute lymphoid leukemia (n = 28), CD34(+) cells (n = 21) and white blood cells (n = 15) specimens. Hundreds of promoter regions in AML showed significant alterations in H3K9me3 levels. H3K9me3 deregulation in AML occurred preferentially as a decrease in H3K9me3 levels at core promoter regions. The altered genomic regions showed an overrepresentation of cis-binding sites for ETS and cyclic adenosine monophosphate response elements (CREs) for transcription factors of the CREB/CREM/ATF1 family. The decrease in H3K9me3 levels at CREs was associated with increased CRE-driven promoter activity in AML blasts in vivo. AML-specific H3K9me3 patterns were not associated with known cytogenetic abnormalities. But a signature derived from H3K9me3 patterns predicted event-free survival in AML patients. When the H3K9me3 signature was combined with established clinical prognostic markers, it outperformed prognosis prediction based on clinical parameters alone. These findings demonstrate widespread changes of H3K9me3 levels at gene promoters in AML. Signatures of histone modification patterns are associated with patient prognosis in AML.

Importance of correlation between gene expression levels: application to the type I interferon signature in rheumatoid arthritis.

PubMed

Reynier, Frédéric; Petit, Fabien; Paye, Malick; Turrel-Davin, Fanny; Imbert, Pierre-Emmanuel; Hot, Arnaud; Mougin, Bruno; Miossec, Pierre

2011-01-01

The analysis of gene expression data shows that many genes display similarity in their expression profiles suggesting some co-regulation. Here, we investigated the co-expression patterns in gene expression data and proposed a correlation-based research method to stratify individuals. Using blood from rheumatoid arthritis (RA) patients, we investigated the gene expression profiles from whole blood using Affymetrix microarray technology. Co-expressed genes were analyzed by a biclustering method, followed by gene ontology analysis of the relevant biclusters. Taking the type I interferon (IFN) pathway as an example, a classification algorithm was developed from the 102 RA patients and extended to 10 systemic lupus erythematosus (SLE) patients and 100 healthy volunteers to further characterize individuals. We developed a correlation-based algorithm referred to as Classification Algorithm Based on a Biological Signature (CABS), an alternative to other approaches focused specifically on the expression levels. This algorithm applied to the expression of 35 IFN-related genes showed that the IFN signature presented a heterogeneous expression between RA, SLE and healthy controls which could reflect the level of global IFN signature activation. Moreover, the monitoring of the IFN-related genes during the anti-TNF treatment identified changes in type I IFN gene activity induced in RA patients. In conclusion, we have proposed an original method to analyze genes sharing an expression pattern and a biological function showing that the activation levels of a biological signature could be characterized by its overall state of correlation.

Topographic Signatures of Meandering Rivers with Differences in Outer Bank Cohesion

NASA Astrophysics Data System (ADS)

Kelly, S. A.; Belmont, P.

2014-12-01

Within a given valley setting, interactions between river hydraulics, sediment, topography, and vegetation determine attributes of channel morphology, including planform, width and depth, slope, and bed and bank properties. These feedbacks also govern river behavior, including migration and avulsion. Bank cohesion, from the addition of fine sediment and/or vegetation has been recognized in flume experiments as a necessary component to create and maintain a meandering channel planform. Greater bank cohesion slows bank erosion, limiting the rate at which a river can adjust laterally and preventing so-called "runaway widening" to a braided state. Feedbacks of bank cohesion on channel hydraulics and sediment transport may thus produce distinct topographic signatures, or patterns in channel width, depth, and point bar transverse slope. We expect that in bends of greater outer bank cohesion the channel will be narrower, deeper, and bars will have greater transverse slopes. Only recently have we recognized that biotic processes may imprint distinct topographic signatures on the landscape. This study explores topographic signatures of three US rivers: the lower Minnesota River, near Mankato, MN, the Le Sueur River, south central MN, and the Fall River, Rocky Mountain National Park, CO. Each of these rivers has variability in outer bank cohesion, quantified based on geotechnical and vegetation properties, and in-channel topography, which was derived from rtkGPS and acoustic bathymetry surveys. We present methods for incorporating biophysical feedbacks into geomorphic transport laws so that models can better simulate the spatial patterns and variability of topographic signatures.

In Vivo Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The φ-Index.

PubMed

Bakas, Spyridon; Akbari, Hamed; Pisapia, Jared; Martinez-Lage, Maria; Rozycki, Martin; Rathore, Saima; Dahmane, Nadia; O'Rourke, Donald M; Davatzikos, Christos

2017-08-15

Purpose: The epidermal growth factor receptor variant III ( EGFRvIII ) mutation has been considered a driver mutation and therapeutic target in glioblastoma, the most common and aggressive brain cancer. Currently, detecting EGFRvIII requires postoperative tissue analyses, which are ex vivo and unable to capture the tumor's spatial heterogeneity. Considering the increasing evidence of in vivo imaging signatures capturing molecular characteristics of cancer, this study aims to detect EGFRvIII in primary glioblastoma noninvasively, using routine clinically acquired imaging. Experimental Design: We found peritumoral infiltration and vascularization patterns being related to EGFRvIII status. We therefore constructed a quantitative within-patient peritumoral heterogeneity index (PHI/φ-index), by contrasting perfusion patterns of immediate and distant peritumoral edema. Application of φ-index in preoperative perfusion scans of independent discovery ( n = 64) and validation ( n = 78) cohorts, revealed the generalizability of this EGFRvIII imaging signature. Results: Analysis in both cohorts demonstrated that the obtained signature is highly accurate (89.92%), specific (92.35%), and sensitive (83.77%), with significantly distinctive ability ( P = 4.0033 × 10 -10 , AUC = 0.8869). Findings indicated a highly infiltrative-migratory phenotype for EGFRvIII + tumors, which displayed similar perfusion patterns throughout peritumoral edema. Contrarily, EGFRvIII - tumors displayed perfusion dynamics consistent with peritumorally confined vascularization, suggesting potential benefit from extensive peritumoral resection/radiation. Conclusions: This EGFRvIII signature is potentially suitable for clinical translation, since obtained from analysis of clinically acquired images. Use of within-patient heterogeneity measures, rather than population-based associations, renders φ-index potentially resistant to inter-scanner variations. Overall, our findings enable noninvasive evaluation of EGFRvIII for patient selection for targeted therapy, stratification into clinical trials, personalized treatment planning, and potentially treatment-response evaluation. Clin Cancer Res; 23(16); 4724-34. ©2017 AACR . ©2017 American Association for Cancer Research.

Feasibility study for locating archaeological village sites by satellite remote sensing techniques. [multispectral photography of Alaska

NASA Technical Reports Server (NTRS)

Cook, J. P. (Principal Investigator); Stringer, W. J.

1974-01-01

The author has identified the following significant results. The objective is to determine the feasibility of detecting large Alaskan archaeological sites by satellite remote sensing techniques and mapping such sites. The approach used is to develop digital multispectral signatures of dominant surface features including vegetation, exposed soils and rock, hydrological patterns and known archaeological sites. ERTS-1 scenes are then printed out digitally in a map-like array with a letter reflecting the most appropriate classification representing each pixel. Preliminary signatures were developed and tested. It was determined that there was a need to tighten up the archaeological site signature by developing accurate signatures for all naturally-occurring vegetation and surface conditions in the vicinity of the test area. These second generation signatures have been tested by means of computer printouts and classified tape displays on the University of Alaska CDU-200 and by comparison with aerial photography. It has been concluded that the archaeological signatures now in use are as good as can be developed. Plans are to print out signatures for the entire test area and locate on topographic maps the likely locations of archaeological sites within the test area.

The spectrum of genomic signatures: from dinucleotides to chaos game representation.

PubMed

Wang, Yingwei; Hill, Kathleen; Singh, Shiva; Kari, Lila

2005-02-14

In the post genomic era, access to complete genome sequence data for numerous diverse species has opened multiple avenues for examining and comparing primary DNA sequence organization of entire genomes. Previously, the concept of a genomic signature was introduced with the observation of species-type specific Dinucleotide Relative Abundance Profiles (DRAPs); dinucleotides were identified as the subsequences with the greatest bias in representation in a majority of genomes. Herein, we demonstrate that DRAP is one particular genomic signature contained within a broader spectrum of signatures. Within this spectrum, an alternative genomic signature, Chaos Game Representation (CGR), provides a unique visualization of patterns in sequence organization. A genomic signature is associated with a particular integer order or subsequence length that represents a measure of the resolution or granularity in the analysis of primary DNA sequence organization. We quantitatively explore the organizational information provided by genomic signatures of different orders through different distance measures, including a novel Image Distance. The Image Distance and other existing distance measures are evaluated by comparing the phylogenetic trees they generate for 26 complete mitochondrial genomes from a diversity of species. The phylogenetic tree generated by the Image Distance is compatible with the known relatedness of species. Quantitative evaluation of the spectrum of genomic signatures may be used to ultimately gain insight into the determinants and biological relevance of the genome signatures.

Home-Based Functional Electrical Stimulation for Long-Term Denervated Human Muscle: History, Basics, Results and Perspectives of the Vienna Rehabilitation Strategy

PubMed Central

Kern, Helmut

2014-01-01

We will here discuss the following points related to Home-based Functional Electrical Stimulation (h-b FES) as treatment for patients with permanently denervated muscles in their legs: 1. Upper (UMN) and lower motor neuron (LMN) damage to the lower spinal cord; 2. Muscle atrophy/hypertrophy versus processes of degeneration, regeneration, and recovery; 3. Recovery of twitch- and tetanic-contractility by h-b FES; 4. Clinical effects of h-b FES using the protocol of the “Vienna School”; 5. Limitations and perspectives. Arguments in favor of using the Vienna protocol include: 1. Increased muscle size in both legs; 2. Improved tetanic force production after 3-5 months of percutaneous stimulation using long stimulus pulses (> 100 msec) of high amplitude (> 80 mAmp), tolerated only in patients with no pain sensibility; 3. Histological and electron microscopic evidence that two years of h-b FES return muscle fibers to a state typical of two weeks denervated muscles with respect to atrophy, disrupted myofibrillar structure, and disorganized Excitation-Contraction Coupling (E-CC) structures; 4. The excitability never recovers to that typical of normal or reinnervated muscles where pulses less than 1 msec in duration and 25 mAmp in intensity excite axons and thereby muscle fibres. It is important to motivate these patients for chronic stimulation throughout life, preferably standing up against the load of the body weight rather than sitting. Only younger and low weight patients can expect to be able to stand-up and do some steps more or less independently. Some patients like to maintain the h-b FES training for decades. Limitations of the procedure are obvious, in part related to the use of multiple, large surface electrodes and the amount of time patients are willing to use for such muscle training. PMID:26913127

Space Weather at Mars: 3-D studies using one-way coupling between the Multi-fluid MHD, M-GITM and M-AMPS models

NASA Astrophysics Data System (ADS)

Dong, Chuanfei

This dissertation presents numerical simulation results of the solar wind interaction with the Martian upper atmosphere by using three comprehensive 3-D models: the Mars Global Ionosphere Thermosphere Model (M-GITM), the Mars exosphere Monte Carlo model Adaptive Mesh Particle Simulator (M-AMPS), and the BATS-R-US Mars multi-fluid MHD (MF-MHD) model. The coupled framework has the potential to provide improved predictions for ion escape rates for comparison with future data to be returned by the MAVEN mission (2014-2016) and thereby improve our understanding of present day escape processes. Estimates of ion escape rates over Mars history must start from properly validated models that can be extrapolated into the past. This thesis aims to build a model library for the NASA Mars Atmosphere and Volatile EvolutioN (MAVEN) mission, which will thus enhance the science return from the MAVEN mission. In this thesis, we aim to address the following four main scientific questions by adopting the one-way coupled framework developed here: (1) What are the Martian ion escape rates at the current epoch and ancient times? (2) What controls the ion escape processes at the current epoch? How are the ion escape variations connected to the solar cycle, crustal field orientation and seasonal variations? (3) How do the variable 3-D cold neutral thermosphere and hot oxygen corona affect the solar wind-Mars interaction? (4) How does the Martian atmosphere respond to extreme variations (e.g., ICMEs) in the solar wind and its interplanetary environment? These questions are closely related to the primary scientific goals of NASA's MAVEN mission and European Space Agency's Mars Express (MEX) mission. We reasonably answer all these four questions at the end of this thesis by employing the one-way coupled framework and comparing the simulation results with both MEX and MAVEN observational data.

F104S c-Mpl responds to a transmembrane domain-binding thrombopoietin receptor agonist: proof of concept that selected receptor mutations in congenital amegakaryocytic thrombocytopenia can be stimulated with alternative thrombopoietic agents.

PubMed

Fox, Norma E; Lim, Jihyang; Chen, Rose; Geddis, Amy E

2010-05-01

To determine whether specific c-Mpl mutations might respond to thrombopoietin receptor agonists. We created cell line models of type II c-Mpl mutations identified in congenital amegakaryocytic thrombocytopenia. We selected F104S c-Mpl for further study because it exhibited surface expression of the receptor. We measured proliferation of cell lines expressing wild-type or F104S c-Mpl in response to thrombopoietin receptor agonists targeting the extracellular (m-AMP4) or transmembrane (LGD-4665) domains of the receptor by 1-methyltetrazole-5-thiol assay. We measured thrombopoietin binding to the mutant receptor using an in vitro thrombopoietin uptake assay and identified F104 as a potentially critical residue for the interaction between the receptor and its ligand by aligning thrombopoietin and erythropoietin receptors from multiple species. Cells expressing F104S c-Mpl proliferated in response to LGD-4665, but not thrombopoietin or m-AMP4. Compared to thrombopoietin, LGD-4665 stimulates signaling with delayed kinetics in both wild-type and F104S c-Mpl-expressing cells. Although F104S c-Mpl is expressed on the cell surface in our BaF3 cell line model, the mutant receptor does not bind thrombopoietin. Comparison to the erythropoietin receptor suggests that F104 engages in hydrogen-bonding interactions that are critical for binding to thrombopoietin. These findings suggest that a small subset of patients with congenital amegakaryocytic thrombocytopenia might respond to treatment with thrombopoietin receptor agonists, but that responsiveness will depend on the type of mutation and agonist used. We postulate that F104 is critical for thrombopoietin binding. The kinetics of signaling in response to a transmembrane domain-binding agonist are delayed in comparison to thrombopoietin. 2010 ISEH Society for Hematology and Stem Cells. Published by Elsevier Inc. All rights reserved.

A methodology to develop computational phantoms with adjustable posture for WBC calibration

NASA Astrophysics Data System (ADS)

Ferreira Fonseca, T. C.; Bogaerts, R.; Hunt, John; Vanhavere, F.

2014-11-01

A Whole Body Counter (WBC) is a facility to routinely assess the internal contamination of exposed workers, especially in the case of radiation release accidents. The calibration of the counting device is usually done by using anthropomorphic physical phantoms representing the human body. Due to such a challenge of constructing representative physical phantoms a virtual calibration has been introduced. The use of computational phantoms and the Monte Carlo method to simulate radiation transport have been demonstrated to be a worthy alternative. In this study we introduce a methodology developed for the creation of realistic computational voxel phantoms with adjustable posture for WBC calibration. The methodology makes use of different software packages to enable the creation and modification of computational voxel phantoms. This allows voxel phantoms to be developed on demand for the calibration of different WBC configurations. This in turn helps to study the major source of uncertainty associated with the in vivo measurement routine which is the difference between the calibration phantoms and the real persons being counted. The use of realistic computational phantoms also helps the optimization of the counting measurement. Open source codes such as MakeHuman and Blender software packages have been used for the creation and modelling of 3D humanoid characters based on polygonal mesh surfaces. Also, a home-made software was developed whose goal is to convert the binary 3D voxel grid into a MCNPX input file. This paper summarizes the development of a library of phantoms of the human body that uses two basic phantoms called MaMP and FeMP (Male and Female Mesh Phantoms) to create a set of male and female phantoms that vary both in height and in weight. Two sets of MaMP and FeMP phantoms were developed and used for efficiency calibration of two different WBC set-ups: the Doel NPP WBC laboratory and AGM laboratory of SCK-CEN in Mol, Belgium.

A methodology to develop computational phantoms with adjustable posture for WBC calibration.

PubMed

Fonseca, T C Ferreira; Bogaerts, R; Hunt, John; Vanhavere, F

2014-11-21

A Whole Body Counter (WBC) is a facility to routinely assess the internal contamination of exposed workers, especially in the case of radiation release accidents. The calibration of the counting device is usually done by using anthropomorphic physical phantoms representing the human body. Due to such a challenge of constructing representative physical phantoms a virtual calibration has been introduced. The use of computational phantoms and the Monte Carlo method to simulate radiation transport have been demonstrated to be a worthy alternative. In this study we introduce a methodology developed for the creation of realistic computational voxel phantoms with adjustable posture for WBC calibration. The methodology makes use of different software packages to enable the creation and modification of computational voxel phantoms. This allows voxel phantoms to be developed on demand for the calibration of different WBC configurations. This in turn helps to study the major source of uncertainty associated with the in vivo measurement routine which is the difference between the calibration phantoms and the real persons being counted. The use of realistic computational phantoms also helps the optimization of the counting measurement. Open source codes such as MakeHuman and Blender software packages have been used for the creation and modelling of 3D humanoid characters based on polygonal mesh surfaces. Also, a home-made software was developed whose goal is to convert the binary 3D voxel grid into a MCNPX input file. This paper summarizes the development of a library of phantoms of the human body that uses two basic phantoms called MaMP and FeMP (Male and Female Mesh Phantoms) to create a set of male and female phantoms that vary both in height and in weight. Two sets of MaMP and FeMP phantoms were developed and used for efficiency calibration of two different WBC set-ups: the Doel NPP WBC laboratory and AGM laboratory of SCK-CEN in Mol, Belgium.

Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA

Treesearch

Brandon M. Lind; Christopher J. Friedline; Jill L. Wegrzyn; Patricia E. Maloney; Detlev R. Vogler; David B. Neale; Andrew J. Eckert

2017-01-01

Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n = 116 231 SNPs) to describe signatures of fine-scale...

Ion channel gene expression predicts survival in glioma patients

PubMed Central

Wang, Rong; Gurguis, Christopher I.; Gu, Wanjun; Ko, Eun A; Lim, Inja; Bang, Hyoweon; Zhou, Tong; Ko, Jae-Hong

2015-01-01

Ion channels are important regulators in cell proliferation, migration, and apoptosis. The malfunction and/or aberrant expression of ion channels may disrupt these important biological processes and influence cancer progression. In this study, we investigate the expression pattern of ion channel genes in glioma. We designate 18 ion channel genes that are differentially expressed in high-grade glioma as a prognostic molecular signature. This ion channel gene expression based signature predicts glioma outcome in three independent validation cohorts. Interestingly, 16 of these 18 genes were down-regulated in high-grade glioma. This signature is independent of traditional clinical, molecular, and histological factors. Resampling tests indicate that the prognostic power of the signature outperforms random gene sets selected from human genome in all the validation cohorts. More importantly, this signature performs better than the random gene signatures selected from glioma-associated genes in two out of three validation datasets. This study implicates ion channels in brain cancer, thus expanding on knowledge of their roles in other cancers. Individualized profiling of ion channel gene expression serves as a superior and independent prognostic tool for glioma patients. PMID:26235283

Application of micro-attenuated total reflectance Fourier transform infrared spectroscopy to ink examination in signatures written with ballpoint pen on questioned documents.

PubMed

Nam, Yun Sik; Park, Jin Sook; Lee, Yeonhee; Lee, Kang-Bong

2014-05-01

Questioned documents examined in a forensic laboratory sometimes contain signatures written with ballpoint pen inks; these signatures were examined to assess the feasibility of micro-attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy as a forensic tool. Micro-ATR FTIR spectra for signatures written with 63 ballpoint pens available commercially in Korea were obtained and used to construct an FTIR spectral database. A library-searching program was utilized to identify the manufacturer, blend, and model of each black ballpoint pen ink based upon their FTIR peak intensities, positions, and patterns in the spectral database. This FTIR technique was also successfully used in determining the sequence of homogeneous line intersections from the crossing lines of two ballpoint pen signatures. We have demonstrated with a set of sample documents that micro-ATR FTIR is a viable nondestructive analytical method that can be used to identify the origin of the ballpoint pen ink used to mark signatures. © 2014 American Academy of Forensic Sciences.

Feature-space-based FMRI analysis using the optimal linear transformation.

PubMed

Sun, Fengrong; Morris, Drew; Lee, Wayne; Taylor, Margot J; Mills, Travis; Babyn, Paul S

2010-09-01

The optimal linear transformation (OLT), an image analysis technique of feature space, was first presented in the field of MRI. This paper proposes a method of extending OLT from MRI to functional MRI (fMRI) to improve the activation-detection performance over conventional approaches of fMRI analysis. In this method, first, ideal hemodynamic response time series for different stimuli were generated by convolving the theoretical hemodynamic response model with the stimulus timing. Second, constructing hypothetical signature vectors for different activity patterns of interest by virtue of the ideal hemodynamic responses, OLT was used to extract features of fMRI data. The resultant feature space had particular geometric clustering properties. It was then classified into different groups, each pertaining to an activity pattern of interest; the applied signature vector for each group was obtained by averaging. Third, using the applied signature vectors, OLT was applied again to generate fMRI composite images with high SNRs for the desired activity patterns. Simulations and a blocked fMRI experiment were employed for the method to be verified and compared with the general linear model (GLM)-based analysis. The simulation studies and the experimental results indicated the superiority of the proposed method over the GLM-based analysis in detecting brain activities.

Cryptoblemes: A New Discovery with Major Economic Implications and Profound Changes to the Geologic Paradigm

NASA Technical Reports Server (NTRS)

Windolph, J., Jr.; Sutton, J.

1997-01-01

Cryptoblemes are subtle impact shock signatures imprinted by cosmic debris on the crustal surfaces of lunar planetary bodes. These signatures constitute a complex cumulative overprinting of topographic, structural geophysical, and tectonic patterns that have a conspicuous radial centric multiringed symmetry. The geometry and distribution of cryptoblemes on Earth is comparable to the size and density of impact features on lunar planetary surfaces. Analysis of satellite imagery, sea-floor sonar, side-looking radar and aerial photographs of specific sites reveals new criteria for the identification and confirmation of impact-shock signatures. These criteria include joint and foliation patterns with asbestiform minerals, ribbon-quartz, spheroidal weathering, domal exfoliation, pencil shale, and shock spheres, which may originate from hydrocavitation of water-saturated sedimentary rocks. Cryptoblemes may also be associated with breccia pipes, sinkholes, buttes, mesas, and bogs, high-Rn anomalies, nodular concentrations, and earthquake epicenters. Major implications of cryptobleme identification include exploratory targeting of hydrocarbon and mineral deposits and the explanation of their origins. Analysis of known mineral deposits, structural traps and sedimentary basins show a direct correlation with cryptobleme patterns. Significant geologic paradigm shifts related to cryptoblemes include mountain building processes, structural orogenies, induced volcanism, earthquake origins, hydrocarbon diagenesis, formation mineral deposits, continental rifting, and plate movements, magnetic overprinting and local regional, and global geologic extinction and speciation patterns. Two figures provide a comparison between a multiring impact overprint in water and multiring cryptobleme in the U.S. basin range. (Additional information is contained in the original document).

Oscillatory patterns in temporal lobe reveal context reinstatement during memory search.

PubMed

Manning, Jeremy R; Polyn, Sean M; Baltuch, Gordon H; Litt, Brian; Kahana, Michael J

2011-08-02

Psychological theories of memory posit that when people recall a past event, they not only recover the features of the event itself, but also recover information associated with other events that occurred nearby in time. The events surrounding a target event, and the thoughts they evoke, may be considered to represent a context for the target event, helping to distinguish that event from similar events experienced at different times. The ability to reinstate this contextual information during memory search has been considered a hallmark of episodic, or event-based, memory. We sought to determine whether context reinstatement may be observed in electrical signals recorded from the human brain during episodic recall. Analyzing electrocorticographic recordings taken as 69 neurosurgical patients studied and recalled lists of words, we uncovered a neural signature of context reinstatement. Upon recalling a studied item, we found that the recorded patterns of brain activity were not only similar to the patterns observed when the item was studied, but were also similar to the patterns observed during study of neighboring list items, with similarity decreasing reliably with positional distance. The degree to which individual patients displayed this neural signature of context reinstatement was correlated with their tendency to recall neighboring list items successively. These effects were particularly strong in temporal lobe recordings. Our findings show that recalling a past event evokes a neural signature of the temporal context in which the event occurred, thus pointing to a neural basis for episodic memory.

Comparative Analysis of P450 Signature Motifs EXXR and CXG in the Large and Diverse Kingdom of Fungi: Identification of Evolutionarily Conserved Amino Acid Patterns Characteristic of P450 Family

PubMed Central

Syed, Khajamohiddin; Mashele, Samson Sitheni

2014-01-01

Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins distributed across the biological kingdoms. P450s are catalytically versatile and play key roles in organisms primary and secondary metabolism. Identification of P450s across the biological kingdoms depends largely on the identification of two P450 signature motifs, EXXR and CXG, in the protein sequence. Once a putative protein has been identified as P450, it will be assigned to a family and subfamily based on the criteria that P450s within a family share more than 40% homology and members of subfamilies share more than 55% homology. However, to date, no evidence has been presented that can distinguish members of a P450 family. Here, for the first time we report the identification of EXXR- and CXG-motifs-based amino acid patterns that are characteristic of the P450 family. Analysis of P450 signature motifs in the under-explored fungal P450s from four different phyla, ascomycota, basidiomycota, zygomycota and chytridiomycota, indicated that the EXXR motif is highly variable and the CXG motif is somewhat variable. The amino acids threonine and leucine are preferred as second and third amino acids in the EXXR motif and proline and glycine are preferred as second and third amino acids in the CXG motif in fungal P450s. Analysis of 67 P450 families from biological kingdoms such as plants, animals, bacteria and fungi showed conservation of a set of amino acid patterns characteristic of a particular P450 family in EXXR and CXG motifs. This suggests that during the divergence of P450 families from a common ancestor these amino acids patterns evolve and are retained in each P450 family as a signature of that family. The role of amino acid patterns characteristic of a P450 family in the structural and/or functional aspects of members of the P450 family is a topic for future research. PMID:24743800

Conic section function neural network circuitry for offline signature recognition.

PubMed

Erkmen, Burcu; Kahraman, Nihan; Vural, Revna A; Yildirim, Tulay

2010-04-01

In this brief, conic section function neural network (CSFNN) circuitry was designed for offline signature recognition. CSFNN is a unified framework for multilayer perceptron (MLP) and radial basis function (RBF) networks to make simultaneous use of advantages of both. The CSFNN circuitry architecture was developed using a mixed mode circuit implementation. The designed circuit system is problem independent. Hence, the general purpose neural network circuit system could be applied to various pattern recognition problems with different network sizes on condition with the maximum network size of 16-16-8. In this brief, CSFNN circuitry system has been applied to two different signature recognition problems. CSFNN circuitry was trained with chip-in-the-loop learning technique in order to compensate typical analog process variations. CSFNN hardware achieved highly comparable computational performances with CSFNN software for nonlinear signature recognition problems.

PYTi-NiCr Signatures in the Columbia Hills are Present in Certain Martian Meteorites

NASA Technical Reports Server (NTRS)

Clark, B. C.; Gellert, R.; Ming, D. W.; Morris, R. V.; Mittlefehldt, D. W.; Squyres, S. W.

2006-01-01

Uniquely high levels of phosphorus and titanium were observed in several samples [1-3] by the APXS x-ray fluorescence measurements as the MER Spirit rover climbed Husband Hill (Columbia Hills, Gusev crater, Mars). A careful study of many such samples and their geochemical variability has revealed additional elements in this pattern, and that the derived multi-element signature is also unambiguously manifested in several martian meteorites.

Profiling of histone H3 lysine 9 trimethylation levels predicts transcription factor activity and survival in acute myeloid leukemia

PubMed Central

Klein, Hans-Ulrich; Hascher, Antje; Isken, Fabienne; Tickenbrock, Lara; Thoennissen, Nils; Agrawal-Singh, Shuchi; Tschanter, Petra; Disselhoff, Christine; Wang, Yipeng; Becker, Anke; Thiede, Christian; Ehninger, Gerhard; zur Stadt, Udo; Koschmieder, Steffen; Seidl, Matthias; Müller, Frank U.; Schmitz, Wilhelm; Schlenke, Peter; McClelland, Michael; Berdel, Wolfgang E.; Dugas, Martin; Serve, Hubert

2010-01-01

Acute myeloid leukemia (AML) is commonly associated with alterations in transcription factors because of altered expression or gene mutations. These changes might induce leukemia-specific patterns of histone modifications. We used chromatin-immunoprecipitation on microarray to analyze histone 3 lysine 9 trimethylation (H3K9me3) patterns in primary AML (n = 108), acute lymphoid leukemia (n = 28), CD34+ cells (n = 21) and white blood cells (n = 15) specimens. Hundreds of promoter regions in AML showed significant alterations in H3K9me3 levels. H3K9me3 deregulation in AML occurred preferentially as a decrease in H3K9me3 levels at core promoter regions. The altered genomic regions showed an overrepresentation of cis-binding sites for ETS and cyclic adenosine monophosphate response elements (CREs) for transcription factors of the CREB/CREM/ATF1 family. The decrease in H3K9me3 levels at CREs was associated with increased CRE-driven promoter activity in AML blasts in vivo. AML-specific H3K9me3 patterns were not associated with known cytogenetic abnormalities. But a signature derived from H3K9me3 patterns predicted event-free survival in AML patients. When the H3K9me3 signature was combined with established clinical prognostic markers, it outperformed prognosis prediction based on clinical parameters alone. These findings demonstrate widespread changes of H3K9me3 levels at gene promoters in AML. Signatures of histone modification patterns are associated with patient prognosis in AML. PMID:20498303

Design and Real-Time Implementation of a Robust APC Coder for Speech Transmission over 16 Kb/s Noisy Channels. Volume II. Real-Time Implementation.

DTIC Science & Technology

1980-12-01

summonsesh~ =Mmam msm am Menem acme- Q so me.~ ml* mmam aa mamP m a m U mob. aN S 1. aN~r% fmF4 1.w V 4l P.N F4 amf em". .4. - do -a.. @ m m die.@ do 5...1& do-E -w SO mbmwlQ %Au 4 a 3 03 ma" Iw 4n0: .0:030. s: Is. 4WD a- 3 0 a11" w Pa I8. r 4u s-U 04o0v",s- Is WON: Pam..www -w ra A am aumes" Menem wa

Patterned wafer geometry grouping for improved overlay control

NASA Astrophysics Data System (ADS)

Lee, Honggoo; Han, Sangjun; Woo, Jaeson; Park, Junbeom; Song, Changrock; Anis, Fatima; Vukkadala, Pradeep; Jeon, Sanghuck; Choi, DongSub; Huang, Kevin; Heo, Hoyoung; Smith, Mark D.; Robinson, John C.

2017-03-01

Process-induced overlay errors from outside the litho cell have become a significant contributor to the overlay error budget including non-uniform wafer stress. Previous studies have shown the correlation between process-induced stress and overlay and the opportunity for improvement in process control, including the use of patterned wafer geometry (PWG) metrology to reduce stress-induced overlay signatures. Key challenges of volume semiconductor manufacturing are how to improve not only the magnitude of these signatures, but also the wafer to wafer variability. This work involves a novel technique of using PWG metrology to provide improved litho-control by wafer-level grouping based on incoming process induced overlay, relevant for both 3D NAND and DRAM. Examples shown in this study are from 19 nm DRAM manufacturing.

Admittance Survey of Type 1 Coronae on Venus: Implications for Elastic Thickness

NASA Technical Reports Server (NTRS)

Hoogenboom, T.; Smrekar, S. E.; Anderson, F. S.; Houseman, G.

2003-01-01

Coronae are volcano-tectonic features on Venus which range from 60km to 2600km and are defined by their nearly circular patterns of fractures. Type 1 (regular) coronae are classified as having >50% complete fracture annuli. Previous work has examined the factors controlling the morphology, size, and fracture pattern of coronae, using lithospheric properties, loading signature and geologic characteristics. However, these studies have been limited to Type 2 (topographic) coronae (e.g. coronaes with <50% fracture annuli), and the factors controlling the formation of Type 1 coronae remain poorly understood. In this study, we apply the methodology of to survey the admittance signature for Type 1 coronae to determine the controlling parameters which govern Type 1 coronae formation.

Differential signatures of bacterial and mammalian IMP dehydrogenase enzymes.

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

Zhang, R.; Evans, G.; Rotella, F.

1999-06-01

IMP dehydrogenase (IMPDH) is an essential enzyme of de novo guanine nucleotide synthesis. IMPDH inhibitors have clinical utility as antiviral, anticancer or immunosuppressive agents. The essential nature of this enzyme suggests its therapeutic applications may be extended to the development of antimicrobial agents. Bacterial IMPDH enzymes show bio- chemical and kinetic characteristics that are different than the mammalian IMPDH enzymes, suggesting IMPDH may be an attractive target for the development of antimicrobial agents. We suggest that the biochemical and kinetic differences between bacterial and mammalian enzymes are a consequence of the variance of specific, identifiable amino acid residues. Identification ofmore » these residues or combination of residues that impart this mammalian or bacterial enzyme signature is a prerequisite for the rational identification of agents that specifically target the bacterial enzyme. We used sequence alignments of IMPDH proteins to identify sequence signatures associated with bacterial or eukaryotic IMPDH enzymes. These selections were further refined to discern those likely to have a role in catalysis using information derived from the bacterial and mammalian IMPDH crystal structures and site-specific mutagenesis. Candidate bacterial sequence signatures identified by this process include regions involved in subunit interactions, the active site flap and the NAD binding region. Analysis of sequence alignments in these regions indicates a pattern of catalytic residues conserved in all enzymes and a secondary pattern of amino acid conservation associated with the major phylogenetic groups. Elucidation of the basis for this mammalian/bacterial IMPDH signature will provide insight into the catalytic mechanism of this enzyme and the foundation for the development of highly specific inhibitors.« less

Gene expression signature in urine for diagnosing and assessing aggressiveness of bladder urothelial carcinoma.

PubMed

Mengual, Lourdes; Burset, Moisès; Ribal, María José; Ars, Elisabet; Marín-Aguilera, Mercedes; Fernández, Manuel; Ingelmo-Torres, Mercedes; Villavicencio, Humberto; Alcaraz, Antonio

2010-05-01

To develop an accurate and noninvasive method for bladder cancer diagnosis and prediction of disease aggressiveness based on the gene expression patterns of urine samples. Gene expression patterns of 341 urine samples from bladder urothelial cell carcinoma (UCC) patients and 235 controls were analyzed via TaqMan Arrays. In a first phase of the study, three consecutive gene selection steps were done to identify a gene set expression signature to detect and stratify UCC in urine. Subsequently, those genes more informative for UCC diagnosis and prediction of tumor aggressiveness were combined to obtain a classification system of bladder cancer samples. In a second phase, the obtained gene set signature was evaluated in a routine clinical scenario analyzing only voided urine samples. We have identified a 12+2 gene expression signature for UCC diagnosis and prediction of tumor aggressiveness on urine samples. Overall, this gene set panel had 98% sensitivity (SN) and 99% specificity (SP) in discriminating between UCC and control samples and 79% SN and 92% SP in predicting tumor aggressiveness. The translation of the model to the clinically applicable format corroborates that the 12+2 gene set panel described maintains a high accuracy for UCC diagnosis (SN = 89% and SP = 95%) and tumor aggressiveness prediction (SN = 79% and SP = 91%) in voided urine samples. The 12+2 gene expression signature described in urine is able to identify patients suffering from UCC and predict tumor aggressiveness. We show that a panel of molecular markers may improve the schedule for diagnosis and follow-up in UCC patients. Copyright 2010 AACR.

Deriving a cardiac ageing signature to reveal MMP-9-dependent inflammatory signalling in senescence.

PubMed

Ma, Yonggang; Chiao, Ying Ann; Clark, Ryan; Flynn, Elizabeth R; Yabluchanskiy, Andriy; Ghasemi, Omid; Zouein, Fouad; Lindsey, Merry L; Jin, Yu-Fang

2015-06-01

Cardiac ageing involves the progressive development of cardiac fibrosis and diastolic dysfunction coordinated by MMP-9. Here, we report a cardiac ageing signature that encompasses macrophage pro-inflammatory signalling in the left ventricle (LV) and distinguishes biological from chronological ageing. Young (6-9 months), middle-aged (12-15 months), old (18-24 months), and senescent (26-34 months) mice of both C57BL/6J wild type (WT) and MMP-9 null were evaluated. Using an identified inflammatory pattern, we were able to define individual mice based on their biological, rather than chronological, age. Bcl6, Ccl24, and Il4 were the strongest inflammatory markers of the cardiac ageing signature. The decline in early-to-late LV filling ratio was most strongly predicted by Bcl6, Il1r1, Ccl24, Crp, and Cxcl13 patterns, whereas LV wall thickness was most predicted by Abcf1, Tollip, Scye1, and Mif patterns. With age, there was a linear increase in cardiac M1 macrophages and a decrease in cardiac M2 macrophages in WT mice; of which, both were prevented by MMP-9 deletion. In vitro, MMP-9 directly activated young macrophage polarization to an M1/M2 mid-transition state. Our results define the cardiac ageing inflammatory signature and assign MMP-9 roles in mediating the inflammaging profile by indirectly and directly modifying macrophage polarization. Our results explain early mechanisms that stimulate ageing-induced cardiac fibrosis and diastolic dysfunction. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2015. For permissions please email: journals.permissions@oup.com.

Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.

PubMed

Tan, Jie; Doing, Georgia; Lewis, Kimberley A; Price, Courtney E; Chen, Kathleen M; Cady, Kyle C; Perchuk, Barret; Laub, Michael T; Hogan, Deborah A; Greene, Casey S

2017-07-26

Cross-experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with denoising autoencoder neural networks, can identify biological patterns, but because ADAGE models, like many neural networks, are over-parameterized, different ADAGE models perform equally well. To enhance model robustness and better build signatures consistent with biological pathways, we developed an ensemble ADAGE (eADAGE) that integrated stable signatures across models. We applied eADAGE to a compendium of Pseudomonas aeruginosa gene expression profiling experiments performed in 78 media. eADAGE revealed a phosphate starvation response controlled by PhoB in media with moderate phosphate and predicted that a second stimulus provided by the sensor kinase, KinB, is required for this PhoB activation. We validated this relationship using both targeted and unbiased genetic approaches. eADAGE, which captures stable biological patterns, enables cross-experiment comparisons that can highlight measured but undiscovered relationships. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Geographic approaches to biodiversity conservation: implications of scale and error to landscape planning

Treesearch

Curtis H. Flather; Kenneth R. Wilson; Susan A. Shriner

2009-01-01

Conservation science is concerned with understanding why distribution and abundance patterns of species vary in time and space. Although these patterns have strong signatures tied to the availability of energy and nutrients, variation in climate, physiographic heterogeneity, and differences in the structural complexity of natural vegetation, it is becoming more...

Benchmarking Data for the Proposed Signature of Used Fuel Casks

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

Rauch, Eric Benton

2016-09-23

A set of benchmarking measurements to test facets of the proposed extended storage signature was conducted on May 17, 2016. The measurements were designed to test the overall concept of how the proposed signature can be used to identify a used fuel cask based only on the distribution of neutron sources within the cask. To simulate the distribution, 4 Cf-252 sources were chosen and arranged on a 3x3 grid in 3 different patterns and raw neutron totals counts were taken at 6 locations around the grid. This is a very simplified test of the typical geometry studied previously in simulationmore » with simulated used nuclear fuel.« less

Spatiotemporal Patterns of Noise-Driven Confined Actin Waves in Living Cells.

PubMed

Bernitt, Erik; Döbereiner, Hans-Günther

2017-01-27

Cells utilize waves of polymerizing actin to reshape their morphologies, which is central to physiological and pathological processes alike. Here, we force dorsal actin waves to propagate on one-dimensional domains with periodic boundary conditions, which results in striking spatiotemporal patterns with a clear signature of noise-driven dynamics. We show that these patterns can be very closely reproduced with a noise-driven active medium at coherence resonance.

Indispensable Role of Proteases in Plant Innate Immunity.

PubMed

Balakireva, Anastasia V; Zamyatnin, Andrey A

2018-02-23

Plant defense is achieved mainly through the induction of microbe-associated molecular patterns (MAMP)-triggered immunity (MTI), effector-triggered immunity (ETI), systemic acquired resistance (SAR), induced systemic resistance (ISR), and RNA silencing. Plant immunity is a highly complex phenomenon with its own unique features that have emerged as a result of the arms race between plants and pathogens. However, the regulation of these processes is the same for all living organisms, including plants, and is controlled by proteases. Different families of plant proteases are involved in every type of immunity: some of the proteases that are covered in this review participate in MTI, affecting stomatal closure and callose deposition. A large number of proteases act in the apoplast, contributing to ETI by managing extracellular defense. A vast majority of the endogenous proteases discussed in this review are associated with the programmed cell death (PCD) of the infected cells and exhibit caspase-like activities. The synthesis of signal molecules, such as salicylic acid, jasmonic acid, and ethylene, and their signaling pathways, are regulated by endogenous proteases that affect the induction of pathogenesis-related genes and SAR or ISR establishment. A number of proteases are associated with herbivore defense. In this review, we summarize the data concerning identified plant endogenous proteases, their effect on plant-pathogen interactions, their subcellular localization, and their functional properties, if available, and we attribute a role in the different types and stages of innate immunity for each of the proteases covered.

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

Patterning of supported gold monolayers via chemical lift-off lithography

PubMed Central

Slaughter, Liane S; Cheung, Kevin M; Kaappa, Sami; Cao, Huan H; Yang, Qing; Young, Thomas D; Serino, Andrew C; Malola, Sami; Olson, Jana M; Link, Stephan

2017-01-01

The supported monolayer of Au that accompanies alkanethiolate molecules removed by polymer stamps during chemical lift-off lithography is a scarcely studied hybrid material. We show that these Au–alkanethiolate layers on poly(dimethylsiloxane) (PDMS) are transparent, functional, hybrid interfaces that can be patterned over nanometer, micrometer, and millimeter length scales. Unlike other ultrathin Au films and nanoparticles, lifted-off Au–alkanethiolate thin films lack a measurable optical signature. We therefore devised fabrication, characterization, and simulation strategies by which to interrogate the nanoscale structure, chemical functionality, stoichiometry, and spectral signature of the supported Au–thiolate layers. The patterning of these layers laterally encodes their functionality, as demonstrated by a fluorescence-based approach that relies on dye-labeled complementary DNA hybridization. Supported thin Au films can be patterned via features on PDMS stamps (controlled contact), using patterned Au substrates prior to lift-off (e.g., selective wet etching), or by patterning alkanethiols on Au substrates to be reactive in selected regions but not others (controlled reactivity). In all cases, the regions containing Au–alkanethiolate layers have a sub-nanometer apparent height, which was found to be consistent with molecular dynamics simulations that predicted the removal of no more than 1.5 Au atoms per thiol, thus presenting a monolayer-like structure. PMID:29259879

Use of mRNA expression signatures to discover small molecule inhibitors of skeletal muscle atrophy

PubMed Central

Adams, Christopher M.; Ebert, Scott M.; Dyle, Michael C.

2017-01-01

Purpose of review Here, we discuss a recently developed experimental strategy for discovering small molecules with potential to prevent and treat skeletal muscle atrophy. Recent findings Muscle atrophy involves and requires widespread changes in skeletal muscle gene expression, which generate complex but measurable patterns of positive and negative changes in skeletal muscle mRNA levels (a.k.a. mRNA expression signatures of muscle atrophy). Many bioactive small molecules generate their own characteristic mRNA expression signatures, and by identifying small molecules whose signatures approximate mirror images of muscle atrophy signatures, one may identify small molecules with potential to prevent and/or reverse muscle atrophy. Unlike a conventional drug discovery approach, this strategy does not rely on a predefined molecular target but rather exploits the complexity of muscle atrophy to identify small molecules that counter the entire spectrum of pathological changes in atrophic muscle. We discuss how this strategy has been used to identify two natural compounds, ursolic acid and tomatidine, that reduce muscle atrophy and improve skeletal muscle function. Summary Discovery strategies based on mRNA expression signatures can elucidate new approaches for preserving and restoring muscle mass and function. PMID:25807353

Use of mRNA expression signatures to discover small molecule inhibitors of skeletal muscle atrophy.

PubMed

Adams, Christopher M; Ebert, Scott M; Dyle, Michael C

2015-05-01

Here, we discuss a recently developed experimental strategy for discovering small molecules with potential to prevent and treat skeletal muscle atrophy. Muscle atrophy involves and requires widespread changes in skeletal muscle gene expression, which generate complex but measurable patterns of positive and negative changes in skeletal muscle mRNA levels (a.k.a. mRNA expression signatures of muscle atrophy). Many bioactive small molecules generate their own characteristic mRNA expression signatures, and by identifying small molecules whose signatures approximate mirror images of muscle atrophy signatures, one may identify small molecules with potential to prevent and/or reverse muscle atrophy. Unlike a conventional drug discovery approach, this strategy does not rely on a predefined molecular target but rather exploits the complexity of muscle atrophy to identify small molecules that counter the entire spectrum of pathological changes in atrophic muscle. We discuss how this strategy has been used to identify two natural compounds, ursolic acid and tomatidine, that reduce muscle atrophy and improve skeletal muscle function. Discovery strategies based on mRNA expression signatures can elucidate new approaches for preserving and restoring muscle mass and function.

Evaluation of algorithms for estimating wheat acreage from multispectral scanner data. [Kansas and Texas

NASA Technical Reports Server (NTRS)

Nalepka, R. F. (Principal Investigator); Richardson, W.; Pentland, A. P.

1976-01-01

The author has identified the following significant results. Fourteen different classification algorithms were tested for their ability to estimate the proportion of wheat in an area. For some algorithms, accuracy of classification in field centers was observed. The data base consisted of ground truth and LANDSAT data from 55 sections (1 x 1 mile) from five LACIE intensive test sites in Kansas and Texas. Signatures obtained from training fields selected at random from the ground truth were generally representative of the data distribution patterns. LIMMIX, an algorithm that chooses a pure signature when the data point is close enough to a signature mean and otherwise chooses the best mixture of a pair of signatures, reduced the average absolute error to 6.1% and the bias to 1.0%. QRULE run with a null test achieved a similar reduction.

Remote sensing and lake eutrophication

NASA Technical Reports Server (NTRS)

Wrigley, R. C.; Horne, A. J.

1974-01-01

An infrared photograph of part of Clear Lake, Cal., shows complex patterns of blue-green algal blooms which were not observed by conventional limnological techniques. Repeated observations of patterns such as these can be used to chart the surface movement of these buoyant algae and can also be used to help control algal scums in eutrophic lakes. Although it is believed that most of the observed patterns resulted from Aphanizomenon (a few were also observed which resulted from suspended sediment), spectral signatures of the algal patterns varied.

Use of forecasting signatures to help distinguish periodicity, randomness, and chaos in ripples and other spatial patterns

USGS Publications Warehouse

Rubin, D.M.

1992-01-01

Forecasting of one-dimensional time series previously has been used to help distinguish periodicity, chaos, and noise. This paper presents two-dimensional generalizations for making such distinctions for spatial patterns. The techniques are evaluated using synthetic spatial patterns and then are applied to a natural example: ripples formed in sand by blowing wind. Tests with the synthetic patterns demonstrate that the forecasting techniques can be applied to two-dimensional spatial patterns, with the same utility and limitations as when applied to one-dimensional time series. One limitation is that some combinations of periodicity and randomness exhibit forecasting signatures that mimic those of chaos. For example, sine waves distorted with correlated phase noise have forecasting errors that increase with forecasting distance, errors that, are minimized using nonlinear models at moderate embedding dimensions, and forecasting properties that differ significantly between the original and surrogates. Ripples formed in sand by flowing air or water typically vary in geometry from one to another, even when formed in a flow that is uniform on a large scale; each ripple modifies the local flow or sand-transport field, thereby influencing the geometry of the next ripple downcurrent. Spatial forecasting was used to evaluate the hypothesis that such a deterministic process - rather than randomness or quasiperiodicity - is responsible for the variation between successive ripples. This hypothesis is supported by a forecasting error that increases with forecasting distance, a greater accuracy of nonlinear relative to linear models, and significant differences between forecasts made with the original ripples and those made with surrogate patterns. Forecasting signatures cannot be used to distinguish ripple geometry from sine waves with correlated phase noise, but this kind of structure can be ruled out by two geometric properties of the ripples: Successive ripples are highly correlated in wavelength, and ripple crests display dislocations such as branchings and mergers. ?? 1992 American Institute of Physics.

Identification of temporal and spatial signatures of broadband shock-associated noise

NASA Astrophysics Data System (ADS)

Pérez Arroyo, C.; Daviller, G.; Puigt, G.; Airiau, C.; Moreau, S.

2018-02-01

Broadband shock-associated noise (BBSAN) is a particular high-frequency noise that is generated in imperfectly expanded jets. BBSAN results from the interaction of turbulent structures and the series of expansion and compression waves which appears downstream of the convergent nozzle exit of moderately under-expanded jets. This paper focuses on the impact of the pressure waves generated by BBSAN from a large eddy simulation of a non-screeching supersonic round jet in the near-field. The flow is under-expanded and is characterized by a high Reynolds number Re_j = 1.25× 10^6 and a transonic Mach number M_j=1.15 . It is shown that BBSAN propagates upstream outside the jet and enters the supersonic region leaving a characteristic pattern in the physical plane. This pattern, also called signature, travels upstream through the shock-cell system with a group velocity between the acoustic speed Uc-a_∞ and the sound speed a_∞ in the frequency-wavenumber domain (U_c is the convective jet velocity). To investigate these characteristic patterns, the pressure signals in the jet and the near-field are decomposed into waves traveling downstream (p^+ ) and waves traveling upstream (p^- ). A novel study based on a wavelet technique is finally applied on such signals in order to extract the BBSAN signatures generated by the most energetic events of the supersonic jet.

Spectral signature verification using statistical analysis and text mining

NASA Astrophysics Data System (ADS)

DeCoster, Mallory E.; Firpi, Alexe H.; Jacobs, Samantha K.; Cone, Shelli R.; Tzeng, Nigel H.; Rodriguez, Benjamin M.

2016-05-01

In the spectral science community, numerous spectral signatures are stored in databases representative of many sample materials collected from a variety of spectrometers and spectroscopists. Due to the variety and variability of the spectra that comprise many spectral databases, it is necessary to establish a metric for validating the quality of spectral signatures. This has been an area of great discussion and debate in the spectral science community. This paper discusses a method that independently validates two different aspects of a spectral signature to arrive at a final qualitative assessment; the textual meta-data and numerical spectral data. Results associated with the spectral data stored in the Signature Database1 (SigDB) are proposed. The numerical data comprising a sample material's spectrum is validated based on statistical properties derived from an ideal population set. The quality of the test spectrum is ranked based on a spectral angle mapper (SAM) comparison to the mean spectrum derived from the population set. Additionally, the contextual data of a test spectrum is qualitatively analyzed using lexical analysis text mining. This technique analyzes to understand the syntax of the meta-data to provide local learning patterns and trends within the spectral data, indicative of the test spectrum's quality. Text mining applications have successfully been implemented for security2 (text encryption/decryption), biomedical3 , and marketing4 applications. The text mining lexical analysis algorithm is trained on the meta-data patterns of a subset of high and low quality spectra, in order to have a model to apply to the entire SigDB data set. The statistical and textual methods combine to assess the quality of a test spectrum existing in a database without the need of an expert user. This method has been compared to other validation methods accepted by the spectral science community, and has provided promising results when a baseline spectral signature is present for comparison. The spectral validation method proposed is described from a practical application and analytical perspective.

Distinct Microbial Signatures Associated With Different Breast Cancer Types

PubMed Central

Banerjee, Sagarika; Tian, Tian; Wei, Zhi; Shih, Natalie; Feldman, Michael D.; Peck, Kristen N.; DeMichele, Angela M.; Alwine, James C.; Robertson, Erle S.

2018-01-01

A dysbiotic microbiome can potentially contribute to the pathogenesis of many different diseases including cancer. Breast cancer is the second leading cause of cancer death in women. Thus, we investigated the diversity of the microbiome in the four major types of breast cancer: endocrine receptor (ER) positive, triple positive, Her2 positive and triple negative breast cancers. Using a whole genome and transcriptome amplification and a pan-pathogen microarray (PathoChip) strategy, we detected unique and common viral, bacterial, fungal and parasitic signatures for each of the breast cancer types. These were validated by PCR and Sanger sequencing. Hierarchical cluster analysis of the breast cancer samples, based on their detected microbial signatures, showed distinct patterns for the triple negative and triple positive samples, while the ER positive and Her2 positive samples shared similar microbial signatures. These signatures, unique or common to the different breast cancer types, provide a new line of investigation to gain further insights into prognosis, treatment strategies and clinical outcome, as well as better understanding of the role of the micro-organisms in the development and progression of breast cancer. PMID:29867857

Methods of extending signatures and training without ground information. [data processing, pattern recognition

NASA Technical Reports Server (NTRS)

Henderson, R. G.; Thomas, G. S.; Nalepka, R. F.

1975-01-01

Methods of performing signature extension, using LANDSAT-1 data, are explored. The emphasis is on improving the performance and cost-effectiveness of large area wheat surveys. Two methods were developed: ASC, and MASC. Two methods, Ratio, and RADIFF, previously used with aircraft data were adapted to and tested on LANDSAT-1 data. An investigation into the sources and nature of between scene data variations was included. Initial investigations into the selection of training fields without in situ ground truth were undertaken.

Brain Representations of Basic Physics Concepts

NASA Astrophysics Data System (ADS)

Just, Marcel Adam

2017-09-01

The findings concerning physics concepts build on the remarkable new ability to determine the neural signature (or activation pattern) corresponding to an individual concept using fMRI brain imaging. Moreover, the neural signatures can be decomposed into meaningful underlying dimensions, identifying the individual, interpretable components of the neural representation of a concept. The investigation of physics concepts representations reveals how relatively recent physics concepts (formalized only in the last few centuries) are stored in the millenia-old information system of the human brain.

Identification and Characteristics of Signature Whistles in Wild Bottlenose Dolphins (Tursiops truncatus) from Namibia

PubMed Central

Elwen, Simon Harvey; Nastasi, Aurora

2014-01-01

A signature whistle type is a learned, individually distinctive whistle type in a dolphin's acoustic repertoire that broadcasts the identity of the whistle owner. The acquisition and use of signature whistles indicates complex cognitive functioning that requires wider investigation in wild dolphin populations. Here we identify signature whistle types from a population of approximately 100 wild common bottlenose dolphins (Tursiops truncatus) inhabiting Walvis Bay, and describe signature whistle occurrence, acoustic parameters and temporal production. A catalogue of 43 repeatedly emitted whistle types (REWTs) was generated by analysing 79 hrs of acoustic recordings. From this, 28 signature whistle types were identified using a method based on the temporal patterns in whistle sequences. A visual classification task conducted by 5 naïve judges showed high levels of agreement in classification of whistles (Fleiss-Kappa statistic, κ = 0.848, Z = 55.3, P<0.001) and supported our categorisation. Signature whistle structure remained stable over time and location, with most types (82%) recorded in 2 or more years, and 4 identified at Walvis Bay and a second field site approximately 450 km away. Whistle acoustic parameters were consistent with those of signature whistles documented in Sarasota Bay (Florida, USA). We provide evidence of possible two-voice signature whistle production by a common bottlenose dolphin. Although signature whistle types have potential use as a marker for studying individual habitat use, we only identified approximately 28% of those from the Walvis Bay population, despite considerable recording effort. We found that signature whistle type diversity was higher in larger dolphin groups and groups with calves present. This is the first study describing signature whistles in a wild free-ranging T. truncatus population inhabiting African waters and it provides a baseline on which more in depth behavioural studies can be based. PMID:25203814

Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers.

PubMed

Meier, Bettina; Volkova, Nadezda V; Hong, Ye; Schofield, Pieta; Campbell, Peter J; Gerstung, Moritz; Gartner, Anton

2018-05-01

Throughout their lifetime, cells are subject to extrinsic and intrinsic mutational processes leaving behind characteristic signatures in the genome. DNA mismatch repair (MMR) deficiency leads to hypermutation and is found in different cancer types. Although it is possible to associate mutational signatures extracted from human cancers with possible mutational processes, the exact causation is often unknown. Here, we use C. elegans genome sequencing of pms-2 and mlh-1 knockouts to reveal the mutational patterns linked to C. elegans MMR deficiency and their dependency on endogenous replication errors and errors caused by deletion of the polymerase ε subunit pole-4 Signature extraction from 215 human colorectal and 289 gastric adenocarcinomas revealed three MMR-associated signatures, one of which closely resembles the C. elegans MMR spectrum and strongly discriminates microsatellite stable and unstable tumors (AUC = 98%). A characteristic difference between human and C. elegans MMR deficiency is the lack of elevated levels of N C G > NTG mutations in C. elegans, likely caused by the absence of cytosine (CpG) methylation in worms . The other two human MMR signatures may reflect the interaction between MMR deficiency and other mutagenic processes, but their exact cause remains unknown. In summary, combining information from genetically defined models and cancer samples allows for better aligning mutational signatures to causal mutagenic processes. © 2018 Meier et al.; Published by Cold Spring Harbor Laboratory Press.

Identification of atypical flight patterns

NASA Technical Reports Server (NTRS)

Statler, Irving C. (Inventor); Ferryman, Thomas A. (Inventor); Amidan, Brett G. (Inventor); Whitney, Paul D. (Inventor); White, Amanda M. (Inventor); Willse, Alan R. (Inventor); Cooley, Scott K. (Inventor); Jay, Joseph Griffith (Inventor); Lawrence, Robert E. (Inventor); Mosbrucker, Chris (Inventor)

2005-01-01

Method and system for analyzing aircraft data, including multiple selected flight parameters for a selected phase of a selected flight, and for determining when the selected phase of the selected flight is atypical, when compared with corresponding data for the same phase for other similar flights. A flight signature is computed using continuous-valued and discrete-valued flight parameters for the selected flight parameters and is optionally compared with a statistical distribution of other observed flight signatures, yielding atypicality scores for the same phase for other similar flights. A cluster analysis is optionally applied to the flight signatures to define an optimal collection of clusters. A level of atypicality for a selected flight is estimated, based upon an index associated with the cluster analysis.

A real-time polymerase chain reaction assay for the detection of Mycoplasma agalactiae.

PubMed

Fitzmaurice, J; Sewell, M; King, C M; McDougall, S; McDonald, W L; O'Keefe, J S

2008-10-01

To develop a real-time PCR for the detection of Mycoplasma agalactiae, using PCR primers targeting the ma-mp81 gene. A group of 15 M. agalactiae isolates, 21 other Mycoplasma spp. isolates and 21 other bacterial isolates was used in evaluation of the assay. All M. agalactiae isolates were detected by the assay and none of the non-target isolates was amplified. The analytical detection limit of the assay was 10 fg of purified genomic DNA and 104 cfu/ml milk inoculated with M. agalactiae. When applied to goat-milk samples collected from three herds free of M. agalactiae infection, the assay had a specificity of 100%. The assay would be useful in a diagnostic laboratory, providing specific, sensitive and rapid detection of M. agalactiae.

Proteomics as a Quality Control Tool of Pharmaceutical Probiotic Bacterial Lysate Products

PubMed Central

Klein, Günter; Schanstra, Joost P.; Hoffmann, Janosch; Mischak, Harald; Siwy, Justyna; Zimmermann, Kurt

2013-01-01

Probiotic bacteria have a wide range of applications in veterinary and human therapeutics. Inactivated probiotics are complex samples and quality control (QC) should measure as many molecular features as possible. Capillary electrophoresis coupled to mass spectrometry (CE/MS) has been used as a multidimensional and high throughput method for the identification and validation of biomarkers of disease in complex biological samples such as biofluids. In this study we evaluate the suitability of CE/MS to measure the consistency of different lots of the probiotic formulation Pro-Symbioflor which is a bacterial lysate of heat-inactivated Escherichia coli and Enterococcus faecalis. Over 5000 peptides were detected by CE/MS in 5 different lots of the bacterial lysate and in a sample of culture medium. 71 to 75% of the total peptide content was identical in all lots. This percentage increased to 87–89% when allowing the absence of a peptide in one of the 5 samples. These results, based on over 2000 peptides, suggest high similarity of the 5 different lots. Sequence analysis identified peptides of both E. coli and E. faecalis and peptides originating from the culture medium, thus confirming the presence of the strains in the formulation. Ontology analysis suggested that the majority of the peptides identified for E. coli originated from the cell membrane or the fimbrium, while peptides identified for E. faecalis were enriched for peptides originating from the cytoplasm. The bacterial lysate peptides as a whole are recognised as highly conserved molecular patterns by the innate immune system as microbe associated molecular pattern (MAMP). Sequence analysis also identified the presence of soybean, yeast and casein protein fragments that are part of the formulation of the culture medium. In conclusion CE/MS seems an appropriate QC tool to analyze complex biological products such as inactivated probiotic formulations and allows determining the similarity between lots. PMID:23840518

Apoplastic peroxidases are required for salicylic acid-mediated defense against Pseudomonas syringae.

PubMed

Mammarella, Nicole D; Cheng, Zhenyu; Fu, Zheng Qing; Daudi, Arsalan; Bolwell, G Paul; Dong, Xinnian; Ausubel, Frederick M

2015-04-01

Reactive oxygen species (ROS) generated by NADPH oxidases or apoplastic peroxidases play an important role in the plant defense response. Diminished expression of at least two Arabidopsis thaliana peroxidase encoding genes, PRX33 (At3g49110) and PRX34 (At3g49120), as a consequence of anti-sense expression of a heterologous French bean peroxidase gene (asFBP1.1), were previously shown to result in reduced levels of ROS following pathogen attack, enhanced susceptibility to a variety of bacterial and fungal pathogens, and reduced levels of callose production and defense-related gene expression in response to the microbe associated molecular pattern (MAMP) molecules flg22 and elf26. These data demonstrated that the peroxidase-dependent oxidative burst plays an important role in the elicitation of pattern-triggered immunity (PTI). Further work reported in this paper, however, shows that asFBP1.1 antisense plants are not impaired in all PTI-associated responses. For example, some but not all flg22-elicited genes are induced to lower levels by flg22 in asFPB1.1, and callose deposition in asFPB1.1 is similar to wild-type following infiltration with a Pseudomonas syringae hrcC mutant or with non-host P. syringae pathovars. Moreover, asFPB1.1 plants did not exhibit any apparent defect in their ability to mount a hypersensitive response (HR). On the other hand, salicylic acid (SA)-mediated activation of PR1 was dramatically impaired in asFPB1.1 plants. In addition, P. syringae-elicited expression of many genes known to be SA-dependent was significantly reduced in asFBP1.1 plants. Consistent with this latter result, in asFBP1.1 plants the key regulator of SA-mediated responses, NPR1, showed both dramatically decreased total protein abundance and a failure to monomerize, which is required for its translocation into the nucleus. Copyright © 2014 Elsevier Ltd. All rights reserved.

Global Three-Dimensional Atmospheric Structure of the Atlantic Multidecadal Oscillation as Revealed by Two Reanalyses

NASA Astrophysics Data System (ADS)

Stuckman, Scott Seele

This study is a first documentation of the structure of the entire AMO life cycle, including extreme and transition phases, throughout the global troposphere. The extreme phase climate signature is constructed based on the strongest and most robust patterns identified by two methods (linear correlation and composite analyses), two reanalysis datasets (the National Centers for Environmental Prediction/National Center for Atmospheric Research and Twentieth Century Reanalysis, supplemented with precipitation data from the University of Delaware dataset) and data from two consecutive AMO cycles. The first characterization of the AMO transition phases uses a transition index based on the time derivative of AMO index. When trying to compare the zonal mean structure of AMO with the El Niño-Southern Oscillation (ENSO), a literature search showed the zonal mean structure of ENSO remained unpublished, despite the otherwise generally well-characterized horizontal structures. Therefore this study includes a seasonal analysis of the ENSO zonal mean structure during boreal winter (DJF) and summer (JJA). The AMO extreme phase is characterized by a blend of low and middle latitude centers of action, with the associated tilt of geopotential height anomaly patterns consistent with off-equatorial heating patterns generated by the Held idealized model. The surface climate signature is connected to the upper air with baroclinic vertical structure over the North Atlantic but barotropic structures elsewhere. The associated zonal mean circulation features three circulation cells globally with strong inter-hemispheric mixing that suggests the traditional view of the AMO involving a Northern-Southern Hemisphere asymmetry is accurate only near the surface. The AMO transition phase features a more equatorial-based climate signature and associated geopotential height anomaly patterns consistent with the Matsuno-Gill idealized model. The zonal mean circulation of the transition phases features six, rather than three, circulation cells globally. The only baroclinic structure, over North America, and several barotropic structures are positioned west of corresponding similar structures during the AMO extreme phase, suggesting an eastward evolution of climate anomalies as the AMO progresses from a cool-to-warm transition phase to warm phase. The Pacific-based climate signature resembles the IPO warm phase and it is proposed the AMO and IPO are different basin-wide expressions of a single multidecadal oscillation. The identification of an AMO transition phase climate signature distinct from the extreme phase suggests transition phases are not neutral and may provide an additional source of information for characterizing climate cycles.

GeoPAT: A toolbox for pattern-based information retrieval from large geospatial databases

NASA Astrophysics Data System (ADS)

Jasiewicz, Jarosław; Netzel, Paweł; Stepinski, Tomasz

2015-07-01

Geospatial Pattern Analysis Toolbox (GeoPAT) is a collection of GRASS GIS modules for carrying out pattern-based geospatial analysis of images and other spatial datasets. The need for pattern-based analysis arises when images/rasters contain rich spatial information either because of their very high resolution or their very large spatial extent. Elementary units of pattern-based analysis are scenes - patches of surface consisting of a complex arrangement of individual pixels (patterns). GeoPAT modules implement popular GIS algorithms, such as query, overlay, and segmentation, to operate on the grid of scenes. To achieve these capabilities GeoPAT includes a library of scene signatures - compact numerical descriptors of patterns, and a library of distance functions - providing numerical means of assessing dissimilarity between scenes. Ancillary GeoPAT modules use these functions to construct a grid of scenes or to assign signatures to individual scenes having regular or irregular geometries. Thus GeoPAT combines knowledge retrieval from patterns with mapping tasks within a single integrated GIS environment. GeoPAT is designed to identify and analyze complex, highly generalized classes in spatial datasets. Examples include distinguishing between different styles of urban settlements using VHR images, delineating different landscape types in land cover maps, and mapping physiographic units from DEM. The concept of pattern-based spatial analysis is explained and the roles of all modules and functions are described. A case study example pertaining to delineation of landscape types in a subregion of NLCD is given. Performance evaluation is included to highlight GeoPAT's applicability to very large datasets. The GeoPAT toolbox is available for download from

Spectral measurements of muzzle flash with multispectral and hyperspectral sensor

NASA Astrophysics Data System (ADS)

Kastek, M.; Dulski, R.; Trzaskawka, P.; Piątkowski, T.; Polakowski, H.

2011-08-01

The paper presents some practical aspects of the measurements of muzzle flash signatures. Selected signatures of sniper shot in typical scenarios has been presented. Signatures registered during all phases of muzzle flash were analyzed. High precision laboratory measurements were made in a special ballistic laboratory and as a result several flash patterns were registered. The field measurements of a muzzle flash were also performed. During the tests several infrared cameras were used, including the measurement class devices with high accuracy and frame rates. The registrations were made in NWIR, SWIR and LWIR spectral bands simultaneously. An ultra fast visual camera was also used for visible spectra registration. Some typical infrared shot signatures were presented. Beside the cameras, the LWIR imaging spectroradiometer HyperCam was also used during the laboratory experiments and the field tests. The signatures collected by the HyperCam device were useful for the determination of spectral characteristics of the muzzle flash, whereas the analysis of thermal images registered during the tests provided the data on temperature distribution in the flash area. As a result of the measurement session the signatures of several types handguns, machine guns and sniper rifles were obtained which will be used in the development of passive infrared systems for sniper detection.

Application of Independent Component Analysis for the Data Mining of Simultaneous EEG-fMRI: Preliminary Experience on Sleep Onset

PubMed Central

Lee, Jong-Hwan; Oh, Sungsuk; Jolesz, Ferenc A.; Park, Hyunwook; Yoo, Seung-Schik

2010-01-01

The simultaneous acquisition of electroencephalogram (EEG) and functional MRI (fMRI) signals is potentially advantageous because of the superior resolution that is achieved in both the temporal and spatial domains, respectively. However, ballistocardiographic artifacts along with the ocular artifacts are a major obstacle for the detection of the EEG signatures of interest. Since the sources corresponding to these artifacts are independent from those producing the EEG signatures, we applied the Infomax-based independent component analysis (ICA) technique to separate the EEG signatures from the artifacts. The isolated EEG signatures were further utilized to model the canonical hemodynamic response functions (HRFs). Subsequently, the brain areas from which these EEG signatures originated were identified as locales of activation patterns from the analysis of fMRI data. Upon the identification and subsequent evaluation of brain areas generating interictal epileptic discharge (IED) spikes from an epileptic subject, the presented method was successfully applied to detect the theta- and alpha-rhythms that are sleep onset related EEG signatures along with the subsequent neural circuitries from a sleep deprived volunteer. These results suggest that the ICA technique may be useful for the preprocessing of simultaneous EEG-fMRI acquisitions, especially when a reference paradigm is unavailable. PMID:19922343

Application of independent component analysis for the data mining of simultaneous Eeg-fMRI: preliminary experience on sleep onset.

PubMed

Lee, Jong-Hwan; Oh, Sungsuk; Jolesz, Ferenc A; Park, Hyunwook; Yoo, Seung-Schik

2009-01-01

The simultaneous acquisition of electroencephalogram (EEG) and functional MRI (fMRI) signals is potentially advantageous because of the superior resolution that is achieved in both the temporal and spatial domains, respectively. However, ballistocardiographic artifacts along with ocular artifacts are a major obstacle for the detection of the EEG signatures of interest. Since the sources corresponding to these artifacts are independent from those producing the EEG signatures, we applied the Infomax-based independent component analysis (ICA) technique to separate the EEG signatures from the artifacts. The isolated EEG signatures were further utilized to model the canonical hemodynamic response functions (HRFs). Subsequently, the brain areas from which these EEG signatures originated were identified as locales of activation patterns from the analysis of fMRI data. Upon the identification and subsequent evaluation of brain areas generating interictal epileptic discharge (IED) spikes from an epileptic subject, the presented method was successfully applied to detect the theta and alpha rhythms that are sleep onset-related EEG signatures along with the subsequent neural circuitries from a sleep-deprived volunteer. These results suggest that the ICA technique may be useful for the preprocessing of simultaneous EEG-fMRI acquisitions, especially when a reference paradigm is unavailable.

Spatial and Temporal Patterns of Dissolved Organic Matter Characteristics in the Upper Willamette River Basin, Oregon

NASA Astrophysics Data System (ADS)

Lee, B. S.; Lajtha, K.

2014-12-01

Dissolved organic matter (DOM) leaching through soil affects soil carbon sequestration and the carbon metabolism of receiving water bodies. Improving our understanding of the sources and fate of DOM at varying spatial and temporal patterns is crucial for land management decisions. However, little is known about how DOM sources change with land use types and seasonal flow patterns. In the Willamette River Basin (WRB), which is home to Oregon's major cities including Portland and Salem, forested headwaters transition to agricultural and urban land. The climate of WRB has a distinctive seasonal pattern with dry warm summers and wet winters driven by winter precipitation and snowmelt runoff between November and March. This study examined DOM fluorescence characteristic in stream water from 21 locations collected monthly and 16 locations collected seasonally to identify the sources and fate of DOM in the upper WRB in contrasting land uses. DOC and dissolved organic nitrogen concentrations increased as the flow rate increased during winter precipitation at all sites. This indicates that increased flow rate increased the connectivity between land and nearby water bodies. DOM fluorescent properties varied among land use types. During the first precipitation event after a long dry summer, a microbial DOM signature in agricultural areas increased along with nitrate concentrations. This may be because accumulated nutrients on land during the dry season flowed to nearby streams during the first rain event and promoted microbial growth in the streams. During the month of the highest flow rate in 2014, sampling sites near forest showed evidence of a greater terrestrial DOM signature compared to its signature during the dry season. This indicates fluorescent DOM characteristics in streams vary as the flow connectivity changes even within the same land type.

A study to explore the use of orbital remote sensing to determine native arid plant distribution. [Arizona

NASA Technical Reports Server (NTRS)

Mcginnies, W. G.; Haase, E. F. (Principal Investigator); Musick, H. B. (Compiler)

1973-01-01

The author has identified the following significant results. Ground truth spectral signature data for various types of scenes, including ground with and without annuals, and various shrubs, were collected. When these signature data are plotted with infrared (MSS band 6 or 7) reflectivity on one axis and red (MSS band 5) reflectivity on the other axis, clusters of data from the various types of scenes are distinct. This method of expressing spectral signature data appears to be more useful for distinguishing types of scenes than a simple infrared to red reflectivity ration. Large areas of varnished desert pavement are visible and mappable on ERTS-1 and high altitude aircraft imagery. A large scale vegetation pattern was found to be correlated with the presence of the desert pavement. The large scale correlation was used in mapping the vegetation of the area. It was found that a distinctive soil type was associated with the presence of the varnished desert pavement. The high salinity and exchangeable sodium percentage of this soil type provide a basis for the explanation of both the large scale and small scale vegetation pattern.

Signatures of microevolutionary processes in phylogenetic patterns.

PubMed

Costa, Carolina L N; Lemos-Costa, Paula; Marquitti, Flavia M D; Fernandes, Lucas D; Ramos, Marlon F; Schneider, David M; Martins, Ayana B; Aguiar, Marcus A M

2018-06-23

Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem we analysed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.

Improved canopy reflectance modeling and scene inference through improved understanding of scene pattern

NASA Technical Reports Server (NTRS)

Franklin, Janet; Simonett, David

1988-01-01

The Li-Strahler reflectance model, driven by LANDSAT Thematic Mapper (TM) data, provided regional estimates of tree size and density within 20 percent of sampled values in two bioclimatic zones in West Africa. This model exploits tree geometry in an inversion technique to predict average tree size and density from reflectance data using a few simple parameters measured in the field (spatial pattern, shape, and size distribution of trees) and in the imagery (spectral signatures of scene components). Trees are treated as simply shaped objects, and multispectral reflectance of a pixel is assumed to be related only to the proportions of tree crown, shadow, and understory in the pixel. These, in turn, are a direct function of the number and size of trees, the solar illumination angle, and the spectral signatures of crown, shadow and understory. Given the variance in reflectance from pixel to pixel within a homogeneous area of woodland, caused by the variation in the number and size of trees, the model can be inverted to give estimates of average tree size and density. Because the inversion is sensitive to correct determination of component signatures, predictions are not accurate for small areas.

Distinguishing Petroleum (Crude Oil and Fuel) From Smoke Exposure within Populations Based on the Relative Blood Levels of Benzene, Toluene, Ethylbenzene, and Xylenes (BTEX), Styrene and 2,5-Dimethylfuran by Pattern Recognition Using Artificial Neural Networks.

PubMed

Chambers, D M; Reese, C M; Thornburg, L G; Sanchez, E; Rafson, J P; Blount, B C; Ruhl, J R E; De Jesús, V R

2018-01-02

Studies of exposure to petroleum (crude oil/fuel) often involve monitoring benzene, toluene, ethylbenzene, xylenes (BTEX), and styrene (BTEXS) because of their toxicity and gas-phase prevalence, where exposure is typically by inhalation. However, BTEXS levels in the general U.S. population are primarily from exposure to tobacco smoke, where smokers have blood levels on average up to eight times higher than nonsmokers. This work describes a method using partition theory and artificial neural network (ANN) pattern recognition to classify exposure source based on relative BTEXS and 2,5-dimethylfuran blood levels. A method using surrogate signatures to train the ANN was validated by comparing blood levels among cigarette smokers from the National Health and Nutrition Examination Survey (NHANES) with BTEXS and 2,5-dimethylfuran signatures derived from the smoke of machine-smoked cigarettes. Classification agreement for an ANN model trained with relative VOC levels was up to 99.8% for nonsmokers and 100.0% for smokers. As such, because there is limited blood level data on individuals exposed to crude oil/fuel, only surrogate signatures derived from crude oil and fuel were used for training the ANN. For the 2007-2008 NHANES data, the ANN model assigned 7 out of 1998 specimens (0.35%) and for the 2013-2014 NHANES data 12 out of 2906 specimens (0.41%) to the crude oil/fuel signature category.

Longitudinal changes in young children’s 0–100 to 0–1000 number-line error signatures

PubMed Central

Reeve, Robert A.; Paul, Jacob M.; Butterworth, Brian

2015-01-01

We use a latent difference score (LDS) model to examine changes in young children’s number-line (NL) error signatures (errors marking numbers on a NL) over 18 months. A LDS model (1) overcomes some of the inference limitations of analytic models used in previous research, and in particular (2) provides a more reliable test of hypotheses about the meaning and significance of changes in NL error signatures over time and task. The NL error signatures of 217 6-year-olds’ (on test occasion one) were assessed three times over 18 months, along with their math ability on two occasions. On the first occasion (T1) children completed a 0–100 NL task; on the second (T2) a 0–100 NL and a 0–1000 NL task; on the third (T3) occasion a 0–1000 NL task. On the third and fourth occasions (T3 and T4), children completed mental calculation tasks. Although NL error signatures changed over time, these were predictable from other NL task error signatures, and predicted calculation accuracy at T3, as well as changes in calculation between T3 and T4. Multiple indirect effects (change parameters) showed that associations between initial NL error signatures (0–100 NL) and later mental calculation ability were mediated by error signatures on the 0–1000 NL task. The pattern of findings from the LDS model highlight the value of identifying direct and indirect effects in characterizing changing relationships in cognitive representations over task and time. Substantively, they support the claim that children’s NL error signatures generalize over task and time and thus can be used to predict math ability. PMID:26029152

Genomic Signature of Kin Selection in an Ant with Obligately Sterile Workers

PubMed Central

Warner, Michael R.; Mikheyev, Alexander S.

2017-01-01

Abstract Kin selection is thought to drive the evolution of cooperation and conflict, but the specific genes and genome-wide patterns shaped by kin selection are unknown. We identified thousands of genes associated with the sterile ant worker caste, the archetype of an altruistic phenotype shaped by kin selection, and then used population and comparative genomic approaches to study patterns of molecular evolution at these genes. Consistent with population genetic theoretical predictions, worker-upregulated genes experienced reduced selection compared with genes upregulated in reproductive castes. Worker-upregulated genes included more taxonomically restricted genes, indicating that the worker caste has recruited more novel genes, yet these genes also experienced reduced selection. Our study identifies a putative genomic signature of kin selection and helps to integrate emerging sociogenomic data with longstanding social evolution theory. PMID:28419349

Sex at the margins: parthenogenesis vs. facultative and obligate sex in a Neotropical ant.

PubMed

Kellner, K; Seal, J N; Heinze, J

2013-01-01

Geographic parthenogenesis is a distribution pattern, in which parthenogenetic populations tend to live in marginal habitats, at higher latitudes and altitudes and island-like habitats compared with the sexual forms. The facultatively parthenogenetic ant Platythyrea punctata is thought to exhibit this general pattern throughout its wide range in Central America and the Caribbean Islands. Workers of P. punctata from the Caribbean produce diploid female offspring from unfertilized eggs by thelytokous parthenogenesis, and mated females and males are rare. In contrast, workers in one colony from Costa Rica were incapable of thelytoky; instead mated workers produced all female offspring. Because sample sizes were very low in former studies, we here use microsatellite markers and explicit tests of thelytoky to examine the population genetic structure of ancestral and derived populations of P. punctata throughout the Caribbean and Central America. Populations from the Caribbean islands were fully capable of parthenogenesis, and population genetic signatures indicate that this is the predominant mode of reproduction, although males are occasionally produced. In contrast, the northernmost population on the mainland (Texas) showed signatures of sexual reproduction, and individuals were incapable of reproduction by thelytoky. Contrary to expectations from a geographic parthenogenesis distribution pattern, most parts of the mainland populations were found to be facultatively thelytokous, with population genetic signatures of both sexual and parthenogenetic reproduction. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Comparing Patterns of Natural Selection across Species Using Selective Signatures

PubMed Central

Shapiro, B. Jesse; Alm, Eric J

2008-01-01

Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 γ-proteobacterial species. We describe the pattern of fast or slow evolution across species as the “selective signature” of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell. PMID:18266472

Fear and the Defense Cascade: Clinical Implications and Management.

PubMed

Kozlowska, Kasia; Walker, Peter; McLean, Loyola; Carrive, Pascal

2015-01-01

Evolution has endowed all humans with a continuum of innate, hard-wired, automatically activated defense behaviors, termed the defense cascade. Arousal is the first step in activating the defense cascade; flight or fight is an active defense response for dealing with threat; freezing is a flight-or-fight response put on hold; tonic immobility and collapsed immobility are responses of last resort to inescapable threat, when active defense responses have failed; and quiescent immobility is a state of quiescence that promotes rest and healing. Each of these defense reactions has a distinctive neural pattern mediated by a common neural pathway: activation and inhibition of particular functional components in the amygdala, hypothalamus, periaqueductal gray, and sympathetic and vagal nuclei. Unlike animals, which generally are able to restore their standard mode of functioning once the danger is past, humans often are not, and they may find themselves locked into the same, recurring pattern of response tied in with the original danger or trauma. Understanding the signature patterns of these innate responses--the particular components that combine to yield the given pattern of defense-is important for developing treatment interventions. Effective interventions aim to activate or deactivate one or more components of the signature neural pattern, thereby producing a shift in the neural pattern and, with it, in mind-body state. The process of shifting the neural pattern is the necessary first step in unlocking the patient's trauma response, in breaking the cycle of suffering, and in helping the patient to adapt to, and overcome, past trauma.

The Effect of Aging on Muscular Dynamics Underlying Movement Patterns Changes.

PubMed

Vernooij, Carlijn A; Rao, Guillaume; Berton, Eric; Retornaz, Frédérique; Temprado, Jean-Jacques

2016-01-01

Introduction: Aging leads to alterations not only within the complex subsystems of the neuro-musculo-skeletal system, but also in the coupling between them. Here, we studied how aging affects functional reorganizations that occur both within and between the behavioral and muscular levels, which must be coordinated to produce goal-directed movements. Using unimanual reciprocal Fitts' task, we examined the behavioral and muscular dynamics of older adults (74.4 ± 3.7 years) and compared them to those found for younger adults (23.2 ± 2.0 years). Methods: To achieve this objective, we manipulated the target size to trigger a phase transition in the behavioral regime and searched for concomitant signatures of a phase transition in the muscular coordination. Here, muscular coordination was derived by using the method of muscular synergy extraction. With this technique, we obtained functional muscular patterns through non-negative matrix factorization of the muscular signals followed by clustering the resulting synergies. Results: Older adults showed a phase transition in behavioral regime, although, in contrast to young participants, their kinematic profiles did not show a discontinuity. In parallel, muscular coordination displayed two typical signatures of a phase transition, that is, increased variability of coordination patterns and a reorganization of muscular synergies. Both signatures confirmed the existence of muscular reorganization in older adults, which is coupled with change in dynamical regime at behavioral level. However, relative to young adults, transition occurred at lower index of difficulty (ID) in older participants and the reorganization of muscular patterns lasted longer (over multiple IDs). Discussion: This implies that consistent changes occur in coordination processes across behavior and muscle. Furthermore, the repertoire of muscular patterns was reduced and somewhat modified for older adults, relative to young participants. This suggests that aging is not only related to changes in individual muscles (e.g., caused by dynapenia) but also in their coordination.

Dynamic transcriptional signatures and network responses for clinical symptoms in influenza-infected human subjects using systems biology approaches.

PubMed

Linel, Patrice; Wu, Shuang; Deng, Nan; Wu, Hulin

2014-10-01

Recent studies demonstrate that human blood transcriptional signatures may be used to support diagnosis and clinical decisions for acute respiratory viral infections such as influenza. In this article, we propose to use a newly developed systems biology approach for time course gene expression data to identify significant dynamically response genes and dynamic gene network responses to viral infection. We illustrate the methodological pipeline by reanalyzing the time course gene expression data from a study with healthy human subjects challenged by live influenza virus. We observed clear differences in the number of significant dynamic response genes (DRGs) between the symptomatic and asymptomatic subjects and also identified DRG signatures for symptomatic subjects with influenza infection. The 505 common DRGs shared by the symptomatic subjects have high consistency with the signature genes for predicting viral infection identified in previous works. The temporal response patterns and network response features were carefully analyzed and investigated.

Assessment of Gamma-Ray-Spectra Analysis Method Utilizing the Fireworks Algorithm for Various Error Measures

DOE PAGES

Alamaniotis, Miltiadis; Tsoukalas, Lefteri H.

2018-01-01

The analysis of measured data plays a significant role in enhancing nuclear nonproliferation mainly by inferring the presence of patterns associated with special nuclear materials. Among various types of measurements, gamma-ray spectra is the widest utilized type of data in nonproliferation applications. In this paper, a method that employs the fireworks algorithm (FWA) for analyzing gamma-ray spectra aiming at detecting gamma signatures is presented. In particular, FWA is utilized to fit a set of known signatures to a measured spectrum by optimizing an objective function, where non-zero coefficients express the detected signatures. FWA is tested on a set of experimentallymore » obtained measurements optimizing various objective functions—MSE, RMSE, Theil-2, MAE, MAPE, MAP—with results exhibiting its potential in providing highly accurate and precise signature detection. Finally and furthermore, FWA is benchmarked against genetic algorithms and multiple linear regression, showing its superiority over those algorithms regarding precision with respect to MAE, MAPE, and MAP measures.« less

A Sensitive and Specific Neural Signature for Picture-Induced Negative Affect

PubMed Central

Chang, Luke J.; Gianaros, Peter J.; Manuck, Stephen B.; Krishnan, Anjali; Wager, Tor D.

2015-01-01

Neuroimaging has identified many correlates of emotion but has not yet yielded brain representations predictive of the intensity of emotional experiences in individuals. We used machine learning to identify a sensitive and specific signature of emotional responses to aversive images. This signature predicted the intensity of negative emotion in individual participants in cross validation (n =121) and test (n = 61) samples (high–low emotion = 93.5% accuracy). It was unresponsive to physical pain (emotion–pain = 92% discriminative accuracy), demonstrating that it is not a representation of generalized arousal or salience. The signature was comprised of mesoscale patterns spanning multiple cortical and subcortical systems, with no single system necessary or sufficient for predicting experience. Furthermore, it was not reducible to activity in traditional “emotion-related” regions (e.g., amygdala, insula) or resting-state networks (e.g., “salience,” “default mode”). Overall, this work identifies differentiable neural components of negative emotion and pain, providing a basis for new, brain-based taxonomies of affective processes. PMID:26098873

Wheat signature modeling and analysis for improved training statistics

NASA Technical Reports Server (NTRS)

Nalepka, R. F. (Principal Investigator); Malila, W. A.; Cicone, R. C.; Gleason, J. M.

1976-01-01

The author has identified the following significant results. The spectral, spatial, and temporal characteristics of wheat and other signatures in LANDSAT multispectral scanner data were examined through empirical analysis and simulation. Irrigation patterns varied widely within Kansas; 88 percent of wheat acreage in Finney was irrigated and 24 percent in Morton, as opposed to less than 3 percent for western 2/3's of the State. The irrigation practice was definitely correlated with the observed spectral response; wheat variety differences produced observable spectral differences due to leaf coloration and different dates of maturation. Between-field differences were generally greater than within-field differences, and boundary pixels produced spectral features distinct from those within field centers. Multiclass boundary pixels contributed much of the observed bias in proportion estimates. The variability between signatures obtained by different draws of training data decreased as the sample size became larger; also, the resulting signatures became more robust and the particular decision threshold value became less important.

Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, nuclear factor-κB and other signal transcription factors in head and neck squamous cell carcinoma

PubMed Central

Yan, Bin; Yang, Xinping; Lee, Tin-Lap; Friedman, Jay; Tang, Jun; Van Waes, Carter; Chen, Zhong

2007-01-01

Background Differentially expressed gene profiles have previously been observed among pathologically defined cancers by microarray technologies, including head and neck squamous cell carcinomas (HNSCCs). However, the molecular expression signatures and transcriptional regulatory controls that underlie the heterogeneity in HNSCCs are not well defined. Results Genome-wide cDNA microarray profiling of ten HNSCC cell lines revealed novel gene expression signatures that distinguished cancer cell subsets associated with p53 status. Three major clusters of over-expressed genes (A to C) were defined through hierarchical clustering, Gene Ontology, and statistical modeling. The promoters of genes in these clusters exhibited different patterns and prevalence of transcription factor binding sites for p53, nuclear factor-κB (NF-κB), activator protein (AP)-1, signal transducer and activator of transcription (STAT)3 and early growth response (EGR)1, as compared with the frequency in vertebrate promoters. Cluster A genes involved in chromatin structure and function exhibited enrichment for p53 and decreased AP-1 binding sites, whereas clusters B and C, containing cytokine and antiapoptotic genes, exhibited a significant increase in prevalence of NF-κB binding sites. An increase in STAT3 and EGR1 binding sites was distributed among the over-expressed clusters. Novel regulatory modules containing p53 or NF-κB concomitant with other transcription factor binding motifs were identified, and experimental data supported the predicted transcriptional regulation and binding activity. Conclusion The transcription factors p53, NF-κB, and AP-1 may be important determinants of the heterogeneous pattern of gene expression, whereas STAT3 and EGR1 may broadly enhance gene expression in HNSCCs. Defining these novel gene signatures and regulatory mechanisms will be important for establishing new molecular classifications and subtyping, which in turn will promote development of targeted therapeutics for HNSCC. PMID:17498291

Supernova signatures of neutrino mass ordering

NASA Astrophysics Data System (ADS)

Scholberg, Kate

2018-01-01

A suite of detectors around the world is poised to measure the flavor-energy-time evolution of the ten-second burst of neutrinos from a core-collapse supernova occurring in the Milky Way or nearby. Next-generation detectors to be built in the next decade will have enhanced flavor sensitivity and statistics. Not only will the observation of this burst allow us to peer inside the dense matter of the extreme event and learn about the collapse processes and the birth of the remnant, but the neutrinos will bring information about neutrino properties themselves. This review surveys some of the physical signatures that the currently-unknown neutrino mass pattern will imprint on the observed neutrino events at Earth, emphasizing the most robust and least model-dependent signatures of mass ordering.

Motor vehicle fuel analyzer

DOEpatents

Hoffheins, B.S.; Lauf, R.J.

1997-08-05

A gas detecting system is described for classifying the type of liquid fuel in a container or tank. The system includes a plurality of semiconductor gas sensors, each of which differs from the other in its response to various organic vapors. The system includes a means of processing the responses of the plurality of sensors such that the responses to any particular organic substance or mixture is sufficiently distinctive to constitute a recognizable ``signature``. The signature of known substances are collected and divided into two classes based on some other known characteristic of the substances. A pattern recognition system classifies the signature of an unknown substance with reference to the two user-defined classes, thereby classifying the unknown substance with regard to the characteristic of interest, such as its suitability for a particular use. 14 figs.

Motor vehicle fuel analyzer

DOEpatents

Hoffheins, Barbara S.; Lauf, Robert J.

1997-01-01

A gas detecting system for classifying the type of liquid fuel in a container or tank. The system includes a plurality of semiconductor gas sensors, each of which differs from the other in its response to various organic vapors. The system includes a means of processing the responses of the plurality of sensors such that the responses to any particular organic substance or mixture is sufficiently distinctive to constitute a recognizable "signature". The signature of known substances are collected and divided into two classes based on some other known characteristic of the substances. A pattern recognition system classifies the signature of an unknown substance with reference to the two user-defined classes, thereby classifying the unknown substance with regard to the characteristic of interest, such as its suitability for a particular use.

Critical Point in Self-Organized Tissue Growth

NASA Astrophysics Data System (ADS)

Aguilar-Hidalgo, Daniel; Werner, Steffen; Wartlick, Ortrud; González-Gaitán, Marcos; Friedrich, Benjamin M.; Jülicher, Frank

2018-05-01

We present a theory of pattern formation in growing domains inspired by biological examples of tissue development. Gradients of signaling molecules regulate growth, while growth changes these graded chemical patterns by dilution and advection. We identify a critical point of this feedback dynamics, which is characterized by spatially homogeneous growth and proportional scaling of patterns with tissue length. We apply this theory to the biological model system of the developing wing of the fruit fly Drosophila melanogaster and quantitatively identify signatures of the critical point.

GRADIENT: Graph Analytic Approach for Discovering Irregular Events, Nascent and Temporal

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

Hogan, Emilie

2015-03-31

Finding a time-ordered signature within large graphs is a computationally complex problem due to the combinatorial explosion of potential patterns. GRADIENT is designed to search and understand that problem space.

GRADIENT: Graph Analytic Approach for Discovering Irregular Events, Nascent and Temporal

ScienceCinema

Hogan, Emilie

2018-01-16

Finding a time-ordered signature within large graphs is a computationally complex problem due to the combinatorial explosion of potential patterns. GRADIENT is designed to search and understand that problem space.

Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers

PubMed Central

2013-01-01

Background Alterations in epigenetic marks, including methylation or acetylation, are common in human cancers. For many epigenetic pathways, however, direct measures of activity are unknown, making their role in various cancers difficult to assess. Gene expression signatures facilitate the examination of patterns of epigenetic pathway activation across and within human cancer types allowing better understanding of the relationships between these pathways. Methods We used Bayesian regression to generate gene expression signatures from normal epithelial cells before and after epigenetic pathway activation. Signatures were applied to datasets from TCGA, GEO, CaArray, ArrayExpress, and the cancer cell line encyclopedia. For TCGA data, signature results were correlated with copy number variation and DNA methylation changes. GSEA was used to identify biologic pathways related to the signatures. Results We developed and validated signatures reflecting downstream effects of enhancer of zeste homolog 2(EZH2), histone deacetylase(HDAC) 1, HDAC4, sirtuin 1(SIRT1), and DNA methyltransferase 2(DNMT2). By applying these signatures to data from cancer cell lines and tumors in large public repositories, we identify those cancers that have the highest and lowest activation of each of these pathways. Highest EZH2 activation is seen in neuroblastoma, hepatocellular carcinoma, small cell lung cancer, and melanoma, while highest HDAC activity is seen in pharyngeal cancer, kidney cancer, and pancreatic cancer. Across all datasets studied, activation of both EZH2 and HDAC4 is significantly underrepresented. Using breast cancer and glioblastoma as examples to examine intrinsic subtypes of particular cancers, EZH2 activation was highest in luminal breast cancers and proneural glioblastomas, while HDAC4 activation was highest in basal breast cancer and mesenchymal glioblastoma. EZH2 and HDAC4 activation are associated with particular chromosome abnormalities: EZH2 activation with aberrations in genes from the TGF and phosphatidylinositol pathways and HDAC4 activation with aberrations in inflammatory and chemokine related genes. Conclusion Gene expression patterns can reveal the activation level of epigenetic pathways. Epigenetic pathways define biologically relevant subsets of human cancers. EZH2 activation and HDAC4 activation correlate with growth factor signaling and inflammation, respectively, and represent two distinct states for cancer cells. This understanding may allow us to identify targetable drivers in these cancer subsets. PMID:24079712

Mechanistic considerations on the wavelength-dependent variations of UVR genotoxicity and mutagenesis in skin: the discrimination of UVA-signature from UV-signature mutation.

PubMed

Ikehata, Hironobu

2018-05-31

Ultraviolet radiation (UVR) predominantly induces UV-signature mutations, C → T and CC → TT base substitutions at dipyrimidine sites, in the cellular and skin genome. I observed in our in vivo mutation studies of mouse skin that these UVR-specific mutations show a wavelength-dependent variation in their sequence-context preference. The C → T mutation occurs most frequently in the 5'-TCG-3' sequence regardless of the UVR wavelength, but is recovered more preferentially there as the wavelength increases, resulting in prominent occurrences exclusively in the TCG sequence in the UVA wavelength range, which I will designate as a "UVA signature" in this review. The preference of the UVB-induced C → T mutation for the sequence contexts shows a mixed pattern of UVC- and UVA-induced mutations, and a similar pattern is also observed for natural sunlight, in which UVB is the most genotoxic component. In addition, the CC → TT mutation hardly occurs at UVA1 wavelengths, although it is detected rarely but constantly in the UVC and UVB ranges. This wavelength-dependent variation in the sequence-context preference of the UVR-specific mutations could be explained by two different photochemical mechanisms of cyclobutane pyrimidine dimer (CPD) formation. The UV-signature mutations observed in the UVC and UVB ranges are known to be caused mainly by CPDs produced through the conventional singlet/triplet excitation of pyrimidine bases after the direct absorption of the UVC/UVB photon energy in those bases. On the other hand, a novel photochemical mechanism through the direct absorption of the UVR energy to double-stranded DNA, which is called "collective excitation", has been proposed for the UVA-induced CPD formation. The UVA photons directly absorbed by DNA produce CPDs with a sequence context preference different from that observed for CPDs caused by the UVC/UVB-mediated singlet/triplet excitation, causing CPD formation preferentially at thymine-containing dipyrimidine sites and probably also preferably at methyl CpG-associated dipyrimidine sites, which include the TCG sequence. In this review, I present a mechanistic consideration on the wavelength-dependent variation of the sequence context preference of the UVR-specific mutations and rationalize the proposition of the UVA-signature mutation, in addition to the UV-signature mutation.

Variability in total ozone associated with baroclinic waves

NASA Technical Reports Server (NTRS)

Mote, Philip W.; Holton, James R.; Wallace, John M.

1991-01-01

One-point regression maps of total ozone formed by regressing the time series of bandpass-filtered geopotential height data have been analyzed against Total Ozone Mapping Spectrometer data. Results obtained reveal a strong signature of baroclinic waves in the ozone variability. The regressed patterns are found to be similar in extent and behavior to the relative vorticity patterns reported by Lim and Wallace (1991).

Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints

PubMed Central

2012-01-01

Background The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa) formed ten clusters of orthologous groups (COG) with genes from the monocot sorghum (Sorghum bicolor) and dicot Arabidopsis (Arabidopsis thaliana). The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns. Results The most apparent pattern observed was the occurrence of spatially conserved ‘core modules’ among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS) classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic) or organ-associated signals, which may be functioning as ‘regulatory fine-tuners’ and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis. Conclusions Patterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in conjunction with lineage-specific or species-specific regulatory fine-tuners. This synergy may be critical for finer-scale spatio-temporal regulation, hence unique expression profiles of homologous transcription factors from different species with distinct zones of ecological adaptation such as rice, sorghum and Arabidopsis. The patterns revealed from these comparisons set the stage for further empirical validation by functional genomics. PMID:22992304

Discrete Neural Signatures of Basic Emotions.

PubMed

Saarimäki, Heini; Gotsopoulos, Athanasios; Jääskeläinen, Iiro P; Lampinen, Jouko; Vuilleumier, Patrik; Hari, Riitta; Sams, Mikko; Nummenmaa, Lauri

2016-06-01

Categorical models of emotions posit neurally and physiologically distinct human basic emotions. We tested this assumption by using multivariate pattern analysis (MVPA) to classify brain activity patterns of 6 basic emotions (disgust, fear, happiness, sadness, anger, and surprise) in 3 experiments. Emotions were induced with short movies or mental imagery during functional magnetic resonance imaging. MVPA accurately classified emotions induced by both methods, and the classification generalized from one induction condition to another and across individuals. Brain regions contributing most to the classification accuracy included medial and inferior lateral prefrontal cortices, frontal pole, precentral and postcentral gyri, precuneus, and posterior cingulate cortex. Thus, specific neural signatures across these regions hold representations of different emotional states in multimodal fashion, independently of how the emotions are induced. Similarity of subjective experiences between emotions was associated with similarity of neural patterns for the same emotions, suggesting a direct link between activity in these brain regions and the subjective emotional experience. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Exocarp Properties and Transcriptomic Analysis of Cucumber (Cucumis sativus) Fruit Expressing Age-Related Resistance to Phytophthora capsici

PubMed Central

Ando, Kaori; Carr, Kevin M.; Colle, Marivi; Mansfeld, Ben N.; Grumet, Rebecca

2015-01-01

Very young cucumber (Cucumis sativus) fruit are highly susceptible to infection by the oomycete pathogen, Phytophthora capsici. As the fruit complete exponential growth, at approximately 10–12 days post pollination (dpp), they transition to resistance. The development of age-related resistance (ARR) is increasingly recognized as an important defense against pathogens, however, underlying mechanisms are largely unknown. Peel sections from cucumber fruit harvested at 8 dpp (susceptible) and 16 dpp (resistant) showed equivalent responses to inoculation as did whole fruit, indicating that the fruit surface plays an important role in defense against P. capsici. Exocarp from 16 dpp fruit had thicker cuticles, and methanolic extracts of peel tissue inhibited growth of P. capsici in vitro, suggesting physical or chemical components to the ARR. Transcripts specifically expressed in the peel vs. pericarp showed functional differentiation. Transcripts predominantly expressed in the peel were consistent with fruit surface associated functions including photosynthesis, cuticle production, response to the environment, and defense. Peel-specific transcripts that exhibited increased expression in 16 dpp fruit relative to 8 dpp fruit, were highly enriched (P<0.0001) for response to stress, signal transduction, and extracellular and transport functions. Specific transcripts included genes associated with potential physical barriers (i.e., cuticle), chemical defenses (flavonoid biosynthesis), oxidative stress, penetration defense, and molecular pattern (MAMP)-triggered or effector-triggered (R-gene mediated) pathways. The developmentally regulated changes in gene expression between peels from susceptible- and resistant- age fruits suggest programming for increased defense as the organ reaches full size. PMID:26528543

Exocarp Properties and Transcriptomic Analysis of Cucumber (Cucumis sativus) Fruit Expressing Age-Related Resistance to Phytophthora capsici.

PubMed

Ando, Kaori; Carr, Kevin M; Colle, Marivi; Mansfeld, Ben N; Grumet, Rebecca

2015-01-01

Very young cucumber (Cucumis sativus) fruit are highly susceptible to infection by the oomycete pathogen, Phytophthora capsici. As the fruit complete exponential growth, at approximately 10-12 days post pollination (dpp), they transition to resistance. The development of age-related resistance (ARR) is increasingly recognized as an important defense against pathogens, however, underlying mechanisms are largely unknown. Peel sections from cucumber fruit harvested at 8 dpp (susceptible) and 16 dpp (resistant) showed equivalent responses to inoculation as did whole fruit, indicating that the fruit surface plays an important role in defense against P. capsici. Exocarp from 16 dpp fruit had thicker cuticles, and methanolic extracts of peel tissue inhibited growth of P. capsici in vitro, suggesting physical or chemical components to the ARR. Transcripts specifically expressed in the peel vs. pericarp showed functional differentiation. Transcripts predominantly expressed in the peel were consistent with fruit surface associated functions including photosynthesis, cuticle production, response to the environment, and defense. Peel-specific transcripts that exhibited increased expression in 16 dpp fruit relative to 8 dpp fruit, were highly enriched (P<0.0001) for response to stress, signal transduction, and extracellular and transport functions. Specific transcripts included genes associated with potential physical barriers (i.e., cuticle), chemical defenses (flavonoid biosynthesis), oxidative stress, penetration defense, and molecular pattern (MAMP)-triggered or effector-triggered (R-gene mediated) pathways. The developmentally regulated changes in gene expression between peels from susceptible- and resistant- age fruits suggest programming for increased defense as the organ reaches full size.

Signature of Hematite in Confidence Hills Martian Rock

NASA Image and Video Library

2014-11-04

This side-by-side comparison shows the X-ray diffraction patterns of two different samples collected from rocks on Mars by NASA Curiosity rover. The images present data obtained by Curiosity Chemistry and Mineralogy instrument CheMin.

Polarization signatures for abandoned agricultural fields in the Manix Basin area of the Mojave Desert

NASA Technical Reports Server (NTRS)

Ray, Terrill W.; Farr, Tom G.; Vanzyl, Jakob J.

1991-01-01

Polarimetric signatures from abandoned circular alfalfa fields in the Manix Basin area of the Mojave desert show systematic changes with length of abandonment. The obliteration of circular planting rows by surface processes could account for the disappearance of bright 'spokes', which seems to be reflection patterns from remnants of the planting rows, with increasing length of abandonment. An observed shift in the location of the maximum L-band copolarization return away from VV, as well as an increase in surface roughness, both occurring with increasing age of abandonment, seems to be attributable to the formation of wind ripple on the relatively vegetationless fields. A Late Pleistocene/Holocene sand bar deposit, which can be identified in the radar images, is probably responsible for the failure of three fields to match the age sequence patterns in roughness and peak shift.

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.

PubMed

Quintales, Luis; Soriano, Ignacio; Vázquez, Enrique; Segurado, Mónica; Antequera, Francisco

2015-04-01

Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition.

The Temporal Signature of Memories: Identification of a General Mechanism for Dynamic Memory Replay in Humans

PubMed Central

Michelmann, Sebastian; Bowman, Howard; Hanslmayr, Simon

2016-01-01

Reinstatement of dynamic memories requires the replay of neural patterns that unfold over time in a similar manner as during perception. However, little is known about the mechanisms that guide such a temporally structured replay in humans, because previous studies used either unsuitable methods or paradigms to address this question. Here, we overcome these limitations by developing a new analysis method to detect the replay of temporal patterns in a paradigm that requires participants to mentally replay short sound or video clips. We show that memory reinstatement is accompanied by a decrease of low-frequency (8 Hz) power, which carries a temporal phase signature of the replayed stimulus. These replay effects were evident in the visual as well as in the auditory domain and were localized to sensory-specific regions. These results suggest low-frequency phase to be a domain-general mechanism that orchestrates dynamic memory replay in humans. PMID:27494601

Automated real-time structure health monitoring via signature pattern recognition

NASA Astrophysics Data System (ADS)

Sun, Fanping P.; Chaudhry, Zaffir A.; Rogers, Craig A.; Majmundar, M.; Liang, Chen

1995-05-01

Described in this paper are the details of an automated real-time structure health monitoring system. The system is based on structural signature pattern recognition. It uses an array of piezoceramic patches bonded to the structure as integrated sensor-actuators, an electric impedance analyzer for structural frequency response function acquisition and a PC for control and graphic display. An assembled 3-bay truss structure is employed as a test bed. Two issues, the localization of sensing area and the sensor temperature drift, which are critical for the success of this technique are addressed and a novel approach of providing temperature compensation using probability correlation function is presented. Due to the negligible weight and size of the solid-state sensor array and its ability to sense incipient-type damage, the system can eventually be implemented on many types of structures such as aircraft, spacecraft, large-span dome roof and steel bridges requiring multilocation and real-time health monitoring.

Apparatus for detecting and recognizing analytes based on their crystallization patterns

DOEpatents

Morozov, Victor; Bailey, Charles L.; Vsevolodov, Nikolai N.; Elliott, Adam

2010-12-14

The invention contemplates apparatuses for recognition of proteins and other biological molecules by imaging morphology, size and distribution of crystalline and amorphous dry residues in droplets (further referred to as "crystallization patterns") containing predetermined amount of certain crystal-forming organic compounds (reporters) to which protein to be analyzed is added. Changes in the crystallization patterns of a number of amino-acids can be used as a "signature" of a protein added. Also, changes in the crystallization patterns, as well as the character of such changes, can be used as recognition elements in analysis of protein molecules.

Geomorphic Processes and Remote Sensing Signatures of Alluvial Fans in the Kun Lun Mountains, China

NASA Technical Reports Server (NTRS)

Farr, Tom G.; Chadwick, Oliver A.

1996-01-01

The timing of alluvial deposition in arid and semiarid areas is tied to land-surface instability caused by regional climate changes. The distribution pattern of dated deposits provides maps of regional land-surface response to past climate change. Sensitivity to differences in surface roughness and composition makes remote sensing techniques useful for regional mapping of alluvial deposits. Radar images from the Spaceborne Radar Laboratory and visible wavelength images from the French SPOT satellite were used to determine remote sensing signatures of alluvial fan units for an area in the Kun Lun Mountains of northwestern China. These data were combined with field observations to compare surface processes and their effects on remote sensing signatures in northwestern China and the southwestern United States. Geomorphic processes affecting alluvial fans in the two areas include aeolian deposition, desert varnish, and fluvial dissection. However, salt weathering is a much more important process in the Kun Lun than in the southwestern United States. This slows the formation of desert varnish and prevents desert pavement from forming. Thus the Kun Lun signatures are characteristic of the dominance of salt weathering, while signatures from the southwestern United States are characteristic of the dominance of desert varnish and pavement processes. Remote sensing signatures are consistent enough in these two regions to be used for mapping fan units over large areas.

Fish debris record the hydrothermal activity in the Atlantis II deep sediments (Red Sea)

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

Oudin, E.; Cocherie, A.

1988-01-01

The REE and U, Th, Zr, Hf, Sc have been analyzed in samples from Atlantis II and Shaban/Jean Charcot Deeps in the Red Sea. The high Zr/Hf ratio in some sediments indicates the presence of fish debris or of finely crystallized apatite. The positive ..sigma..REE vs P/sub 2/O/sub 5/ and ..sigma..REE vs Zr/Hf correlations show that fish debris and finely crystallized apatite are the main REE sink in Atlantis II Deep sediments as in other marine environments. The hydrothermal sediments and the fish debris concentrates have similar REE patterns, characterized by a LREE enrichment and a large positive Eu anomaly.more » This REE pattern is also observed in E.P.R. hydrothermal solutions. Fish debris from marine environments acquire their REE content and signature mostly from sea water during early diagenesis. The hydrothermal REE signature of Atlantis II Deep fish debris indicate that they probably record the REE signature of their hydrothermal sedimentation and diagenetic environment. The different REE signatures of the Shaban/Jean Charcot and Atlantis II Deep hydrothermal sediments suggest a sea water-dominated brine in the Shaban/Jean Charcot Deep as opposed to the predominantly hydrothermal brine in Atlantis II Deep. Atlantis II Deep fish debris are also characterized by their high U but low Th contents. Their low Th contents probably reflect the low Th content of the various possible sources (sea water, brine, sediments). Their U contents are probably controlled by the redox conditions of sedimentation.« less

Changes in Gene Expression Predicting Local Control in Cervical Cancer: Results from Radiation Therapy Oncology Group 0128

PubMed Central

Weidhaas, Joanne B.; Li, Shu-Xia; Winter, Kathryn; Ryu, Janice; Jhingran, Anuja; Miller, Bridgette; Dicker, Adam P.; Gaffney, David

2009-01-01

Purpose To evaluate the potential of gene expression signatures to predict response to treatment in locally advanced cervical cancer treated with definitive chemotherapy and radiation. Experimental Design Tissue biopsies were collected from patients participating in Radiation Therapy Oncology Group (RTOG) 0128, a phase II trial evaluating the benefit of celecoxib in addition to cisplatin chemotherapy and radiation for locally advanced cervical cancer. Gene expression profiling was done and signatures of pretreatment, mid-treatment (before the first implant), and “changed” gene expression patterns between pre- and mid-treatment samples were determined. The ability of the gene signatures to predict local control versus local failure was evaluated. Two-group t test was done to identify the initial gene set separating these end points. Supervised classification methods were used to enrich the gene sets. The results were further validated by leave-one-out and 2-fold cross-validation. Results Twenty-two patients had suitable material from pretreatment samples for analysis, and 13 paired pre- and mid-treatment samples were obtained. The changed gene expression signatures between the pre- and mid-treatment biopsies predicted response to treatment, separating patients with local failures from those who achieved local control with a seven-gene signature. The in-sample prediction rate, leave-one-out prediction rate, and 2-fold prediction rate are 100% for this seven-gene signature. This signature was enriched for cell cycle genes. Conclusions Changed gene expression signatures during therapy in cervical cancer can predict outcome as measured by local control. After further validation, such findings could be applied to direct additional therapy for cervical cancer patients treated with chemotherapy and radiation. PMID:19509178

Patterns of brain structural connectivity differentiate normal weight from overweight subjects

PubMed Central

Gupta, Arpana; Mayer, Emeran A.; Sanmiguel, Claudia P.; Van Horn, John D.; Woodworth, Davis; Ellingson, Benjamin M.; Fling, Connor; Love, Aubrey; Tillisch, Kirsten; Labus, Jennifer S.

2015-01-01

Background Alterations in the hedonic component of ingestive behaviors have been implicated as a possible risk factor in the pathophysiology of overweight and obese individuals. Neuroimaging evidence from individuals with increasing body mass index suggests structural, functional, and neurochemical alterations in the extended reward network and associated networks. Aim To apply a multivariate pattern analysis to distinguish normal weight and overweight subjects based on gray and white-matter measurements. Methods Structural images (N = 120, overweight N = 63) and diffusion tensor images (DTI) (N = 60, overweight N = 30) were obtained from healthy control subjects. For the total sample the mean age for the overweight group (females = 32, males = 31) was 28.77 years (SD = 9.76) and for the normal weight group (females = 32, males = 25) was 27.13 years (SD = 9.62). Regional segmentation and parcellation of the brain images was performed using Freesurfer. Deterministic tractography was performed to measure the normalized fiber density between regions. A multivariate pattern analysis approach was used to examine whether brain measures can distinguish overweight from normal weight individuals. Results 1. White-matter classification: The classification algorithm, based on 2 signatures with 17 regional connections, achieved 97% accuracy in discriminating overweight individuals from normal weight individuals. For both brain signatures, greater connectivity as indexed by increased fiber density was observed in overweight compared to normal weight between the reward network regions and regions of the executive control, emotional arousal, and somatosensory networks. In contrast, the opposite pattern (decreased fiber density) was found between ventromedial prefrontal cortex and the anterior insula, and between thalamus and executive control network regions. 2. Gray-matter classification: The classification algorithm, based on 2 signatures with 42 morphological features, achieved 69% accuracy in discriminating overweight from normal weight. In both brain signatures regions of the reward, salience, executive control and emotional arousal networks were associated with lower morphological values in overweight individuals compared to normal weight individuals, while the opposite pattern was seen for regions of the somatosensory network. Conclusions 1. An increased BMI (i.e., overweight subjects) is associated with distinct changes in gray-matter and fiber density of the brain. 2. Classification algorithms based on white-matter connectivity involving regions of the reward and associated networks can identify specific targets for mechanistic studies and future drug development aimed at abnormal ingestive behavior and in overweight/obesity. PMID:25737959

Fear and the Defense Cascade: Clinical Implications and Management

PubMed Central

Kozlowska, Kasia; Walker, Peter; McLean, Loyola; Carrive, Pascal

2015-01-01

Abstract Evolution has endowed all humans with a continuum of innate, hard-wired, automatically activated defense behaviors, termed the defense cascade. Arousal is the first step in activating the defense cascade; flight or fight is an active defense response for dealing with threat; freezing is a flight-or-fight response put on hold; tonic immobility and collapsed immobility are responses of last resort to inescapable threat, when active defense responses have failed; and quiescent immobility is a state of quiescence that promotes rest and healing. Each of these defense reactions has a distinctive neural pattern mediated by a common neural pathway: activation and inhibition of particular functional components in the amygdala, hypothalamus, periaqueductal gray, and sympathetic and vagal nuclei. Unlike animals, which generally are able to restore their standard mode of functioning once the danger is past, humans often are not, and they may find themselves locked into the same, recurring pattern of response tied in with the original danger or trauma. Understanding the signature patterns of these innate responses—the particular components that combine to yield the given pattern of defense—is important for developing treatment interventions. Effective interventions aim to activate or deactivate one or more components of the signature neural pattern, thereby producing a shift in the neural pattern and, with it, in mind-body state. The process of shifting the neural pattern is the necessary first step in unlocking the patient’s trauma response, in breaking the cycle of suffering, and in helping the patient to adapt to, and overcome, past trauma. PMID:26062169

Shifting Quaternary migration patterns in the Bahamian archipelago: Evidence from the Zamia pumila complex at the northern limits of the Caribbean island biodiversity hotspot.

PubMed

Salas-Leiva, Dayana E; Meerow, Alan W; Calonje, Michael; Francisco-Ortega, Javier; Griffith, M Patrick; Nakamura, Kyoko; Sánchez, Vanessa; Knowles, Lindy; Knowles, David

2017-05-01

The Bahamas archipelago is formed by young, tectonically stable carbonate banks that harbor direct geological evidence of global ice-volume changes. We sought to detect signatures of major changes on gene flow patterns and reconstruct the phylogeographic history of the monophyletic Zamia pumila complex across the Bahamas. Nuclear molecular markers with both high and low mutation rates were used to capture two different time scale signatures and test several gene flow and demographic hypotheses. Single-copy nuclear genes unveiled apparent ancestral admixture on Andros, suggesting a significant role of this island as main hub of diversity of the archipelago. We detected demographic and spatial expansion of the Zamia pumila complex on both paleo-provinces around the Piacenzian (Pliocene)/Gelasian (Pleistocene). Populations evidenced signatures of different migration models that have occurred at two different times. Populations on Long Island ( Z. lucayana ) may either represent a secondary colonization of the Bahamas by Zamia or a rapid and early-divergence event of at least one population on the Bahamas. Despite changes in migration patterns with global climate, expected heterozygosity with both marker systems remains within the range reported for cycads, but with significant levels of increased inbreeding detected by the microsatellites. This finding is likely associated with reduced gene flow between and within paleo-provinces, accompanied by genetic drift, as rising seas enforced isolation. Our study highlights the importance of the maintenance of the predominant direction of genetic exchange and the role of overseas dispersion among the islands during climate oscillations. © 2017 Botanical Society of America.

Landscape cultivation alters δ30Si signature in terrestrial ecosystems

PubMed Central

Vandevenne, Floor I.; Delvaux, Claire; Hughes, Harold J.; André, Luc; Ronchi, Benedicta; Clymans, Wim; Barão, Lúcia; Govers, Gerard; Meire, Patrick; Struyf, Eric

2015-01-01

Despite increasing recognition of the relevance of biological cycling for Si cycling in ecosystems and for Si export from soils to fluvial systems, effects of human cultivation on the Si cycle are still relatively understudied. Here we examined stable Si isotope (δ30Si) signatures in soil water samples across a temperate land use gradient. We show that – independent of geological and climatological variation – there is a depletion in light isotopes in soil water of intensive croplands and managed grasslands relative to native forests. Furthermore, our data suggest a divergence in δ30Si signatures along the land use change gradient, highlighting the imprint of vegetation cover, human cultivation and intensity of disturbance on δ30Si patterns, on top of more conventionally acknowledged drivers (i.e. mineralogy and climate). PMID:25583031

Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India.

PubMed

Kulkarni, Smita S; Lapedes, Alan; Tang, Haili; Gnanakaran, S; Daniels, Marcus G; Zhang, Ming; Bhattacharya, Tanmoy; Li, Ming; Polonis, Victoria R; McCutchan, Francine E; Morris, Lynn; Ellenberger, Dennis; Butera, Salvatore T; Bollinger, Robert C; Korber, Bette T; Paranjape, Ramesh S; Montefiori, David C

2009-03-15

Little is known about the neutralization properties of HIV-1 in India to optimally design and test vaccines. For this reason, a functional Env clone was obtained from each of ten newly acquired, heterosexually transmitted HIV-1 infections in Pune, Maharashtra. These clones formed a phylogenetically distinct genetic lineage within subtype C. As Env-pseudotyped viruses the clones were mostly resistant to IgG1b12, 2G12 and 2F5 but all were sensitive to 4E10. When compared to a large multi-subtype panel of Env-pseudotyped viruses (subtypes B, C and CRF02_AG) in neutralization assays with a multi-subtype panel of HIV-1-positive plasma samples, the Indian Envs were remarkably complex. With the exception of the Indian Envs, results of a hierarchical clustering analysis showed a strong subtype association with the patterns of neutralization susceptibility. From these patterns we were able to identify 19 neutralization cluster-associated amino acid signatures in gp120 and 14 signatures in the ectodomain and cytoplasmic tail of gp41. We conclude that newly transmitted Indian Envs are antigenically complex in spite of close genetic similarity. Delineation of neutralization-associated amino acid signatures provides a deeper understanding of the antigenic structure of HIV-1 Env.

Observation of the human body thermoregulation and extraction of its vein signature using NIR and MWIR imaging

NASA Astrophysics Data System (ADS)

Bouzida, Nabila; Bendada, Abdelhakim; Maldague, Xavier P.

2009-05-01

The article aims first to present a new study on the thermal regulatory response of the human skin surface while exposed to a cold environment. Our work has shown that when a cold stress is applied to the left hand, thermal infrared imaging (MWIR spectral band: 3-5 μm) allows a clear observation of a temperature rise on the right hand. Moreover, a frequency analysis was also carried out upon selected vein pixels of the images monitored during the same cold stress experiment. The objective was to identify the specific frequencies that could be linked to some physiological mechanisms of the human body. This kind of study could be very useful for the characterization of possible thermo-physiological pathologies. Besides thermoregulation, we also present in this article some results on the extraction of the hand vein pattern. Firstly, we show some vein extraction results obtained after image processing of the thermal images recorded in the thermal band (MWIR), then we compare this vein pattern to the signature obtained with a camera operating in the NIR spectral band (0.85-1.7 μm). This method could be used as a complementary means for finger print signatures in biometrics.

Electroencephalogram Signatures of Ketamine-Induced Unconsciousness

PubMed Central

Akeju, Oluwaseun; Song, Andrew H.; Hamilos, Allison E.; Pavone, Kara J.; Flores, Francisco J.; Brown, Emery N.; Purdon, Patrick L.

2016-01-01

Objectives Ketamine is an N-methyl-D-aspartate receptor antagonist commonly administered as a general anesthetic. However, circuit level mechanisms to explain ketamine-induced unconsciousness in humans are yet to be clearly defined. Disruption of frontal-parietal network connectivity has been proposed as a mechanism to explain this brain state. However, this mechanism was recently demonstrated at subanesthetic doses of ketamine in awake-patients. Therefore we investigated whether there is an electroencephalogram (EEG) marker for ketamine-induced unconsciousness. Methods We retrospectively studied the EEG in 12 patients who received ketamine for the induction of general anesthesia. We analyzed the EEG dynamics using power spectral and coherence methods. Results Following the administration of a bolus dose of ketamine to induce unconsciousness, we observed a “gamma burst” EEG pattern that consisted of alternating slow-delta (0.1-4 Hz) and gamma (~27-40 Hz) oscillations. This pattern was also associated with increased theta oscillations (~4-8 Hz) and decreased alpha/beta oscillations (~10-24 Hz). Conclusions Ketamine-induced unconsciousness is associated with a gamma burst EEG pattern. Significance We postulate that the gamma burst pattern is a thalamocortical rhythm based on insights previously obtained from cat neurophysiological experiments. This EEG signature of ketamine-induced unconsciousness may offer new insights into general anesthesia induced brain states. PMID:27178861

Security authentication using phase-encoded nanoparticle structures and polarized light.

PubMed

Carnicer, Artur; Hassanfiroozi, Amir; Latorre-Carmona, Pedro; Huang, Yi-Pai; Javidi, Bahram

2015-01-15

Phase-encoded nanostructures such as quick response (QR) codes made of metallic nanoparticles are suggested to be used in security and authentication applications. We present a polarimetric optical method able to authenticate random phase-encoded QR codes. The system is illuminated using polarized light, and the QR code is encoded using a phase-only random mask. Using classification algorithms, it is possible to validate the QR code from the examination of the polarimetric signature of the speckle pattern. We used Kolmogorov-Smirnov statistical test and Support Vector Machine algorithms to authenticate the phase-encoded QR codes using polarimetric signatures.

Optical implementation of neocognitron and its applications to radar signature discrimination

NASA Technical Reports Server (NTRS)

Chao, Tien-Hsin; Stoner, William W.

1991-01-01

A feature-extraction-based optoelectronic neural network is introduced. The system implementation approach applies the principle of the neocognitron paradigm first introduced by Fukushima et al. (1983). A multichannel correlator is used as a building block of a generic single layer of the neocognitron for shift-invariant feature correlation. Multilayer processing is achieved by iteratively feeding back the output of the feature correlator to the input spatial light modulator. Successful pattern recognition with intraclass fault tolerance and interclass discrimination is achieved using this optoelectronic neocognitron. Detailed system analysis is described. Experimental demonstration of radar signature processing is also provided.

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures

PubMed Central

Shiraishi, Yuichi; Tremmel, Georg; Miyano, Satoru; Stephens, Matthew

2015-01-01

Recent advances in sequencing technologies have enabled the production of massive amounts of data on somatic mutations from cancer genomes. These data have led to the detection of characteristic patterns of somatic mutations or “mutation signatures” at an unprecedented resolution, with the potential for new insights into the causes and mechanisms of tumorigenesis. Here we present new methods for modelling, identifying and visualizing such mutation signatures. Our methods greatly simplify mutation signature models compared with existing approaches, reducing the number of parameters by orders of magnitude even while increasing the contextual factors (e.g. the number of flanking bases) that are accounted for. This improves both sensitivity and robustness of inferred signatures. We also provide a new intuitive way to visualize the signatures, analogous to the use of sequence logos to visualize transcription factor binding sites. We illustrate our new method on somatic mutation data from urothelial carcinoma of the upper urinary tract, and a larger dataset from 30 diverse cancer types. The results illustrate several important features of our methods, including the ability of our new visualization tool to clearly highlight the key features of each signature, the improved robustness of signature inferences from small sample sizes, and more detailed inference of signature characteristics such as strand biases and sequence context effects at the base two positions 5′ to the mutated site. The overall framework of our work is based on probabilistic models that are closely connected with “mixed-membership models” which are widely used in population genetic admixture analysis, and in machine learning for document clustering. We argue that recognizing these relationships should help improve understanding of mutation signature extraction problems, and suggests ways to further improve the statistical methods. Our methods are implemented in an R package pmsignature (https://github.com/friend1ws/pmsignature) and a web application available at https://friend1ws.shinyapps.io/pmsignature_shiny/. PMID:26630308

KM3NeT/ORCA status and plans

NASA Astrophysics Data System (ADS)

Samtleben, Dorothea F. E.

2016-04-01

Neutrinos created in interactions of cosmic rays with the atmosphere can serve as a powerful tool to unveil the neutrino mass hierarchy (NMH). At low energies, around a few GeV, matter effects from the transition through the Earth are expected to imprint a distinct but also subtle signature on the oscillation pattern, specific to the ordering of the neutrino masses. KM3NeT/ORCA (Oscillations Research with Cosmics in the Abyss), a densely instrumented building block of the upcoming KM3NeT neutrino telescope, will be designated to measuring this signature in the Mediterranean Sea. Using detailed simulations the sensitivity towards this signature has been evaluated. The multi-PMT detectors allow in the water for an accurate reconstruction of GeV neutrino event signatures and distinction of neutrino flavours. For the determination of the mass hierarchy a median significance of 2-6σ has been estimated for three years of data taking, depending on the actual hierarchy and the oscillation parameters. At the same time the values of several oscillation parameters like θ23 will be determined to unprecedented precision.

Microbes: Agents of Isotopic Change

NASA Astrophysics Data System (ADS)

Fogel, M. L.

2012-12-01

Microbes drive many of the important oxidation and reduction reactions on Earth; digest almost all forms of organic matter; and can serve as both primary and secondary producers. Because of their versatile biochemistry and physiology, they impart unique isotopic signatures to organic and inorganic materials, which have proven to be key measurements for understanding elemental cycling now and throughout Earth's history. Understanding microbial isotope fractionations in laboratory experiments has been important for interpreting isotopic patterns measured in natural settings. In fact, the pairing of simple experiment with natural observation has been the pathway for interpreting the fingerprint of microbial processes in ancient sediments and rocks. Examples of how key experiments have explained stable isotope fractionations by microbes and advanced the field of microbial ecology will be presented. Learning the isotopic signatures of Earth's microbes is a valuable exercise for predicting what isotopic signatures could be displayed by possible extant or extinct extraterrestrial life. Given the potential for discovery on Mars, Enceladus, and other solar system bodies, new methods and techniques for pinpointing what is unique about microbial isotope signatures is particularly relevant.

Disaster relief through composite signatures

NASA Astrophysics Data System (ADS)

Hawley, Chadwick T.; Hyde, Brian; Carpenter, Tom; Nichols, Steve

2012-06-01

A composite signature is a group of signatures that are related in such a way to more completely or further define a target or operational endeavor at a higher fidelity. This paper builds on previous work developing innovative composite signatures associated with civil disasters, including physical, chemical and pattern/behavioral. For the composite signature approach to be successful it requires effective data fusion and visualization. This plays a key role in both preparedness and the response and recovery which are critical to saving lives. Visualization tools enhance the overall understanding of the crisis by pulling together and analyzing the data, and providing a clear and complete analysis of the information to the organizations/agencies dependant on it for a successful operation. An example of this, Freedom Web, is an easy-to-use data visualization and collaboration solution for use in homeland security, emergency preparedness, situational awareness, and event management. The solution provides a nationwide common operating picture for all levels of government through a web based, map interface. The tool was designed to be utilized by non-geospatial experts and is easily tailored to the specific needs of the users. Consisting of standard COTS and open source databases and a web server, users can view, edit, share, and highlight information easily and quickly through a standard internet browser.

Pattern recognition monitoring of PEM fuel cell

DOEpatents

Meltser, M.A.

1999-08-31

The CO-concentration in the H{sub 2} feed stream to a PEM fuel cell stack is monitored by measuring current and voltage behavior patterns from an auxiliary cell attached to the end of the stack. The auxiliary cell is connected to the same oxygen and hydrogen feed manifolds that supply the stack, and discharges through a constant load. Pattern recognition software compares the current and voltage patterns from the auxiliary cell to current and voltage signature determined from a reference cell similar to the auxiliary cell and operated under controlled conditions over a wide range of CO-concentrations in the H{sub 2} fuel stream. 4 figs.

Pattern recognition monitoring of PEM fuel cell

DOEpatents

Meltser, Mark Alexander

1999-01-01

The CO-concentration in the H.sub.2 feed stream to a PEM fuel cell stack is monitored by measuring current and voltage behavior patterns from an auxiliary cell attached to the end of the stack. The auxiliary cell is connected to the same oxygen and hydrogen feed manifolds that supply the stack, and discharges through a constant load. Pattern recognition software compares the current and voltage patterns from the auxiliary cell to current and voltage signature determined from a reference cell similar to the auxiliary cell and operated under controlled conditions over a wide range of CO-concentrations in the H.sub.2 fuel stream.

Genome-wide signals of positive selection in human evolution

PubMed Central

Enard, David; Messer, Philipp W.; Petrov, Dmitri A.

2014-01-01

The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci, and the genome-wide patterns of polymorphism show signatures consistent with frequent positive selection. On the other hand, recent studies have argued that many of the candidate loci are false positives and that most genome-wide signatures of adaptation are in fact due to reduction of neutral diversity by linked deleterious mutations, known as background selection. Here we analyze human polymorphism data from the 1000 Genomes Project and detect signatures of positive selection once we correct for the effects of background selection. We show that levels of neutral polymorphism are lower near amino acid substitutions, with the strongest reduction observed specifically near functionally consequential amino acid substitutions. Furthermore, amino acid substitutions are associated with signatures of recent adaptation that should not be generated by background selection, such as unusually long and frequent haplotypes and specific distortions in the site frequency spectrum. We use forward simulations to argue that the observed signatures require a high rate of strongly adaptive substitutions near amino acid changes. We further demonstrate that the observed signatures of positive selection correlate better with the presence of regulatory sequences, as predicted by the ENCODE Project Consortium, than with the positions of amino acid substitutions. Our results suggest that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson that adaptive divergence is primarily driven by regulatory changes. PMID:24619126

EEG signatures of arm isometric exertions in preparation, planning and execution.

PubMed

Nasseroleslami, Bahman; Lakany, Heba; Conway, Bernard A

2014-04-15

The electroencephalographic (EEG) activity patterns in humans during motor behaviour provide insight into normal motor control processes and for diagnostic and rehabilitation applications. While the patterns preceding brisk voluntary movements, and especially movement execution, are well described, there are few EEG studies that address the cortical activation patterns seen in isometric exertions and their planning. In this paper, we report on time and time-frequency EEG signatures in experiments in normal subjects (n=8), using multichannel EEG during motor preparation, planning and execution of directional centre-out arm isometric exertions performed at the wrist in the horizontal plane, in response to instruction-delay visual cues. Our observations suggest that isometric force exertions are accompanied by transient and sustained event-related potentials (ERP) and event-related (de-)synchronisations (ERD/ERS), comparable to those of a movement task. Furthermore, the ERPs and ERD/ERS are also observed during preparation and planning of the isometric task. Comparison of ear-lobe-referenced and surface Laplacian ERPs indicates the contribution of superficial sources in supplementary and pre-motor (FC(z)), parietal (CP(z)) and primary motor cortical areas (C₁ and FC₁) to ERPs (primarily negative peaks in frontal and positive peaks in parietal areas), but contribution of deep sources to sustained time-domain potentials (negativity in planning and positivity in execution). Transient and sustained ERD patterns in μ and β frequency bands of ear-lobe-referenced and surface Laplacian EEG indicate the contribution of both superficial and deep sources to ERD/ERS. As no physical displacement happens during the task, we can infer that the underlying mechanisms of motor-related ERPs and ERD/ERS patterns do not only depend on change in limb coordinate or muscle-length-dependent ascending sensory information and are primary generated by motor preparation, direction-dependent planning and execution of isometric motor tasks. The results contribute to our understanding of the functions of different brain regions during voluntary motor tasks and their activity signatures in EEG can shed light on the relationships between large-scale recordings such as EEG and other recordings such as single unit activity and fMRI in this context. Copyright © 2013 Elsevier Inc. All rights reserved.

Particle-in-cell simulations of asymmetric guide-field reconnection: quadrupolar structure of Hall magnetic field

NASA Astrophysics Data System (ADS)

Schmitz, R. G.; Alves, M. V.; Barbosa, M. V. G.

2017-12-01

One of the most important processes that occurs in Earth's magnetosphere is known as magnetic reconnection (MR). This process can be symmetric or asymmetric, depending basically on the plasma density and magnetic field in both sides of the current sheet. A good example of symmetric reconnection in terrestrial magnetosphere occurs in the magnetotail, where these quantities are similar on the north and south lobes. In the dayside magnetopause MR is asymmetric, since the plasma regimes and magnetic fields of magnetosheath and magnetosphere are quite different. Symmetric reconnection has some unique signatures. For example, the formation of a quadrupolar structure of Hall magnetic field and a bipolar Hall electric field that points to the center of the current sheet. The different particle motions in the presence of asymmetries change these signatures, causing the quadrupolar pattern to be distorted and forming a bipolar structure. Also, the bipolar Hall electric field is modified and gives rise to a single peak pointing toward the magnetosheat, considering an example of magnetopause reconnection. The presence of a guide-field can also distort the quadrupolar pattern, by giving a shear angle across the current sheet and altering the symmetric patterns, according to previous simulations and observations. Recently, a quadrupolar structure was observed in an asymmetric guide-field MR event using MMS (Magnetospheric Multiscale) mission data [Peng et al., JGR, 2017]. This event shows clearly that the density asymmetry and the guide-field were not sufficient to form signatures of asymmetric reconnection. Using the particle-in-cell code iPIC3D [Markidis et al, Mathematics and Computers in Simulation, 2010] with the MMS data from this event used to define input parameters, we found a quadrupolar structure of Hall magnetic field and a bipolar pattern of Hall electric field in ion scales, showing that our results are in an excellent agreement with the MMS observations. To our knowledge, this is the first time PIC simulations show this kind of results, since previous simulations have predicted bipolar pattern in the asymmetric guide-field reconnection.

Geodynamic implications for zonal and meridional isotopic patterns across the northern Lau and North Fiji Basins

NASA Astrophysics Data System (ADS)

Price, Allison A.; Jackson, Matthew G.; Blichert-Toft, Janne; Kurz, Mark D.; Gill, Jim; Blusztajn, Jerzy; Jenner, Frances; Brens, Raul; Arculus, Richard

2017-03-01

We present new Sr-Nd-Pb-Hf-He isotopic data for 65 volcanic samples from the northern Lau and North Fiji Basins. This includes 47 lavas obtained from 40 dredge sites spanning an east-west transect across the Lau and North Fiji basins, 10 ocean island basalt (OIB)-type lavas collected from seven Fijian islands, and eight OIB lavas sampled on Rotuma. For the first time, we are able to map clear north-south and east-west geochemical gradients in 87Sr/86Sr across the northern Lau and North Fiji Basins: lavas with the most geochemically enriched radiogenic isotopic signatures are located in the northeast Lau Basin, while signatures of geochemical enrichment are diminished to the south and west away from the Samoan hot spot. Based on these geochemical patterns and plate reconstructions of the region, these observations are best explained by the addition of Samoa, Rurutu, and Rarotonga hot spot material over the past 4 Ma. We suggest that underplated Samoan material has been advected into the Lau Basin over the past ˜4 Ma. As the slab migrated west (and toward the Samoan plume) via rollback over time, younger and hotter (and therefore less viscous) underplated Samoan plume material was entrained. Thus, entrainment efficiency of underplated plume material was enhanced, and Samoan plume signatures in the Lau Basin became stronger as the trench approached the Samoan hot spot. The addition of subducted volcanoes from the Cook-Austral Volcanic Lineament first from the Rarotonga hot spot, then followed by the Rurutu hot spot, contributes to the extreme geochemical signatures observed in the northeast Lau Basin.

The role of parasite-driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica).

PubMed

Wenzel, Marius A; Douglas, Alex; James, Marianne C; Redpath, Steve M; Piertney, Stuart B

2016-01-01

Landscape genomics promises to provide novel insights into how neutral and adaptive processes shape genome-wide variation within and among populations. However, there has been little emphasis on examining whether individual-based phenotype-genotype relationships derived from approaches such as genome-wide association (GWAS) manifest themselves as a population-level signature of selection in a landscape context. The two may prove irreconcilable as individual-level patterns become diluted by high levels of gene flow and complex phenotypic or environmental heterogeneity. We illustrate this issue with a case study that examines the role of the highly prevalent gastrointestinal nematode Trichostrongylus tenuis in shaping genomic signatures of selection in red grouse (Lagopus lagopus scotica). Individual-level GWAS involving 384 SNPs has previously identified five SNPs that explain variation in T. tenuis burden. Here, we examine whether these same SNPs display population-level relationships between T. tenuis burden and genetic structure across a small-scale landscape of 21 sites with heterogeneous parasite pressure. Moreover, we identify adaptive SNPs showing signatures of directional selection using F(ST) outlier analysis and relate population- and individual-level patterns of multilocus neutral and adaptive genetic structure to T. tenuis burden. The five candidate SNPs for parasite-driven selection were neither associated with T. tenuis burden on a population level, nor under directional selection. Similarly, there was no evidence of parasite-driven selection in SNPs identified as candidates for directional selection. We discuss these results in the context of red grouse ecology and highlight the broader consequences for the utility of landscape genomics approaches for identifying signatures of selection. © 2015 John Wiley & Sons Ltd.

Microarray-based gene expression profiling in patients with cryopyrin-associated periodic syndromes defines a disease-related signature and IL-1-responsive transcripts.

PubMed

Balow, James E; Ryan, John G; Chae, Jae Jin; Booty, Matthew G; Bulua, Ariel; Stone, Deborah; Sun, Hong-Wei; Greene, James; Barham, Beverly; Goldbach-Mansky, Raphaela; Kastner, Daniel L; Aksentijevich, Ivona

2013-06-01

To analyse gene expression patterns and to define a specific gene expression signature in patients with the severe end of the spectrum of cryopyrin-associated periodic syndromes (CAPS). The molecular consequences of interleukin 1 inhibition were examined by comparing gene expression patterns in 16 CAPS patients before and after treatment with anakinra. We collected peripheral blood mononuclear cells from 22 CAPS patients with active disease and from 14 healthy children. Transcripts that passed stringent filtering criteria (p values≤false discovery rate 1%) were considered as differentially expressed genes (DEG). A set of DEG was validated by quantitative reverse transcription PCR and functional studies with primary cells from CAPS patients and healthy controls. We used 17 CAPS and 66 non-CAPS patient samples to create a set of gene expression models that differentiates CAPS patients from controls and from patients with other autoinflammatory conditions. Many DEG include transcripts related to the regulation of innate and adaptive immune responses, oxidative stress, cell death, cell adhesion and motility. A set of gene expression-based models comprising the CAPS-specific gene expression signature correctly classified all 17 samples from an independent dataset. This classifier also correctly identified 15 of 16 post-anakinra CAPS samples despite the fact that these CAPS patients were in clinical remission. We identified a gene expression signature that clearly distinguished CAPS patients from controls. A number of DEG were in common with other systemic inflammatory diseases such as systemic onset juvenile idiopathic arthritis. The CAPS-specific gene expression classifiers also suggest incomplete suppression of inflammation at low doses of anakinra.

Microarray-based gene expression profiling in patients with cryopyrin-associated periodic syndromes defines a disease-related signature and IL-1-responsive transcripts

PubMed Central

Balow, James E; Ryan, John G; Chae, Jae Jin; Booty, Matthew G; Bulua, Ariel; Stone, Deborah; Sun, Hong-Wei; Greene, James; Barham, Beverly; Goldbach-Mansky, Raphaela; Kastner, Daniel L; Aksentijevich, Ivona

2014-01-01

Objective To analyse gene expression patterns and to define a specific gene expression signature in patients with the severe end of the spectrum of cryopyrin-associated periodic syndromes (CAPS). The molecular consequences of interleukin 1 inhibition were examined by comparing gene expression patterns in 16 CAPS patients before and after treatment with anakinra. Methods We collected peripheral blood mononuclear cells from 22 CAPS patients with active disease and from 14 healthy children. Transcripts that passed stringent filtering criteria (p values ≤ false discovery rate 1%) were considered as differentially expressed genes (DEG). A set of DEG was validated by quantitative reverse transcription PCR and functional studies with primary cells from CAPS patients and healthy controls. We used 17 CAPS and 66 non-CAPS patient samples to create a set of gene expression models that differentiates CAPS patients from controls and from patients with other autoinflammatory conditions. Results Many DEG include transcripts related to the regulation of innate and adaptive immune responses, oxidative stress, cell death, cell adhesion and motility. A set of gene expression-based models comprising the CAPS-specific gene expression signature correctly classified all 17 samples from an independent dataset. This classifier also correctly identified 15 of 16 postanakinra CAPS samples despite the fact that these CAPS patients were in clinical remission. Conclusions We identified a gene expression signature that clearly distinguished CAPS patients from controls. A number of DEG were in common with other systemic inflammatory diseases such as systemic onset juvenile idiopathic arthritis. The CAPS-specific gene expression classifiers also suggest incomplete suppression of inflammation at low doses of anakinra. PMID:23223423

Stable isotope patterns in micronekton from the Mozambique Channel

NASA Astrophysics Data System (ADS)

Ménard, Frédéric; Benivary, Hermann Doris; Bodin, Nathalie; Coffineau, Nathalie; Le Loc'h, François; Mison, Thomas; Richard, Pierre; Potier, Michel

2014-02-01

We measured the stable carbon (δ13C) and nitrogen (δ15N) isotopic composition of tissues of micronektonic organisms (fishes, squids, crustaceans and gelatinous organisms) collected in the Mozambique Channel during two scientific cruises in 2008 and 2009. The oceanic circulation in the Mozambique Channel is dominated by mesoscale cyclonic and anticyclonic eddies which play a key role in biological processes of less-productive deep-sea ecosystems. We investigated the potential impact of mesoscale features on the δ13C and δ15N values of 32 taxa of micronekton. Fishes, squids, crustaceans and gelatinous organisms encompassed a wide range of isotopic niches, with large overlaps among species. Our results showed that mesoscale features did not really influence the isotopic signatures of the sampled organisms, although cyclonic eddies can occasionally impact the nitrogen signatures of micronekton. We show that δ13C values were intermediate between standard offshore and nearshore signatures, suggesting that pelagic production in the Mozambique Channel could be partly supported by the transport and export of inorganic and organic particles from the Mozambican coast toward the offshore area. Trophic levels calculated from δ15N values ranged from 2.6 to 4.2, showing that micronekton taxa can be tertiary consumers in the Mozambique Channel. Our findings evidenced clusters of micronektonic organisms according to their δ15N or δ13C isotopic signatures, but variations in stable isotope values reflect a complex set of embedded processes linked to physical mesoscale dynamics (rotational dynamics of eddies) and basic biology and ecology of micronektonic organisms (vertical habitat, migration pattern, dietary habits, body length) that are discussed with regard to the stable isotope method based on time-integrated assimilated food.

Complex Pattern of Resistance-Associated Substitutions of Hepatitis C Virus after Daclatasvir/Asunaprevir Treatment Failure

PubMed Central

Hasebe, Chitomi; Osaki, Yukio; Joko, Kouji; Yagisawa, Hitoshi; Sakita, Shinya; Okushin, Hiroaki; Satou, Takashi; Hisai, Hiroyuki; Abe, Takehiko; Tsuji, Keiji; Tamada, Takashi; Kobashi, Haruhiko; Mitsuda, Akeri; Ide, Yasushi; Ogawa, Chikara; Tsuruta, Syotaro; Takaguchi, Kouichi; Murakawa, Miyako; Asahina, Yasuhiro; Enomoto, Nobuyuki; Izumi, Namiki

2016-01-01

Backgrounds & Aims We aimed to clarify the characteristics of resistance-associated substitutions (RASs) after treatment failure with NS5A inhibitor, daclatasvir (DCV) in combination with NS3/4A inhibitor, asunaprevir (ASV), in patients with chronic hepatitis C virus genotype 1b infection. Methods This is a nationwide multicenter study conducted by the Japanese Red Cross Liver Study Group. The sera were obtained from 68 patients with virological failure after 24 weeks of DCV/ASV treatment. RASs in NS5A and NS3 were determined by population sequencing. Results The frequency of signature RASs at position D168 of NS3 was 68%, and at positions L31 and Y93 of NS5A was 79 and 76%, respectively. The frequency of dual signature RASs in NS5A (L31-RAS and Y93-RAS) was 63%. RASs at L28, R30, P32, Q54, P58, and A92 in addition to dual signature RAS were detected in 5, 5, 1, 22, 2, and 0 patients, respectively. In total, triple, quadruple, and quintuple RASs in combination with dual signature RAS were detected in 35, 10, and 1.5% patients, respectively. These RASs were detected in patients without baseline RASs or who prematurely discontinued therapy. Co-existence of D168 RAS in NS3 and L31 and/or Y93 RAS in NS5A was observed in 62% of patients. Conclusion Treatment-emergent RASs after failure with DCV/ASV combination therapy are highly complex in more than 50% of the patients. The identification of complex RAS patterns, which may indicate high levels of resistance to NS5A inhibitors, highlights the need for RAS sequencing when considering re-treatment with regimens including NS5A inhibitors. PMID:27776192

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.

PubMed

Hanghøj, Kristian; Seguin-Orlando, Andaine; Schubert, Mikkel; Madsen, Tobias; Pedersen, Jakob Skou; Willerslev, Eske; Orlando, Ludovic

2016-12-01

The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Th-2 signature in chronic airway diseases: towards the extinction of asthma-COPD overlap syndrome?

PubMed

Cosío, Borja G; Pérez de Llano, Luis; Lopez Viña, Antolin; Torrego, Alfons; Lopez-Campos, Jose Luis; Soriano, Joan B; Martinez Moragon, Eva; Izquierdo, Jose Luis; Bobolea, Irina; Callejas, Javier; Plaza, Vicente; Miravitlles, Marc; Soler-Catalunya, Juan Jose

2017-05-01

We aimed to describe the differences and similarities between patients with chronic obstructive airway disease classified on the basis of classical diagnostic labels (asthma, chronic obstructive pulmonary disease (COPD), or asthma-COPD overlap (ACOS)) or according to the underlying inflammatory pattern (Th-2 signature, either Th-2-high or Th-2-low).We performed a cross-sectional study of patients aged ≥40 years and with a post-bronchodilator forced expiratory volume in 1 s to forced vital capacity ratio ≤0.7 with a previous diagnosis of asthma (non-smoking asthmatics (NSA)), COPD or ACOS, the latter including both smoking asthmatics (SA) and patients with eosinophilic COPD (COPD-e). Clinical, functional and inflammatory parameters (blood eosinophil count, IgE and exhaled nitric oxide fraction ( F eNO )) were compared between groups. Th-2 signature was defined by a blood eosinophil count ≥300 cells·μL -1 and/or a sputum eosinophil count ≥3%.Overall, 292 patients were included in the study: 89 with COPD, 94 NSA and 109 with ACOS (44 SA and 65 with COPD-e). No differences in symptoms or exacerbation rate were found between the three groups. With regards the underlying inflammatory pattern, 94 patients (32.2%) were characterised as Th-2-high and 198 (67.8%) as Th-2-low. The Th-2 signature was found in 49% of NSA, 3.3% of patients with COPD, 30% of SA and 49.3% of patients with COPD-e. This classification yielded significant differences in demographic, functional and inflammatory characteristics.We conclude that a classification based upon the inflammatory profile, irrespective of the taxonomy, provides a more clear distinction of patients with chronic obstructive airway disease. Copyright ©ERS 2017.

Patterns of larval source distribution and mixing in early life stages of Pacific cod (Gadus macrocephalus) in the southeastern Bering Sea

NASA Astrophysics Data System (ADS)

Miller, Jessica A.; DiMaria, Ruth A.; Hurst, Thomas P.

2016-12-01

Effective and sustainable management depends on knowledge of spawning locations and their relative contributions to marine fish populations. Pacific cod (Gadus macrocephalus) in the southeastern Bering Sea aggregate at discrete spawning locations but there is little information on patterns of larval dispersal and the relative contribution of specific spawning areas to nursery habitats. Age-0 Pacific cod from two cohorts (2006 and 2008) were examined to address the following questions: (1) does size, age, and otolith chemistry vary among known capture locations; (2) can variation in elemental composition of the otolith cores (early larval signatures) be used to infer the number of chemically distinct sources contributing to juvenile recruits in the Bering Sea; and (3) to what extent are juvenile collection locations represented by groups of fish with similar chemical histories throughout their early life history? Hierarchical cluster (HCA) and discriminant function analyses (DFA) were used to examine variation in otolith chemistry at discrete periods throughout the early life history. HCA identified five chemically distinct groups of larvae in the 2006 cohort and three groups in 2008; however, three sources accounted for 80-100% of the juveniles in each year. DFA of early larval signatures indicated that there were non-random spatial distributions of early larvae in both years, which may reflect interannual variation in regional oceanography. There was also a detectable and substantial level of coherence in chemical signatures within groups of fish throughout the early life history. The variation in elemental signatures throughout the early life history (hatch to capture) indicates that otolith chemical analysis could be an effective tool to further clarify larval sources and dispersal, identify juvenile nursery habitats, and estimate the contributions of juvenile nursery habitats to the adult population within the southeastern Bering Sea.

Comparing spatial and temporal patterns of river water isotopes across networks

EPA Science Inventory

A detailed understanding of the spatial and temporal dynamics of water sources across river networks is central to managing the impacts of climate change. Because the stable isotope composition of precipitation varies geographically, variation in surface-water isotope signatures ...

Higher Order Crossings from a Parametric Family of Linear Filters

DTIC Science & Technology

1989-09-01

ultrasound echo signatures obtained from bonded aluminum specimens that underwent different surface treatment prior to bonding. To measure de- viation from...feature of their adaptation to aquatic existence (Schevill and Watkins (1962).) Tracking and identification of distinctive whistle patterns of whales

Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses

PubMed Central

Castel, Guillaume; Razzauti, Maria; Jousselin, Emmanuelle; Kergoat, Gael J.; Cosson, Jean-François

2014-01-01

In the last 50 years, hantaviruses have significantly affected public health worldwide, but the exact extent of the distribution of hantavirus diseases, species and lineages and the risk of their emergence into new geographic areas are still poorly known. In particular, the determinants of molecular evolution of hantaviruses circulating in different geographical areas or different host species are poorly documented. Yet, this understanding is essential for the establishment of more accurate scenarios of hantavirus emergence under different climatic and environmental constraints. In this study, we focused on Murinae-associated hantaviruses (mainly Seoul Dobrava and Hantaan virus) using sequences available in GenBank and conducted several complementary phylogenetic inferences. We sought for signatures of selection and changes in patterns and rates of diversification in order to characterize hantaviruses’ molecular evolution at different geographical scales (global and local). We then investigated whether these events were localized in particular geographic areas. Our phylogenetic analyses supported the assumption that RNA virus molecular variations were under strong evolutionary constraints and revealed changes in patterns of diversification during the evolutionary history of hantaviruses. These analyses provide new knowledge on the molecular evolution of hantaviruses at different scales of time and space. PMID:24618811

A Review of Pacific Interdecadal Climate Variability: Possible Mechanisms and Surface Climate Signatures in the Pacific Sector

NASA Astrophysics Data System (ADS)

Mantua, N. J.

2004-12-01

Many investigators have examined historical surface climate records from the Pacific sector and identified a relatively small number of spatial patterns varying at decadal to interdecadal time scales. "Pacific Decadal Variability" (PDV) is a label that has been used to describe this family of climate variations. Some patterns of PDV are contained completely within the northern extratropics, while others have signatures throughout the Pacific hemisphere on both sides of the equator. Mechanisms for observed patterns of PDV are not yet known, though a wide variety of hypotheses have been proposed. Various ocean-atmosphere mechanisms for PDV are contained within the extratropics, others within the tropics, while others involve tropical-extratropical interactions. Some investigators have proposed external forcing (solar, lunar, or volcanic) as potentially important for driving PDV. A relatively simple hypothesis couples ENSO forcing with upper ocean heat storage for extratropical PDV, and it suggests PDV predictability may be limited to ~2 year lead times. Paleo-PDV reconstructions have been based on materials throughout the Pacific sector using such things as extratropical tree-rings, tropical corals, extratropical clam shell growth rings, and ice cores. These different proxy records have generally provided different perspectives on paleo-PDV behavior.

Ionospheric convection signatures observed by DE 2 during northward interplanetary magnetic field

NASA Technical Reports Server (NTRS)

Heelis, R. A.; Hanson, W. B.; Reiff, P. H.; Winningham, J. D.

1986-01-01

Observations of the ionospheric convection signature at high latitudes are examined during periods of prolonged northward interplanetary magnetic field (IMF). The data from Dynamics Explorer 2 show that a four-cell convection pattern can frequently be observed in a region that is displaced to the sunward side of the dawn-dusk meridian regardless of season. In the eclipsed ionosphere, extremely structured or turbulent flow exists with no identifiable connection to a more coherent pattern that may simultaneously exist in the dayside region. The two highest-latitude convection cells that form part of the coherent dayside pattern show a dependence on the y component of the IMF. This dependence is such that a clockwise circulating cell displaced toward dawn dominates the high-latitude region when B(Y) is positive. Anti-clockwise circulation displaced toward dusk dominates the highest latitudes when B(Y) is negative. Examination of the simultaneously observed energetic particle environment suggests that both open and closed field lines may be associated with the high-latitude convection cells. On occasions these entire cells can exist on open field lines. The existence of closed field lines in regions of sunward flow is also apparent in the data.

Individuality embedded in the isolation calls of captive beluga whales (Delphinapterus leucas).

PubMed

Mishima, Yuka; Morisaka, Tadamichi; Itoh, Miho; Matsuo, Ikuo; Sakaguchi, Aiko; Miyamoto, Yoshinori

2015-01-01

Species with fission-fusion social systems tend to exchange individualized contact calls to maintain group cohesion. Signature whistles by bottlenose dolphins are unique compared to the contact calls of other non-human animals in that they include identity information independent of voice cues. Further, dolphins copy the signatures of conspecifics and use them to label specific individuals. Increasing our knowledge of the contact calls of other cetaceans that have a fluid social structure may thus help us better understand the evolutionary and adaptive significance of all forms of individually distinctive calls. It was recently reported that one type of broadband pulsed sounds (PS1), rather than whistles, may function as individualized contact calls in captive belugas. The objective of this study was to assess the function and individual distinctiveness of PS1 calls in an isolation context. Recordings were made from five captive belugas, including both sexes and various ages. PS1 was the predominant call type (38 % in total) out of five broader sound categories. One sub-adult and three adults had individually distinctive and stereotyped pulse repetition pattern in PS1; one calf showed no clear stereotyped pulse repetition pattern. While visual inspection of the PS1 power spectra uncovered no apparent individual specificity, statistical analyses revealed that both temporal and spectral parameters had inter-individual differences and that there was greater inter-individual than intra-individual variability. Discriminant function analysis based on five temporal and spectral parameters classified PS1 calls into individuals with an overall correct classification rate of 80.5 %, and the most informative parameter was the average Inter-pulse interval, followed by peak frequency. These results suggest that belugas use individually distinctive contact calls in an isolation context. If belugas encode signature information in PS1 calls, as seen in bottlenose dolphins, the pulse repetition pattern may be the carrier, as it is individually stereotyped and appears to require vocal development. This idea is supported by the finding that the average inter-pulse interval is the most powerful discriminator in discriminant analysis. Playback experiments will elucidate which parameters are perceived as individual characteristics, and whether one of the parameters functions as a signature.

Electromagnetic signatures of the preclinical and prodromal stages of Alzheimer's disease.

PubMed

Nakamura, Akinori; Cuesta, Pablo; Fernández, Alberto; Arahata, Yutaka; Iwata, Kaori; Kuratsubo, Izumi; Bundo, Masahiko; Hattori, Hideyuki; Sakurai, Takashi; Fukuda, Koji; Washimi, Yukihiko; Endo, Hidetoshi; Takeda, Akinori; Diers, Kersten; Bajo, Ricardo; Maestú, Fernando; Ito, Kengo; Kato, Takashi

2018-05-01

Biomarkers useful for the predementia stages of Alzheimer's disease are needed. Electroencephalography and magnetoencephalography (MEG) are expected to provide potential biomarker candidates for evaluating the predementia stages of Alzheimer's disease. However, the physiological relevance of EEG/MEG signal changes and their role in pathophysiological processes such as amyloid-β deposition and neurodegeneration need to be elucidated. We evaluated 28 individuals with mild cognitive impairment and 38 cognitively normal individuals, all of whom were further classified into amyloid-β-positive mild cognitive impairment (n = 17, mean age 74.7 ± 5.4 years, nine males), amyloid-β-negative mild cognitive impairment (n = 11, mean age 73.8 ± 8.8 years, eight males), amyloid-β-positive cognitively normal (n = 13, mean age 71.8 ± 4.4 years, seven males), and amyloid-β-negative cognitively normal (n = 25, mean age 72.5 ± 3.4 years, 11 males) individuals using Pittsburgh compound B-PET. We measured resting state MEG for 5 min with the eyes closed, and investigated regional spectral patterns of MEG signals using atlas-based region of interest analysis. Then, the relevance of the regional spectral patterns and their associations with pathophysiological backgrounds were analysed by integrating information from Pittsburgh compound B-PET, fluorodeoxyglucose-PET, structural MRI, and cognitive tests. The results demonstrated that regional spectral patterns of resting state activity could be separated into several types of MEG signatures as follows: (i) the effects of amyloid-β deposition were expressed as the alpha band power augmentation in medial frontal areas; (ii) the delta band power increase in the same region was associated with disease progression within the Alzheimer's disease continuum and was correlated with entorhinal atrophy and an Alzheimer's disease-like regional decrease in glucose metabolism; and (iii) the global theta power augmentation, which was previously considered to be an Alzheimer's disease-related EEG/MEG signature, was associated with general cognitive decline and hippocampal atrophy, but was not specific to Alzheimer's disease because these changes could be observed in the absence of amyloid-β deposition. The results suggest that these MEG signatures may be useful as unique biomarkers for the predementia stages of Alzheimer's disease.

Biofloc technology application in aquaculture to support sustainable development goals.

PubMed

Bossier, Peter; Ekasari, Julie

2017-09-01

Biofloc technology (BFT) application offers benefits in improving aquaculture production that could contribute to the achievement of sustainable development goals. This technology could result in higher productivity with less impact to the environment. Furthermore, biofloc systems may be developed and performed in integration with other food production, thus promoting productive integrated systems, aiming at producing more food and feed from the same area of land with fewer input. The biofloc technology is still in its infant stage. A lot more research is needed to optimise the system (in relation to operational parameters) e.g. in relation to nutrient recycling, MAMP production, immunological effects. In addition research findings will need to be communicated to farmers as the implementation of biofloc technology will require upgrading their skills. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

A solid colorimetric sensor for the analysis of amphetamine-like street samples.

PubMed

Argente-García, A; Jornet-Martínez, N; Herráez-Hernández, R; Campíns-Falcó, P

2016-11-02

A solid sensor obtained by embedding 1,2-naphthoquinone-4-sulfonate (NQS) into polydimethylsiloxane/tetraethylortosilicate/silicon dioxide nanoparticles composite has been developed to identify and determine amphetamine (AMP), methamphetamine (MAMP), 3,4-methylenedioxymetamphetamine (MDMA) and 3,4-methylenedioxyamphetamine (MDA). The analytes are derivatized inside the composite for 10 min to create a colored product which can be then quantified by measuring the diffuse reflectance or the color intensity after processing the digitalized image. Satisfactory limits of detection (0.002-0.005 g mL -1 ) and relative standard deviations (<10%) have been achieved. The proposed kit has been successfully validated and applied to the analysis of amphetamine-like drugs street samples. The kit allows the in-situ screening of the mentioned illicit drugs owing to its simplicity, rapidity and portability, with excellent sensor stability and at a very low-cost. Copyright © 2016 Elsevier B.V. All rights reserved.

Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography.

PubMed

Buzalewicz, Igor; Kujawińska, Małgorzata; Krauze, Wojciech; Podbielska, Halina

2016-01-01

The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH), which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an innovative approach to the subject.

Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography

PubMed Central

Buzalewicz, Igor; Kujawińska, Małgorzata; Krauze, Wojciech; Podbielska, Halina

2016-01-01

The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH), which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an innovative approach to the subject. PMID:26943121

Criticality meets learning: Criticality signatures in a self-organizing recurrent neural network

PubMed Central

Del Papa, Bruno; Priesemann, Viola

2017-01-01

Many experiments have suggested that the brain operates close to a critical state, based on signatures of criticality such as power-law distributed neuronal avalanches. In neural network models, criticality is a dynamical state that maximizes information processing capacities, e.g. sensitivity to input, dynamical range and storage capacity, which makes it a favorable candidate state for brain function. Although models that self-organize towards a critical state have been proposed, the relation between criticality signatures and learning is still unclear. Here, we investigate signatures of criticality in a self-organizing recurrent neural network (SORN). Investigating criticality in the SORN is of particular interest because it has not been developed to show criticality. Instead, the SORN has been shown to exhibit spatio-temporal pattern learning through a combination of neural plasticity mechanisms and it reproduces a number of biological findings on neural variability and the statistics and fluctuations of synaptic efficacies. We show that, after a transient, the SORN spontaneously self-organizes into a dynamical state that shows criticality signatures comparable to those found in experiments. The plasticity mechanisms are necessary to attain that dynamical state, but not to maintain it. Furthermore, onset of external input transiently changes the slope of the avalanche distributions – matching recent experimental findings. Interestingly, the membrane noise level necessary for the occurrence of the criticality signatures reduces the model’s performance in simple learning tasks. Overall, our work shows that the biologically inspired plasticity and homeostasis mechanisms responsible for the SORN’s spatio-temporal learning abilities can give rise to criticality signatures in its activity when driven by random input, but these break down under the structured input of short repeating sequences. PMID:28552964

The Human Airway Epithelial Basal Cell Transcriptome

PubMed Central

Wang, Rui; Zwick, Rachel K.; Ferris, Barbara; Witover, Bradley; Salit, Jacqueline; Crystal, Ronald G.

2011-01-01

Background The human airway epithelium consists of 4 major cell types: ciliated, secretory, columnar and basal cells. During natural turnover and in response to injury, the airway basal cells function as stem/progenitor cells for the other airway cell types. The objective of this study is to better understand human airway epithelial basal cell biology by defining the gene expression signature of this cell population. Methodology/Principal Findings Bronchial brushing was used to obtain airway epithelium from healthy nonsmokers. Microarrays were used to assess the transcriptome of basal cells purified from the airway epithelium in comparison to the transcriptome of the differentiated airway epithelium. This analysis identified the “human airway basal cell signature” as 1,161 unique genes with >5-fold higher expression level in basal cells compared to differentiated epithelium. The basal cell signature was suppressed when the basal cells differentiated into a ciliated airway epithelium in vitro. The basal cell signature displayed overlap with genes expressed in basal-like cells from other human tissues and with that of murine airway basal cells. Consistent with self-modulation as well as signaling to other airway cell types, the human airway basal cell signature was characterized by genes encoding extracellular matrix components, growth factors and growth factor receptors, including genes related to the EGF and VEGF pathways. Interestingly, while the basal cell signature overlaps that of basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels. Conclusion/Significance The human airway epithelial basal cell signature identified in the present study provides novel insights into the molecular phenotype and biology of the stem/progenitor cells of the human airway epithelium. PMID:21572528

Origin of Bermuda's clay-rich Quaternary paleosols and their paleoclimatic significance

USGS Publications Warehouse

Herwitz, S.R.; Muhs, D.R.; Prospero, J.M.; Mahan, S.; Vaughn, B.

1996-01-01

Red clayey paleosols that are chiefly the product of aerosolic dust deposition are interbedded in the Quaternary carbonate formations of the Bermuda oceanic island system. These paleosols provide a basis for reconstructing Quaternary atmospheric circulation patterns in the northwestern Atlantic. Geochemical analyses were performed on representative paleosol samples to identify their parent dust source. Fine-grained fractions were analyzed by energy-dispersive X ray fluorescence to determine trace element (Zr, Y, La, Ti, and Nb) concentrations and to derive geochemical signatures based on immobile element ratios. These ratios were compared with geochemical signatures determined for three possible sources of airborne dust: (1) Great Plains loess, (2) Mississippi River Valley loess, and (3) Saharan dust. The Zr/Y and Zr/La ratios provided the clearest distinction between the hypothesized dust sources. The low ratios in the paleosol B horizons most closely resemble Saharan dust in the <2-??m size class fraction. Contributions from the two North American loessial source areas could not be clearly detected. Thus Bermuda paleosols have a predominantly Saharan aerosolic dust signature. Saharan dust deposition on Bermuda during successive Quaternary glacial periods is consistent with patterns of general circulation models, which indicate that during glacial maxima the northeast summer trade winds were stronger than at present and reached latitudes higher than 30 ?? N despite lower-than-present sea surface temperatures in the North Atlantic.

Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases.

PubMed

Narayanan, Manikandan; Huynh, Jimmy L; Wang, Kai; Yang, Xia; Yoo, Seungyeul; McElwee, Joshua; Zhang, Bin; Zhang, Chunsheng; Lamb, John R; Xie, Tao; Suver, Christine; Molony, Cliona; Melquist, Stacey; Johnson, Andrew D; Fan, Guoping; Stone, David J; Schadt, Eric E; Casaccia, Patrizia; Emilsson, Valur; Zhu, Jun

2014-07-30

Using expression profiles from postmortem prefrontal cortex samples of 624 dementia patients and non-demented controls, we investigated global disruptions in the co-regulation of genes in two neurodegenerative diseases, late-onset Alzheimer's disease (AD) and Huntington's disease (HD). We identified networks of differentially co-expressed (DC) gene pairs that either gained or lost correlation in disease cases relative to the control group, with the former dominant for both AD and HD and both patterns replicating in independent human cohorts of AD and aging. When aligning networks of DC patterns and physical interactions, we identified a 242-gene subnetwork enriched for independent AD/HD signatures. This subnetwork revealed a surprising dichotomy of gained/lost correlations among two inter-connected processes, chromatin organization and neural differentiation, and included DNA methyltransferases, DNMT1 and DNMT3A, of which we predicted the former but not latter as a key regulator. To validate the inter-connection of these two processes and our key regulator prediction, we generated two brain-specific knockout (KO) mice and show that Dnmt1 KO signature significantly overlaps with the subnetwork (P = 3.1 × 10(-12)), while Dnmt3a KO signature does not (P = 0.017). Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

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

Sablock, J.

A trace element signature, a characteristic pattern of enrichment and depletion of trace elements, was determined for a group of siliciclastic-carbonate Oxfordian and Kimmeridgian sedimentary strata, collected from outcrops in western Montana, southeastern British Columbia and southern Alberta. The average values, by petrofacies, of 10 major and 18 trace elements were measured for 40 samples. These data were normalized to Upper Continental Crust (UCC), and plotted against averaged published values of graywackes from the same facies. The rare earth elements (REEs), as well as Ti, Zr, Nb and Y are considered immobile even through diagenesis, and at least low levelmore » metamorphism. So these elements should form a reliable part of the geochemical signature. Compared to UCC and average graywacke, Jurassic samples are very depleted in Zr, Nb and Y. Oxfordian samples have slightly higher rare earth element values, i.e. La, Ce and Nd, than either other Jurassic samples or average graywacke. The most likely source of REE values are garnets and tourmaline which occur as inclusions in monocrystalline quartz grains. This pattern, and petrological study, point to a sedimentary source area, deficient in feldspar, heavy minerals and rock fragments. The consistency of the signature throughout this time may indicate slow uplift of a widespread sedimentary source area, or could be an effect of greater mixing and shorter residence time of dissolved materials in an epeiric sea.« less

Some fundamental concepts in remote sensing

NASA Technical Reports Server (NTRS)

1982-01-01

The term remote sensing is defined as well as ideas such as class, pattern, feature, pattern recognition, feature extraction, and theme. The electromagnetic spectrum is examined especially those wavelength regions available to remote sensing. Relevant energy and wave propagation laws are discussed and the characteristics of emitted and reflected radiation and their detection are investigated. The identification of classes by their spectral signatures, the multispectral approach, and the principal types of sensors and platforms used in remote sensing are also considered.

Silica Retention and Enrichment in Open-System Chemical Weathering on Mars

NASA Technical Reports Server (NTRS)

Yen, A. S.; Ming, D. W.; Gellert, R.; Clark, B. C.; Mittlefehldt, D. W.; Morris, R. V.; Thompson, L. M.; Berger, J.

2015-01-01

Chemical signatures of weathering are evident in the Alpha Particle X-ray Spectrometer (APXS) datasets from Gusev Crater, Meridiani Planum, and Gale Crater. Comparisons across the landing sites show consistent patterns indicating silica retention and/or enrichment in open-system aqueous alteration.

Canonical Genetic Signatures of the Adult Human Brain

PubMed Central

Hawrylycz, Michael; Miller, Jeremy A.; Menon, Vilas; Feng, David; Dolbeare, Tim; Guillozet-Bongaarts, Angela L.; Jegga, Anil G.; Aronow, Bruce J.; Lee, Chang-Kyu; Bernard, Amy; Glasser, Matthew F.; Dierker, Donna L.; Menche, Jörge; Szafer, Aaron; Collman, Forrest; Grange, Pascal; Berman, Kenneth A.; Mihalas, Stefan; Yao, Zizhen; Stewart, Lance; Barabási, Albert-László; Schulkin, Jay; Phillips, John; Ng, Lydia; Dang, Chinh; Haynor, David R.; Jones, Allan; Van Essen, David C.; Koch, Christof; Lein, Ed

2015-01-01

The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure, and function. We applied a correlation-based metric of “differential stability” (DS) to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing meso-scale genetic organization. The highest DS genes are highly biologically relevant, with enrichment for brain-related biological annotations, disease associations, drug targets, and literature citations. Using high DS genes we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components, and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely-patterned genes displayed dramatic shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry. PMID:26571460

A Plastic Temporal Brain Code for Conscious State Generation

PubMed Central

Dresp-Langley, Birgitta; Durup, Jean

2009-01-01

Consciousness is known to be limited in processing capacity and often described in terms of a unique processing stream across a single dimension: time. In this paper, we discuss a purely temporal pattern code, functionally decoupled from spatial signals, for conscious state generation in the brain. Arguments in favour of such a code include Dehaene et al.'s long-distance reverberation postulate, Ramachandran's remapping hypothesis, evidence for a temporal coherence index and coincidence detectors, and Grossberg's Adaptive Resonance Theory. A time-bin resonance model is developed, where temporal signatures of conscious states are generated on the basis of signal reverberation across large distances in highly plastic neural circuits. The temporal signatures are delivered by neural activity patterns which, beyond a certain statistical threshold, activate, maintain, and terminate a conscious brain state like a bar code would activate, maintain, or inactivate the electronic locks of a safe. Such temporal resonance would reflect a higher level of neural processing, independent from sensorial or perceptual brain mechanisms. PMID:19644552

Minimal methylation classifier (MIMIC): A novel method for derivation and rapid diagnostic detection of disease-associated DNA methylation signatures.

PubMed

Schwalbe, E C; Hicks, D; Rafiee, G; Bashton, M; Gohlke, H; Enshaei, A; Potluri, S; Matthiesen, J; Mather, M; Taleongpong, P; Chaston, R; Silmon, A; Curtis, A; Lindsey, J C; Crosier, S; Smith, A J; Goschzik, T; Doz, F; Rutkowski, S; Lannering, B; Pietsch, T; Bailey, S; Williamson, D; Clifford, S C

2017-10-18

Rapid and reliable detection of disease-associated DNA methylation patterns has major potential to advance molecular diagnostics and underpin research investigations. We describe the development and validation of minimal methylation classifier (MIMIC), combining CpG signature design from genome-wide datasets, multiplex-PCR and detection by single-base extension and MALDI-TOF mass spectrometry, in a novel method to assess multi-locus DNA methylation profiles within routine clinically-applicable assays. We illustrate the application of MIMIC to successfully identify the methylation-dependent diagnostic molecular subgroups of medulloblastoma (the most common malignant childhood brain tumour), using scant/low-quality samples remaining from the most recently completed pan-European medulloblastoma clinical trial, refractory to analysis by conventional genome-wide DNA methylation analysis. Using this approach, we identify critical DNA methylation patterns from previously inaccessible cohorts, and reveal novel survival differences between the medulloblastoma disease subgroups with significant potential for clinical exploitation.

Differentiation of bacterial colonies and temporal growth patterns using hyperspectral imaging

NASA Astrophysics Data System (ADS)

Mehrübeoglu, Mehrube; Buck, Gregory W.; Livingston, Daniel W.

2014-09-01

Detection and identification of bacteria are important for health and safety. Hyperspectral imaging offers the potential to capture unique spectral patterns and spatial information from bacteria which can then be used to detect and differentiate bacterial species. Here, hyperspectral imaging has been used to characterize different bacterial colonies and investigate their growth over time. Six bacterial species (Pseudomonas fluorescens, Escherichia coli, Serratia marcescens, Salmonella enterica, Staphylococcus aureus, Enterobacter aerogenes) were grown on tryptic soy agar plates. Hyperspectral data were acquired immediately after, 24 hours after, and 96 hours after incubation. Spectral signatures from bacterial colonies demonstrated repeatable measurements for five out of six species. Spatial variations as well as changes in spectral signatures were observed across temporal measurements within and among species at multiple wavelengths due to strengthening or weakening reflectance signals from growing bacterial colonies based on their pigmentation. Between-class differences and within-class similarities were the most prominent in hyperspectral data collected 96 hours after incubation.

Partial bisulfite conversion for unique template sequencing

PubMed Central

Kumar, Vijay; Rosenbaum, Julie; Wang, Zihua; Forcier, Talitha; Ronemus, Michael; Wigler, Michael

2018-01-01

Abstract We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone. PMID:29161423

The multiscale nature of magnetic pattern on the solar surface

NASA Astrophysics Data System (ADS)

Scardigli, S.; Del Moro, D.; Berrilli, F.

Multiscale magnetic underdense regions (voids) appear in high resolution magnetograms of quiet solar surface. These regions may be considered a signature of the underlying convective structure. The study of the associated pattern paves the way for the study of turbulent convective scales from granular to global. In order to address the question of magnetic pattern driven by turbulent convection we used a novel automatic void detection method to calculate void distributions. The absence of preferred scales of organization in the calculated distributions supports the multiscale nature of flows on the solar surface and the absence of preferred convective scales.

Acute intraperitoneal lipopolysaccharide influences the immune system in the absence of gut dysbiosis.

PubMed

Sylvia, Kristyn E; Demas, Gregory E

2018-03-01

There is bidirectional communication between the immune system and the gut microbiome, however the precise mechanisms regulating this crosstalk are not well understood. Microbial-associated molecular patterns (MAMPs) within the gut, including lipopolysaccharide (LPS) that produces a quick and robust activation of the immune system, may be one way by which these interactions occur. Endogenous levels of LPS in the gut are low enough that they do not usually cause disease, although, in times of increased LPS loads, they may be capable of increasing vulnerability of the gut to pathogenic bacteria. Furthermore, chronic, low-grade inflammation can have lasting effects on the gut, but the effects of acute inflammation on gut communities have not been thoroughly assessed. In this study, we first investigated whether a single modest dose of LPS administered to adult male and female Siberian hamsters (Phodopus sungorus) activated the immune system by measuring levels of circulating cortisol and the proinflammatory cytokine TNF-α in the liver compared with saline-treated animals. We then investigated whether this same acute dose of LPS altered the microbiome 48 h after treatment. We found that, although LPS increased cortisol and liver cytokine levels, and produced changes in food intake and body mass in both sexes, immunological changes were independent of gut dysbiosis 48 h after LPS injection. These data suggest that an acute immune activation may not be capable of altering the gut microbiome in healthy individuals. It is likely, however, that this type of immune challenge may have other physiological impacts on the gut's vulnerability, and future studies will investigate these relationships further. © 2018 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

Identification of lipopolysaccharide-interacting plasma membrane-type proteins in Arabidopsis thaliana.

PubMed

Vilakazi, Cornelius S; Dubery, Ian A; Piater, Lizelle A

2017-02-01

Lipopolysaccharide (LPS) is an amphiphatic bacterial glycoconjugate found on the external membrane of Gram-negative bacteria. This endotoxin is considered as a microbe-associated molecular pattern (MAMP) molecule and has been shown to elicit defense responses in plants. Here, LPS-interacting proteins from Arabidopsis thaliana plasma membrane (PM)-type fractions were captured and identified in order to investigate those involved in LPS perception and linked to triggering of innate immune responses. A novel proteomics-based affinity-capture strategy coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed for the enrichment and identification of LPS-interacting proteins. As such, LPS isolated from Burkholderia cepacia (LPS B.cep. ) was immobilized on three independent and distinct affinity-based matrices to serve as bait for interacting proteins from A. thaliana leaf and callus tissue. These were resolved by 1D electrophoresis and identified by mass spectrometry. Proteins specifically bound to LPS B.cep. have been implicated in membrane structure (e.g. COBRA-like and tubulin proteins), membrane trafficking and/or transport (e.g. soluble NSF attachment protein receptor (SNARE) proteins, patellin, aquaporin, PM instrinsic proteins (PIP) and H + -ATPase), signal transduction (receptor-like kinases and calcium-dependent protein kinases) as well as defense/stress responses (e.g. hypersensitive-induced response (HIR) proteins, jacalin-like lectin domain-containing protein and myrosinase-binding proteins). The novel affinity-capture strategy for the enrichment of LPS-interacting proteins proved to be effective, especially in the binding of proteins involved in plant defense responses, and can thus be used to elucidate LPS-mediated molecular recognition and disease mechanism(s). Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

PubMed Central

2014-01-01

Background Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. Methods By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation. Results For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1. Conclusions The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance. PMID:24592996

Identification of positive selection signatures in pigs by comparing linkage disequilibrium variances.

PubMed

Li, X; Yang, S; Dong, K; Tang, Z; Li, K; Fan, B; Wang, Z; Liu, B

2017-10-01

Selection affects the patterns of linkage disequilibrium (LD) around the site of a beneficial allele with an increase in LD among the hitchhiking alleles. Comparing the differences in regional LD between pig populations could help to identify putative genomic regions with potential adaptations for economic traits. In this study, using Illumina Porcine SNP60K BeadChip genotyping data from 207 Chinese indigenous, 117 South American village and 408 Large White pigs, we estimated the variation of genome-wide LD between populations using the varld program. The top 0.1% standardized VarLD scores were used as a criterion for all comparisons, and compared with LD blocks, a total of four selection signatures on Sus scrofa chromosome (SSC) 7, 9, 13 and 14 were identified in all populations. These signatures overlapped with quantitative trait loci for linoleic acid content, age at puberty, number of muscle fibers per unit area, hip structure and body weight traits in pigs. Among them, one of the signatures (56.5-56.6 Mb on SSC7) in Large White pigs harbored the ADAMTSL3 gene, which is known to affect body length. The findings of this study seem to point toward recent selection in different pig populations. Further investigations are encouraged to confirm the selection signatures detected by varld in the present study. © 2017 Stichting International Foundation for Animal Genetics.

Global simulation of flux transfer events: Generation mechanism and spacecraft signatures

NASA Astrophysics Data System (ADS)

Raeder, J.

We use global MHD simulations of Earth's magnetosphere to show that for southward IMF conditions: a) steady reconnection preferentially occurs without FTEs when the stagnation flow line nearly coincides with the X-line location, which requires small dipole tilt and nearly due southward IMF, b) FTEs occur when the flow/field symmetry is broken, which requires either a large dipole tilt and/or a substantial east-west component of the IMF, c) the predicted spacecraft signature and the repetition frequency of FTEs in the simulations agrees very well with typical observations, lending credibility to the the model, d) the fundamental process that leads to FTE formation is multiple X-line formation caused by the flow and field patterns in the magnetosheath and requires no intrinsic plasma property variations like variable resistivity, e) if the dipole tilt breaks the symmetry FTEs occur only in the winter hemisphere whereas the reconnection signatures in the summer hemisphere are steady with no bipolar FTE-like signatures, f) if the IMF east-west field component breaks the symmetry FTEs occur in both hemispheres but are least likely observed near the subsolar point, and g) FTE formation depends on sufficient resolution and low diffusion in the model. Too coarse resolution and/or too high diffusivity lead to flow-through reconnection signatures that appear unphysical given the frequent observation of FTEs.

Vehicle NOx emission plume isotopic signatures: Spatial variability across the eastern United States

NASA Astrophysics Data System (ADS)

Miller, David J.; Wojtal, Paul K.; Clark, Sydney C.; Hastings, Meredith G.

2017-04-01

On-road vehicle nitrogen oxide (NOx) sources currently dominate the U.S. anthropogenic emission budgets, yet vehicle NOx emissions have uncertain contributions to oxidized nitrogen (N) deposition patterns. Isotopic signatures serve as a potentially valuable observational tool to trace source contributions to NOx chemistry and N deposition, yet in situ emission signatures are underconstrained. We characterize the spatiotemporal variability of vehicle NOx emission isotopic signatures (δ15N-NOx) representative of U.S. vehicle fleet-integrated emission plumes. A novel combination of on-road mobile and stationary urban measurements is performed using a field and laboratory-verified technique for actively capturing NOx in solution to quantify δ15N-NOx at hourly resolution. On-road δ15N-NOx upwind of Providence, RI, ranged from -7 to -3‰. Simultaneous urban background δ15N-NOx observations showed comparable range and variations with on-road measurements, suggesting that vehicles dominate NOx emissions in the Providence area. On-road spatial δ15N-NOx variations of -9 to -2‰ were observed under various driving conditions in six urban metropolitan areas and rural interstate highways during summer and autumn in the U.S. Northeast and Midwest. Although isotopic signatures were insensitive to on-road driving mode variations, statistically significant correlations were found between δ15N-NOx and NOx emission factor extremes associated with heavy diesel emitter contributions. Overall, these results constrain an isotopic signature of fleet-integrated roadway NOx emission plumes, which have important implications for distinguishing vehicle NOx from other sources and tracking emission contributions to NOx chemistry and N deposition.

Preliminary airborne measurements for the SR-71 sonic boom propagation experiment

NASA Technical Reports Server (NTRS)

Haering, Edward A., Jr.; Ehernberger, L. J.; Whitmore, Stephen A.

1995-01-01

SR-71 sonic boom signatures were measured to validate sonic boom propagation prediction codes. An SR-71 aircraft generated sonic booms from Mach 1.25 to Mach 1.6, at altitudes of 31,000 to 48,000 ft, and at various gross weights. An F-16XL aircraft measured the SR-71 near-field shock waves from close to the aircraft to more than 8,000 ft below, gathering 105 signatures. A YO-3A aircraft measured the SR-71 sonic booms from 21,000 to 38,000 feet below, recording 17 passes. The sonic booms at ground level and atmospheric data were recorded for each flight. Data analysis is underway. Preliminary results show that shock wave patterns and coalescence vary with SR-71 gross weight, Mach number, and altitude. For example, noncoalesced shock wave signatures were measured by the YO-3A at 21,000 ft below the SR-71 aircraft while at a low gross weight, Mach 1.25, and 31,000-ft altitude. This paper describes the design and execution of the flight research experiment. Instrumentation and flight maneuvers of the SR-71, F-16XL, and YO-3A aircraft and sample sonic boom signatures are included.

Extraction of human gait signatures: an inverse kinematic approach using Groebner basis theory applied to gait cycle analysis

NASA Astrophysics Data System (ADS)

Barki, Anum; Kendricks, Kimberly; Tuttle, Ronald F.; Bunker, David J.; Borel, Christoph C.

2013-05-01

This research highlights the results obtained from applying the method of inverse kinematics, using Groebner basis theory, to the human gait cycle to extract and identify lower extremity gait signatures. The increased threat from suicide bombers and the force protection issues of today have motivated a team at Air Force Institute of Technology (AFIT) to research pattern recognition in the human gait cycle. The purpose of this research is to identify gait signatures of human subjects and distinguish between subjects carrying a load to those subjects without a load. These signatures were investigated via a model of the lower extremities based on motion capture observations, in particular, foot placement and the joint angles for subjects affected by carrying extra load on the body. The human gait cycle was captured and analyzed using a developed toolkit consisting of an inverse kinematic motion model of the lower extremity and a graphical user interface. Hip, knee, and ankle angles were analyzed to identify gait angle variance and range of motion. Female subjects exhibited the most knee angle variance and produced a proportional correlation between knee flexion and load carriage.

RIDES: Robust Intrusion Detection System for IP-Based Ubiquitous Sensor Networks

PubMed Central

Amin, Syed Obaid; Siddiqui, Muhammad Shoaib; Hong, Choong Seon; Lee, Sungwon

2009-01-01

The IP-based Ubiquitous Sensor Network (IP-USN) is an effort to build the “Internet of things”. By utilizing IP for low power networks, we can benefit from existing well established tools and technologies of IP networks. Along with many other unresolved issues, securing IP-USN is of great concern for researchers so that future market satisfaction and demands can be met. Without proper security measures, both reactive and proactive, it is hard to envisage an IP-USN realm. In this paper we present a design of an IDS (Intrusion Detection System) called RIDES (Robust Intrusion DEtection System) for IP-USN. RIDES is a hybrid intrusion detection system, which incorporates both Signature and Anomaly based intrusion detection components. For signature based intrusion detection this paper only discusses the implementation of distributed pattern matching algorithm with the help of signature-code, a dynamically created attack-signature identifier. Other aspects, such as creation of rules are not discussed. On the other hand, for anomaly based detection we propose a scoring classifier based on the SPC (Statistical Process Control) technique called CUSUM charts. We also investigate the settings and their effects on the performance of related parameters for both of the components. PMID:22412321

RIDES: Robust Intrusion Detection System for IP-Based Ubiquitous Sensor Networks.

PubMed

Amin, Syed Obaid; Siddiqui, Muhammad Shoaib; Hong, Choong Seon; Lee, Sungwon

2009-01-01

The IP-based Ubiquitous Sensor Network (IP-USN) is an effort to build the "Internet of things". By utilizing IP for low power networks, we can benefit from existing well established tools and technologies of IP networks. Along with many other unresolved issues, securing IP-USN is of great concern for researchers so that future market satisfaction and demands can be met. Without proper security measures, both reactive and proactive, it is hard to envisage an IP-USN realm. In this paper we present a design of an IDS (Intrusion Detection System) called RIDES (Robust Intrusion DEtection System) for IP-USN. RIDES is a hybrid intrusion detection system, which incorporates both Signature and Anomaly based intrusion detection components. For signature based intrusion detection this paper only discusses the implementation of distributed pattern matching algorithm with the help of signature-code, a dynamically created attack-signature identifier. Other aspects, such as creation of rules are not discussed. On the other hand, for anomaly based detection we propose a scoring classifier based on the SPC (Statistical Process Control) technique called CUSUM charts. We also investigate the settings and their effects on the performance of related parameters for both of the components.

Spatial and Temporal Variability of Elemental Signautres in Juvenile Winter Flounder (Psuedopleuronectes americanus): Implications for Natal Connectivity

EPA Science Inventory

Elemental signatures in otoliths (fish ear-stones) have become a powerful tool in fisheries science for identifying fish migration patterns, reconstructing environmental histories, and for delineating the nursery origins of adult fish populations. Assessing connectivity between a...

ELEMENTAL FINGERPRINTS OF JUVENILE WINTER FLOUNDER OTOLITHS FROM NARRAGNSETT BAY, RI AND SURROUNDING COASTAL PONDS

EPA Science Inventory

Elemental fingerprinting has become a powerful tool in fisheries science for identifying fish migration patterns, seasonal changes in habitat use, and for delineating the nursery origins of adult fish populations. In this study we investigated whether elemental signatures in juve...

Earth's Coming of Age: Isotopically Tracking the Global Transformation from the Hadean to the Geologically Modern Earth

NASA Astrophysics Data System (ADS)

Bennett, V. C.; Nutman, A. P.

2017-12-01

Some of the strongest direct evidence that documents fundamental changes in the chemistry and organisation of Earth's interior derives from radiogenic isotopic compositions that include both long-lived (particularly 176Lu-176Hf and 147Sm-143Nd) and short-lived, i.e., now extinct parent isotope, systems (182Hf-182W, 146Sm-142Nd). Changes in patterns of isotopic evolution are linked to changes in mantle dynamics such that tracking these signatures in geologically well-characterised rocks can be used to discover the the nature and evolution of tectonic processes. Over the past decade, intensive geochemical investigations by various groups focussing on the oldest (> 4.0 Ga to 3.6 Ga) rock record, as preserved in several localities, have revealed isotopic distinctions in the early Earth compared with those in Proterozoic and younger rocks. For example, whilst the major and trace element compositions of Eoarchean gneisses have analogs in younger rocks in accord with a continuum of crust formation processes, radiogenic isotopic signatures from both long and short half-life decay schemes record an image of the Earth in transition from early differentiation processes, likely associated with planetary accretion and formation, to more modern style characterised by plate tectonics. The emerging image is that many Eoarchean rocks possess extinct nuclide anomalies in the form of 142Nd and 182Hf isotopic signatures that are absent in modern terrestrial samples; these signatures are evidence of chemical fractionation processes occuring within the first ca. 10-300 million years of Solar System history. In addition, viewing the global database, patterns of long-half life isotope signatures i.e., 143Nd and 176Hf differ from those seen in younger (<3.6 Ga) rocks, again providing a tracer of mantle dynamics and reflecting the influence of early processes. It is becoming increasingly apparent that the well demonstrated "coupled" 176Hf-143Nd isotopic evolution generated by plate tectonic processes and characterizing Phanerozoic and Proterozoic mantle derived rocks is absent in the Eoarchean record. Here, we track this isotopic transition in key regions and demonstrate how this places limits on the timing and style of transition from early to modern Earth.

Conservation of Chitin-Induced MAPK Signaling Pathways in Rice and Arabidopsis.

PubMed

Yamada, Kenta; Yamaguchi, Koji; Yoshimura, Satomi; Terauchi, Akira; Kawasaki, Tsutomu

2017-06-01

Perception of microbe-associated molecular patterns (MAMPs) including chitin by pattern recognition receptors (PRRs) rapidly induces activation of mitogen-activated protein kinase (MAPK) cascades. However, how PRRs transmit immune signals to the MAPK cascade is largely unknown. Recently, Arabidopsis receptor-like cytoplasmic kinase PBL27 has been reported to activate MAPKs through phosphorylation of AtMAPKKK5 in the chitin signaling pathway. In this study, we found that OsRLCK185, a rice ortholog of PBL27, regulates chitin-induced MAPK activation in a similar fashion to PBL27 in rice. Upon chitin perception, OsRLCK185 is phosphorylated by OsCERK1, a component of the chitin receptor complex. OsRLCK185 interacted with OsMAPKKK11 and OsMAPKKK18, rice orthologs of AtMAPKKK5, in yeast two-hybrid assays. Silencing of both OsMAPKKK11 and OsMAPKKK18 significantly reduced chitin-induced activation of OsMPK3 and OsMPK6. Expression levels of OsMAPKKK18 were much higher than that of OsMAPKKK11 in rice cells, which was consistent with the fact that the Osmapkkk11 single mutation did not affect MAPK activation. This result suggested that OsMAPKKK18 plays a more important role than OsMAPKKK11 in the chitin-induced activation of OsMPK3 and OsMPK6. The bimolecular fluorescence complementation (BiFC) experiment indicated that OsRLCK185 interacted with OsMAPKKK18 at the plasma membrane in planta. In vitro phosphorylation experiments showed that OsRLCK185 directly phosphorylates OsMAPKKK18. Furthermore, OsMAPKKK18 interacted with the MAPKK OsMKK4, the upstream component of OsMPK3/6. These results suggested that OsRLCK185 connects the chitin receptor to the MAPK cascade consisting of OsMAPKKK18-OsMKK4-OsMPK3/6. Our data revealed that chitin-induced MAPK activation in rice and Arabidopsis is regulated by common homologous elements. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

400 Years of summer hydroclimate from stable isotopes in Iberian trees

NASA Astrophysics Data System (ADS)

Andreu-Hayles, Laia; Ummenhofer, Caroline C.; Barriendos, Mariano; Schleser, Gerhard H.; Helle, Gerhard; Leuenberger, Markus; Gutiérrez, Emilia; Cook, Edward R.

2017-07-01

Tree rings are natural archives that annually record distinct types of past climate variability depending on the parameters measured. Here, we use ring-width and stable isotopes in cellulose of trees from the northwestern Iberian Peninsula (IP) to understand regional summer hydroclimate over the last 400 years and the associated atmospheric patterns. Correlations between tree rings and climate data demonstrate that isotope signatures in the targeted Iberian pine forests are very sensitive to water availability during the summer period, and are mainly controlled by stomatal conductance. Non-linear methods based on extreme events analysis allow for capturing distinct seasonal climatic variability recorded by tree-ring parameters and asymmetric signals of the associated atmospheric features. Moreover, years with extreme high (low) values in the tree-ring records were characterised by coherent large-scale atmospheric circulation patterns with reduced (enhanced) moisture transport onto the northwestern IP. These analyses of extremes revealed that high/low proxy values do not necessarily correspond to mirror images in the atmospheric anomaly patterns, suggesting different drivers of these patterns and the corresponding signature recorded in the proxies. Regional hydroclimate features across the broader IP and western Europe during extreme wet/dry summers detected by the northwestern IP trees compare favourably to independent multicentury sea level pressure and drought reconstructions for Europe. Historical records also validate our findings that attribute non-linear moisture signals recorded by extreme tree-ring values to distinct large-scale atmospheric patterns and allow for 400-year reconstructions of the frequency of occurrence of extreme conditions in late spring and summer hydroclimate.

400 years of summer hydroclimate from stable isotopes in Iberian trees

NASA Astrophysics Data System (ADS)

Andreu-Hayles, Laia; Ummenhofer, Caroline C.; Barriendos, Mariano; Schleser, Gerhard H.; Helle, Gerhard; Leuenberger, Markus; Gutierrez, Emilia; Cook, Edward R.

2017-04-01

Tree rings are natural archives that annually record distinct types of past climate variability depending on the parameters measured. Here, we use ring-width and stable isotopes in cellulose of trees from the northwestern Iberian Peninsula (IP) to understand regional summer hydroclimate over the last 400 years and the associated atmospheric patterns. Correlations between tree rings and climate data demonstrate that isotope signatures in the targeted Iberian pine forests are very sensitive to water availability during the summer period, and are mainly controlled by stomatal conductance. Non-linear methods based on extreme events analysis allow for capturing distinct seasonal climatic variability recorded by tree-ring parameters and asymmetric signals of the associated atmospheric features. Moreover, years with extreme high (low) values in the tree-ring records were characterised by coherent large-scale atmospheric circulation patterns with reduced (enhanced) moisture transport onto the northwestern IP. These analyses of extremes revealed that high/low proxy values do not necessarily correspond to mirror images in the atmospheric anomaly patterns, suggesting different drivers of these patterns and the corresponding signature recorded in the proxies. Regional hydroclimate features across the broader IP and western Europe during extreme wet/dry summers detected by the northwestern IP trees compare favourably to an independent multicentury sea level pressure and drought reconstruction for Europe. Historical records also validate our findings that attribute non-linear moisture signals recorded by extreme tree-ring values to distinct large-scale atmospheric patterns and allow for 400-yr reconstructions of the frequency of occurrence of extreme conditions in summer hydroclimate. We will discuss how the results for Lillo compare with other records.

Memory, executive, and multidomain subtle cognitive impairment: clinical and biomarker findings.

PubMed

Toledo, Jon B; Bjerke, Maria; Chen, Kewei; Rozycki, Martin; Jack, Clifford R; Weiner, Michael W; Arnold, Steven E; Reiman, Eric M; Davatzikos, Christos; Shaw, Leslie M; Trojanowski, John Q

2015-07-14

We studied the biomarker signatures and prognoses of 3 different subtle cognitive impairment (SCI) groups (executive, memory, and multidomain) as well as the subjective memory complaints (SMC) group. We studied 522 healthy controls in the Alzheimer's Disease Neuroimaging Initiative (ADNI). Cutoffs for executive, memory, and multidomain SCI were defined using participants who remained cognitively normal (CN) for 7 years. CSF Alzheimer disease (AD) biomarkers, composite and region-of-interest (ROI) MRI, and fluorodeoxyglucose-PET measures were compared in these participants. Using a stringent cutoff (fifth percentile), 27.6% of the ADNI participants were classified as SCI. Most single ROI or global-based measures were not sensitive to detect differences between groups. Only MRI-SPARE-AD (Spatial Pattern of Abnormalities for Recognition of Early AD), a quantitative MRI pattern-based global index, showed differences between all groups, excluding the executive SCI group. Atrophy patterns differed in memory SCI and SMC. The CN and the SMC groups presented a similar distribution of preclinical dementia stages. Fifty percent of the participants with executive, memory, and multidomain SCI progressed to mild cognitive impairment or dementia at 7, 5, and 2 years, respectively. Our results indicate that (1) the different SCI categories have different clinical prognoses and biomarker signatures, (2) longitudinally followed CN subjects are needed to establish clinical cutoffs, (3) subjects with SMC show a frontal pattern of brain atrophy, and (4) pattern-based analyses outperform commonly used single ROI-based neuroimaging biomarkers and are needed to detect initial stages of cognitive impairment. © 2015 American Academy of Neurology.

Decoding fMRI Signatures of Real-world Autobiographical Memory Retrieval.

PubMed

Rissman, Jesse; Chow, Tiffany E; Reggente, Nicco; Wagner, Anthony D

2016-04-01

Extant neuroimaging data implicate frontoparietal and medial-temporal lobe regions in episodic retrieval, and the specific pattern of activity within and across these regions is diagnostic of an individual's subjective mnemonic experience. For example, in laboratory-based paradigms, memories for recently encoded faces can be accurately decoded from single-trial fMRI patterns [Uncapher, M. R., Boyd-Meredith, J. T., Chow, T. E., Rissman, J., & Wagner, A. D. Goal-directed modulation of neural memory patterns: Implications for fMRI-based memory detection. Journal of Neuroscience, 35, 8531-8545, 2015; Rissman, J., Greely, H. T., & Wagner, A. D. Detecting individual memories through the neural decoding of memory states and past experience. Proceedings of the National Academy of Sciences, U.S.A., 107, 9849-9854, 2010]. Here, we investigated the neural patterns underlying memory for real-world autobiographical events, probed at 1- to 3-week retention intervals as well as whether distinct patterns are associated with different subjective memory states. For 3 weeks, participants (n = 16) wore digital cameras that captured photographs of their daily activities. One week later, they were scanned while making memory judgments about sequences of photos depicting events from their own lives or events captured by the cameras of others. Whole-brain multivoxel pattern analysis achieved near-perfect accuracy at distinguishing correctly recognized events from correctly rejected novel events, and decoding performance did not significantly vary with retention interval. Multivoxel pattern classifiers also differentiated recollection from familiarity and reliably decoded the subjective strength of recollection, of familiarity, or of novelty. Classification-based brain maps revealed dissociable neural signatures of these mnemonic states, with activity patterns in hippocampus, medial PFC, and ventral parietal cortex being particularly diagnostic of recollection. Finally, a classifier trained on previously acquired laboratory-based memory data achieved reliable decoding of autobiographical memory states. We discuss the implications for neuroscientific accounts of episodic retrieval and comment on the potential forensic use of fMRI for probing experiential knowledge.

Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection

PubMed Central

Huang, Yongsheng; Zaas, Aimee K.; Rao, Arvind; Dobigeon, Nicolas; Woolf, Peter J.; Veldman, Timothy; Øien, N. Christine; McClain, Micah T.; Varkey, Jay B.; Nicholson, Bradley; Carin, Lawrence; Kingsmore, Stephen; Woods, Christopher W.; Ginsburg, Geoffrey S.; Hero, Alfred O.

2011-01-01

Exposure to influenza viruses is necessary, but not sufficient, for healthy human hosts to develop symptomatic illness. The host response is an important determinant of disease progression. In order to delineate host molecular responses that differentiate symptomatic and asymptomatic Influenza A infection, we inoculated 17 healthy adults with live influenza (H3N2/Wisconsin) and examined changes in host peripheral blood gene expression at 16 timepoints over 132 hours. Here we present distinct transcriptional dynamics of host responses unique to asymptomatic and symptomatic infections. We show that symptomatic hosts invoke, simultaneously, multiple pattern recognition receptors-mediated antiviral and inflammatory responses that may relate to virus-induced oxidative stress. In contrast, asymptomatic subjects tightly regulate these responses and exhibit elevated expression of genes that function in antioxidant responses and cell-mediated responses. We reveal an ab initio molecular signature that strongly correlates to symptomatic clinical disease and biomarkers whose expression patterns best discriminate early from late phases of infection. Our results establish a temporal pattern of host molecular responses that differentiates symptomatic from asymptomatic infections and reveals an asymptomatic host-unique non-passive response signature, suggesting novel putative molecular targets for both prognostic assessment and ameliorative therapeutic intervention in seasonal and pandemic influenza. PMID:21901105

Signatures of a globally optimal searching strategy in the three-dimensional foraging flights of bumblebees

NASA Astrophysics Data System (ADS)

Lihoreau, Mathieu; Ings, Thomas C.; Chittka, Lars; Reynolds, Andy M.

2016-07-01

Simulated annealing is a powerful stochastic search algorithm for locating a global maximum that is hidden among many poorer local maxima in a search space. It is frequently implemented in computers working on complex optimization problems but until now has not been directly observed in nature as a searching strategy adopted by foraging animals. We analysed high-speed video recordings of the three-dimensional searching flights of bumblebees (Bombus terrestris) made in the presence of large or small artificial flowers within a 0.5 m3 enclosed arena. Analyses of the three-dimensional flight patterns in both conditions reveal signatures of simulated annealing searches. After leaving a flower, bees tend to scan back-and forth past that flower before making prospecting flights (loops), whose length increases over time. The search pattern becomes gradually more expansive and culminates when another rewarding flower is found. Bees then scan back and forth in the vicinity of the newly discovered flower and the process repeats. This looping search pattern, in which flight step lengths are typically power-law distributed, provides a relatively simple yet highly efficient strategy for pollinators such as bees to find best quality resources in complex environments made of multiple ephemeral feeding sites with nutritionally variable rewards.

Effects Of Hydrothermal Alteration On Magnetic Properties And Magnetic Signatures - Implications For Predictive Magnetic Exploration Models

NASA Astrophysics Data System (ADS)

Clark, D.

2012-12-01

Magnetics is the most widely used geophysical method in hard rock exploration and magnetic surveys are an integral part of exploration programs for many types of mineral deposit, including porphyry Cu, intrusive-related gold, volcanic-hosted epithermal Au, IOCG, VMS, and Ni sulfide deposits. However, the magnetic signatures of ore deposits and their associated mineralized systems are extremely variable and exploration that is based simply on searching for signatures that resemble those of known deposits and systems is rarely successful. Predictive magnetic exploration models are based upon well-established geological models, combined with magnetic property measurements and geological information from well-studied deposits, and guided by magnetic petrological understanding of the processes that create, destroy and modify magnetic minerals in rocks. These models are designed to guide exploration by predicting magnetic signatures that are appropriate to specific geological settings, taking into account factors such as tectonic province; protolith composition; post-formation tilting/faulting/ burial/ exhumation and partial erosion; and metamorphism. Patterns of zoned hydrothermal alteration are important indicators of potentially mineralized systems and, if properly interpreted, can provided vectors to ore. Magnetic signatures associated with these patterns at a range of scales can provide valuable information on prospectivity and can guide drilling, provided they are correctly interpreted in geological terms. This presentation reviews effects of the important types of hydrothermal alteration on magnetic properties within mineralized systems, with particular reference to porphyry copper and IOCG deposits. For example, an unmodified gold-rich porphyry copper system, emplaced into mafic-intermediate volcanic host rocks (such as Bajo de la Alumbrera, Argentina) exhibits an inner potassic zone that is strongly mineralized and magnetite-rich, which is surrounded by an outer potassic zone that contains less abundant, but still significant, magnetite. The inner potassic zone represents relatively intense development of qtz-mt-Kfsp veins, whereas the outer potassic zone corresponds to bio-Kfsp-qtz-mt alteration. A shell of magnetite-destructive phyllic alteration with very low susceptibility envelops the potassic zones. The phyllic zone is surrounded by a zone of intense propylitic alteration, which is partially magnetite-destructive, which passes out into weak propylitic alteration and then into unaltered, moderately magnetic volcanics. For such a system, emplaced into magnetic intermediate-mafic igneous host rocks and exposed after removal by erosion of ~ 1 km of overburden, a strong central RTP high is surrounded by a relatively weak annular low over the phyllic zone, gradually returning to background levels over the propylitic zone (an "archery target" signature). For a completely buried system, however, the signature is basically an alteration low due to the large volume of magnetite-destructive alteration surrounding the deeply buried magnetic core.

Ants regulate colony spatial organization using multiple chemical road-signs

PubMed Central

Heyman, Yael; Shental, Noam; Brandis, Alexander; Hefetz, Abraham; Feinerman, Ofer

2017-01-01

Communication provides the basis for social life. In ant colonies, the prevalence of local, often chemically mediated, interactions introduces strong links between communication networks and the spatial distribution of ants. It is, however, unknown how ants identify and maintain nest chambers with distinct functions. Here, we combine individual tracking, chemical analysis and machine learning to decipher the chemical signatures present on multiple nest surfaces. We present evidence for several distinct chemical ‘road-signs' that guide the ants' movements within the dark nest. These chemical signatures can be used to classify nest chambers with different functional roles. Using behavioural manipulations, we demonstrate that at least three of these chemical signatures are functionally meaningful and allow ants from different task groups to identify their specific nest destinations, thus facilitating colony coordination and stabilization. The use of multiple chemicals that assist spatiotemporal guidance, segregation and pattern formation is abundant in multi-cellular organisms. Here, we provide a rare example for the use of these principles in the ant colony. PMID:28569746

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

PubMed

Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

2016-01-19

Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

Prediction of meat spectral patterns based on optical properties and concentrations of the major constituents.

PubMed

ElMasry, Gamal; Nakauchi, Shigeki

2016-03-01

A simulation method for approximating spectral signatures of minced meat samples was developed depending on concentrations and optical properties of the major chemical constituents. Minced beef samples of different compositions scanned on a near-infrared spectroscopy and on a hyperspectral imaging system were examined. Chemical composition determined heuristically and optical properties collected from authenticated references were simulated to approximate samples' spectral signatures. In short-wave infrared range, the resulting spectrum equals the sum of the absorption of three individual absorbers, that is, water, protein, and fat. By assuming homogeneous distributions of the main chromophores in the mince samples, the obtained absorption spectra are found to be a linear combination of the absorption spectra of the major chromophores present in the sample. Results revealed that developed models were good enough to derive spectral signatures of minced meat samples with a reasonable level of robustness of a high agreement index value more than 0.90 and ratio of performance to deviation more than 1.4.

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

PubMed Central

Paige, Sharon L.; Thomas, Sean; Stoick-Cooper, Cristi L.; Wang, Hao; Maves, Lisa; Sandstrom, Richard; Pabon, Lil; Reinecke, Hans; Pratt, Gabriel; Keller, Gordon; Moon, Randall T.; Stamatoyannopoulos, John; Murry, Charles E.

2012-01-01

Summary Directed differentiation of human embryonic stem cells (ESCs) into cardiovascular cells provides a model for studying molecular mechanisms of human cardiovascular development. Though it is known that chromatin modification patterns in ESCs differ markedly from those in lineage-committed progenitors and differentiated cells, the temporal dynamics of chromatin alterations during differentiation along a defined lineage have not been studied. We show that differentiation of human ESCs into cardiovascular cells is accompanied by programmed temporal alterations in chromatin structure that distinguish key regulators of cardiovascular development from other genes. We used this temporal chromatin signature to identify regulators of cardiac development, including the homeobox gene MEIS2. We demonstrate using the zebrafish model that MEIS2 is critical for proper heart tube formation and subsequent cardiac looping. Temporal chromatin signatures should be broadly applicable to other models of stem cell differentiation to identify regulators and provide key insights into major developmental decisions. PMID:22981225

Ants regulate colony spatial organization using multiple chemical road-signs.

PubMed

Heyman, Yael; Shental, Noam; Brandis, Alexander; Hefetz, Abraham; Feinerman, Ofer

2017-06-01

Communication provides the basis for social life. In ant colonies, the prevalence of local, often chemically mediated, interactions introduces strong links between communication networks and the spatial distribution of ants. It is, however, unknown how ants identify and maintain nest chambers with distinct functions. Here, we combine individual tracking, chemical analysis and machine learning to decipher the chemical signatures present on multiple nest surfaces. We present evidence for several distinct chemical 'road-signs' that guide the ants' movements within the dark nest. These chemical signatures can be used to classify nest chambers with different functional roles. Using behavioural manipulations, we demonstrate that at least three of these chemical signatures are functionally meaningful and allow ants from different task groups to identify their specific nest destinations, thus facilitating colony coordination and stabilization. The use of multiple chemicals that assist spatiotemporal guidance, segregation and pattern formation is abundant in multi-cellular organisms. Here, we provide a rare example for the use of these principles in the ant colony.

Advanced process and defect characterization methodology to support process development of advanced patterning structures

NASA Astrophysics Data System (ADS)

Ketkar, Supriya; Lee, Junhan; Asokamani, Sen; Cho, Winston; Mishra, Shailendra

2018-03-01

This paper discusses the approach and solution adopted by GLOBALFOUNDRIES, a high volume manufacturing (HVM) foundry, for dry-etch related edge-signature surface particle defects issue facing the sub-nm node in the gate-etch sector. It is one of the highest die killers for the company in the 14-nm node. We have used different approaches to attack and rectify the edge signature surface particle defect. Several process-related & hardware changes have been successively implemented to achieve defect reduction improvement by 63%. Each systematic process and/or hardware approach has its own unique downstream issues and they have been dealt in a route-cause-effect technique to address the issue.

Widespread iron limitation of phytoplankton in the south pacific ocean

PubMed

Behrenfeld; Kolber

1999-02-05

Diel fluorescence patterns were discovered in phytoplankton sampled over 7000 kilometers of the South Pacific Ocean that appear indicative of iron-limiting growth conditions. These patterns were rapidly lost after in situ iron enrichment and were not observed during a 15,000-kilometer transect in the Atlantic Ocean where iron concentrations are relatively high. Laboratory studies of marine Synechococcus sp. indicated that the patterns in the South Pacific are a unique manifestation of iron limitation on the fluorescence signature of state transitions. Results suggest that primary productivity is iron limited not only throughout the equatorial Pacific but also over much of the vast South Pacific gyre.

Detection and recognition of analytes based on their crystallization patterns

DOEpatents

Morozov, Victor [Manassas, VA; Bailey, Charles L [Cross Junction, VA; Vsevolodov, Nikolai N [Kensington, MD; Elliott, Adam [Manassas, VA

2008-05-06

The invention contemplates a method for recognition of proteins and other biological molecules by imaging morphology, size and distribution of crystalline and amorphous dry residues in droplets (further referred to as "crystallization pattern") containing predetermined amount of certain crystal-forming organic compounds (reporters) to which protein to be analyzed is added. It has been shown that changes in the crystallization patterns of a number of amino-acids can be used as a "signature" of a protein added. It was also found that both the character of changer in the crystallization patter and the fact of such changes can be used as recognition elements in analysis of protein molecules.

Thermal signatures of voluntary deception in ecological conditions

PubMed Central

Panasiti, Maria Serena; Cardone, Daniela; Pavone, Enea F.; Mancini, Alessandra; Merla, Arcangelo; Aglioti, Salvatore M.

2016-01-01

Deception is a pervasive phenomenon that greatly influences dyadic, groupal and societal interactions. Behavioural, physiological and neural signatures of this phenomenon have imporant implications for theoretical and applied research, but, because it is difficult for a laboratory to replicate the natural context in which deception occurs, contemporary research is still struggling to find such signatures. In this study, we tracked the facial temperature of participants who decided whether or not to deceive another person, in situations where their reputation was at risk or not. We used a high-sensitivity infrared device to track temperature changes to check for unique patterns of autonomic reactivity. Using a region-of-interest based approach we found that prior to any response there was a minimal increase in periorbital temperature (which indexes sympathetic activation, together with reduced cheek temperature) for the self-gain lies in the reputation-risk condition. Crucially, we found a rise in nose temperature (which indexes parasympathetic activation) for self-gain lies in the reputation-risk condition, not only during response preparation but also after the choice was made. This finding suggests that the entire deception process may be tracked by the nose region. Furthermore, this nasal temperature modulation was negatively correlated with machiavellian traits, indicating that sympathetic/parasympathetic regulation is less important for manipulative individuals who may care less about the consequences of lie-related moral violations. Our results highlight a unique pattern of autonomic reactivity for spontaneous deception in ecological contexts. PMID:27734927

Cosmological Signatures of a Mirror Twin Higgs

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

Chacko, Zackaria; Curtin, David; Geller, Michael

We explore the cosmological signatures associated with the twin baryons, electrons, photons and neutrinos in the Mirror Twin Higgs framework. We consider a scenario in which the twin baryons constitute a subcomponent of dark matter, and the contribution of the twin photon and neutrinos to dark radiation is suppressed due to late asymmetric reheating, but remains large enough to be detected in future cosmic microwave background (CMB) experiments. We show that this framework can lead to distinctive signals in large scale structure and in the cosmic microwave background. Baryon acoustic oscillations in the mirror sector prior to recombination lead tomore » a suppression of structure on large scales, and leave a residual oscillatory pattern in the matter power spectrum. This pattern depends sensitively on the relative abundances and ionization energies of both twin hydrogen and helium, and is therefore characteristic of this class of models. Although both mirror photons and neutrinos constitute dark radiation in the early universe, their effects on the CMB are distinct. This is because prior to recombination the twin neutrinos free stream, while the twin photons are prevented from free streaming by scattering off twin electrons. In the Mirror Twin Higgs framework the relative contributions of these two species to the energy density in dark radiation is predicted, leading to testable effects in the CMB. These highly distinctive cosmological signatures may allow this class of models to be discovered, and distinguished from more general dark sectors.« less

Metabolic Signatures of Bacterial Vaginosis

PubMed Central

Morgan, Martin T.; Fiedler, Tina L.; Djukovic, Danijel; Hoffman, Noah G.; Raftery, Daniel; Marrazzo, Jeanne M.

2015-01-01

ABSTRACT Bacterial vaginosis (BV) is characterized by shifts in the vaginal microbiota from Lactobacillus dominant to a microbiota with diverse anaerobic bacteria. Few studies have linked specific metabolites with bacteria found in the human vagina. Here, we report dramatic differences in metabolite compositions and concentrations associated with BV using a global metabolomics approach. We further validated important metabolites using samples from a second cohort of women and a different platform to measure metabolites. In the primary study, we compared metabolite profiles in cervicovaginal lavage fluid from 40 women with BV and 20 women without BV. Vaginal bacterial representation was determined using broad-range PCR with pyrosequencing and concentrations of bacteria by quantitative PCR. We detected 279 named biochemicals; levels of 62% of metabolites were significantly different in women with BV. Unsupervised clustering of metabolites separated women with and without BV. Women with BV have metabolite profiles marked by lower concentrations of amino acids and dipeptides, concomitant with higher levels of amino acid catabolites and polyamines. Higher levels of the signaling eicosanoid 12-hydroxyeicosatetraenoic acid (12-HETE), a biomarker for inflammation, were noted in BV. Lactobacillus crispatus and Lactobacillus jensenii exhibited similar metabolite correlation patterns, which were distinct from correlation patterns exhibited by BV-associated bacteria. Several metabolites were significantly associated with clinical signs and symptoms (Amsel criteria) used to diagnose BV, and no metabolite was associated with all four clinical criteria. BV has strong metabolic signatures across multiple metabolic pathways, and these signatures are associated with the presence and concentrations of particular bacteria. PMID:25873373

Inferring individual-level processes from population-level patterns in cultural evolution.

PubMed

Kandler, Anne; Wilder, Bryan; Fortunato, Laura

2017-09-01

Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data, we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution.

Genome-wide introgression among distantly related Heliconius butterfly species.

PubMed

Zhang, Wei; Dasmahapatra, Kanchon K; Mallet, James; Moreira, Gilson R P; Kronforst, Marcus R

2016-02-27

Although hybridization is thought to be relatively rare in animals, the raw genetic material introduced via introgression may play an important role in fueling adaptation and adaptive radiation. The butterfly genus Heliconius is an excellent system to study hybridization and introgression but most studies have focused on closely related species such as H. cydno and H. melpomene. Here we characterize genome-wide patterns of introgression between H. besckei, the only species with a red and yellow banded 'postman' wing pattern in the tiger-striped silvaniform clade, and co-mimetic H. melpomene nanna. We find a pronounced signature of putative introgression from H. melpomene into H. besckei in the genomic region upstream of the gene optix, known to control red wing patterning, suggesting adaptive introgression of wing pattern mimicry between these two distantly related species. At least 39 additional genomic regions show signals of introgression as strong or stronger than this mimicry locus. Gene flow has been on-going, with evidence of gene exchange at multiple time points, and bidirectional, moving from the melpomene to the silvaniform clade and vice versa. The history of gene exchange has also been complex, with contributions from multiple silvaniform species in addition to H. besckei. We also detect a signature of ancient introgression of the entire Z chromosome between the silvaniform and melpomene/cydno clades. Our study provides a genome-wide portrait of introgression between distantly related butterfly species. We further propose a comprehensive and efficient workflow for gene flow identification in genomic data sets.

Changes in spatial point patterns of pioneer woody plants across a large tropical landslide

NASA Astrophysics Data System (ADS)

Velázquez, Eduardo; De la Cruz, Marcelino; Gómez-Sal, Antonio

2014-11-01

We assessed whether the relative importance of positive and negative interactions in early successional communities varied across a large landslide on Casita Volcano (Nicaragua). We tested several hypotheses concerning the signatures of these processes in the spatial patterns of woody pioneer plants, as well as those of mortality and recruitment events, in several zones of the landslide differing in substrate stability and fertility, over a period of two years (2001 and 2002). We identified all woody individuals with a diameter >1 cm and mapped them in 28 plots measuring 10 × 10-m. On these maps, we performed a spatial point pattern analysis using univariate and bivariate pair-correlation functions; g (r) and g12 (r), and pairwise differences of univariate and bivariate functions. Spatial signatures of positive and negative interactions among woody plants were more prevalent in the most and least stressful zones of the landslide, respectively. Natural and human-induced disturbances such as the occurrence of fire, removal of newly colonizing plants through erosion and clearcutting of pioneer trees were also identified as potentially important pattern-creating processes. These results are in agreement with the stress-gradient hypothesis, which states that the relative importance of facilitation and competition varies inversely across gradients of abiotic stress. Our findings also indicate that the assembly of early successional plant communities in large heterogeneous landslides might be driven by a much larger array of processes than previously thought.

Differential transmission of the molecular signature of RBSP3, LIMD1 and CDC25A in basal/ parabasal versus spinous of normal epithelium during head and neck tumorigenesis: A mechanistic study.

PubMed

Sarkar, Shreya; Alam, Neyaz; Mandal, Syam Sundar; Chatterjee, Kabita; Ghosh, Supratim; Roychoudhury, Susanta; Panda, Chinmay Kumar

2018-01-01

Head and neck squamous cell carcinoma (HNSCC) is a global disease and mortality burden, necessitating the elucidation of its molecular progression for effective disease management. The study aims to understand the molecular profile of three candidate cell cycle regulatory genes, RBSP3, LIMD1 and CDC25A in the basal/ parabasal versus spinous layer of normal oral epithelium and during head and neck tumorigenesis. Immunohistochemical expression and promoter methylation was used to determine the molecular signature in normal oral epithelium. The mechanism of alteration transmission of this profile during tumorigenesis was then explored through additional deletion and mutation in HPV/ tobacco etiological groups, followed byclinico-pathological correlation. In basal/parabasal layer, the molecular signature of the genes was low protein expression/ high promoter methylation of RBSP3, high expression/ low methylation of LIMD1 and high expression of CDC25A. Dysplastic epithelium maintained the signature of RBSP3 through high methylation/ additional deletion with loss of the signatures of LIMD1 and CDC25A via deletion/ additional methylation. Similarly, maintenance and / or loss of signature in invasive tumors was by recurrent deletion/ methylation. Thus, differential patterns of alteration of the genes might be pre-requisite for the development of dysplastic and invasive lesions. Etiological factors played a key role in promoting genetic alterations and determining prognosis. Tobacco negative HNSCC patients had significantly lower alterations of LIMD1 and CDC25A, along with better survival among tobacco negative/ HPV positive patients. Our data suggests the necessity for perturbation of normal molecular profile of RBSP3, LIMD1 and CDC25A in conjunction with etiological factors for head and neck tumorigenesis, implying their diagnostic and prognostic significance.

Multiwaveband simulation-based signature analysis of camouflaged human dismounts in cluttered environments with TAIThermIR and MuSES

NASA Astrophysics Data System (ADS)

Packard, Corey D.; Klein, Mark D.; Viola, Timothy S.; Hepokoski, Mark A.

2016-10-01

The ability to predict electro-optical (EO) signatures of diverse targets against cluttered backgrounds is paramount for signature evaluation and/or management. Knowledge of target and background signatures is essential for a variety of defense-related applications. While there is no substitute for measured target and background signatures to determine contrast and detection probability, the capability to simulate any mission scenario with desired environmental conditions is a tremendous asset for defense agencies. In this paper, a systematic process for the thermal and visible-through-infrared simulation of camouflaged human dismounts in cluttered outdoor environments is presented. This process, utilizing the thermal and EO/IR radiance simulation tool TAIThermIR (and MuSES), provides a repeatable and accurate approach for analyzing contrast, signature and detectability of humans in multiple wavebands. The engineering workflow required to combine natural weather boundary conditions and the human thermoregulatory module developed by ThermoAnalytics is summarized. The procedure includes human geometry creation, human segmental physiology description and transient physical temperature prediction using environmental boundary conditions and active thermoregulation. Radiance renderings, which use Sandford-Robertson BRDF optical surface property descriptions and are coupled with MODTRAN for the calculation of atmospheric effects, are demonstrated. Sensor effects such as optical blurring and photon noise can be optionally included, increasing the accuracy of detection probability outputs that accompany each rendering. This virtual evaluation procedure has been extensively validated and provides a flexible evaluation process that minimizes the difficulties inherent in human-subject field testing. Defense applications such as detection probability assessment, camouflage pattern evaluation, conspicuity tests and automatic target recognition are discussed.

CT-based radiomics signature for differentiating Borrmann type IV gastric cancer from primary gastric lymphoma.

PubMed

Ma, Zelan; Fang, Mengjie; Huang, Yanqi; He, Lan; Chen, Xin; Liang, Cuishan; Huang, Xiaomei; Cheng, Zixuan; Dong, Di; Liang, Changhong; Xie, Jiajun; Tian, Jie; Liu, Zaiyi

2017-06-01

To evaluate the value of CT-based radiomics signature for differentiating Borrmann type IV gastric cancer (GC) from primary gastric lymphoma (PGL). 40 patients with Borrmann type IV GC and 30 patients with PGL were retrospectively recruited. 485 radiomics features were extracted and selected from the portal venous CT images to build a radiomics signature. Subjective CT findings, including gastric wall peristalsis, perigastric fat infiltration, lymphadenopathy below the renal hila and enhancement pattern, were assessed to construct a subjective findings model. The radiomics signature, subjective CT findings, age and gender were integrated into a combined model by multivariate analysis. The diagnostic performance of these three models was assessed with receiver operating characteristics curves (ROC) and were compared using DeLong test. The subjective findings model, the radiomics signature and the combined model showed a diagnostic accuracy of 81.43% (AUC [area under the curve], 0.806; 95% CI [confidence interval]: 0.696-0.917; sensitivity, 63.33%; specificity, 95.00%), 84.29% (AUC, 0.886 [95% CI: 0.809-0.963]; sensitivity, 86.67%; specificity, 82.50%), 87.14% (AUC, 0.903 [95%CI: 0.831-0.975]; sensitivity, 70.00%; specificity, 100%), respectively. There were no significant differences in AUC among these three models (P=0.051-0.422). Radiomics analysis has the potential to accurately differentiate Borrmann type IV GC from PGL. Copyright © 2017 Elsevier B.V. All rights reserved.

Electromagnetic signatures of the preclinical and prodromal stages of Alzheimer’s disease

PubMed Central

Cuesta, Pablo; Fernández, Alberto; Arahata, Yutaka; Iwata, Kaori; Kuratsubo, Izumi; Bundo, Masahiko; Hattori, Hideyuki; Sakurai, Takashi; Fukuda, Koji; Washimi, Yukihiko; Endo, Hidetoshi; Takeda, Akinori; Diers, Kersten; Bajo, Ricardo; Maestú, Fernando; Ito, Kengo; Kato, Takashi

2018-01-01

Abstract Biomarkers useful for the predementia stages of Alzheimer’s disease are needed. Electroencephalography and magnetoencephalography (MEG) are expected to provide potential biomarker candidates for evaluating the predementia stages of Alzheimer’s disease. However, the physiological relevance of EEG/MEG signal changes and their role in pathophysiological processes such as amyloid-β deposition and neurodegeneration need to be elucidated. We evaluated 28 individuals with mild cognitive impairment and 38 cognitively normal individuals, all of whom were further classified into amyloid-β-positive mild cognitive impairment (n = 17, mean age 74.7 ± 5.4 years, nine males), amyloid-β-negative mild cognitive impairment (n = 11, mean age 73.8 ± 8.8 years, eight males), amyloid-β-positive cognitively normal (n = 13, mean age 71.8 ± 4.4 years, seven males), and amyloid-β-negative cognitively normal (n = 25, mean age 72.5 ± 3.4 years, 11 males) individuals using Pittsburgh compound B-PET. We measured resting state MEG for 5 min with the eyes closed, and investigated regional spectral patterns of MEG signals using atlas-based region of interest analysis. Then, the relevance of the regional spectral patterns and their associations with pathophysiological backgrounds were analysed by integrating information from Pittsburgh compound B-PET, fluorodeoxyglucose-PET, structural MRI, and cognitive tests. The results demonstrated that regional spectral patterns of resting state activity could be separated into several types of MEG signatures as follows: (i) the effects of amyloid-β deposition were expressed as the alpha band power augmentation in medial frontal areas; (ii) the delta band power increase in the same region was associated with disease progression within the Alzheimer’s disease continuum and was correlated with entorhinal atrophy and an Alzheimer’s disease-like regional decrease in glucose metabolism; and (iii) the global theta power augmentation, which was previously considered to be an Alzheimer’s disease-related EEG/MEG signature, was associated with general cognitive decline and hippocampal atrophy, but was not specific to Alzheimer’s disease because these changes could be observed in the absence of amyloid-β deposition. The results suggest that these MEG signatures may be useful as unique biomarkers for the predementia stages of Alzheimer’s disease. PMID:29522156

Contextual and Developmental Differences in the Neural Architecture of Cognitive Control.

PubMed

Petrican, Raluca; Grady, Cheryl L

2017-08-09

Because both development and context impact functional brain architecture, the neural connectivity signature of a cognitive or affective predisposition may similarly vary across different ages and circumstances. To test this hypothesis, we investigated the effects of age and cognitive versus social-affective context on the stable and time-varying neural architecture of inhibition, the putative core cognitive control component, in a subsample ( N = 359, 22-36 years, 174 men) of the Human Connectome Project. Among younger individuals, a neural signature of superior inhibition emerged in both stable and dynamic connectivity analyses. Dynamically, a context-free signature emerged as stronger segregation of internal cognition (default mode) and environmentally driven control (salience, cingulo-opercular) systems. A dynamic social-affective context-specific signature was observed most clearly in the visual system. Stable connectivity analyses revealed both context-free (greater default mode segregation) and context-specific (greater frontoparietal segregation for higher cognitive load; greater attentional and environmentally driven control system segregation for greater reward value) signatures of inhibition. Superior inhibition in more mature adulthood was typified by reduced segregation in the default network with increasing reward value and increased ventral attention but reduced cingulo-opercular and subcortical system segregation with increasing cognitive load. Failure to evidence this neural profile after the age of 30 predicted poorer life functioning. Our results suggest that distinguishable neural mechanisms underlie individual differences in cognitive control during different young adult stages and across tasks, thereby underscoring the importance of better understanding the interplay among dispositional, developmental, and contextual factors in shaping adaptive versus maladaptive patterns of thought and behavior. SIGNIFICANCE STATEMENT The brain's functional architecture changes across different contexts and life stages. To test whether the neural signature of a trait similarly varies, we investigated cognitive versus social-affective context effects on the stable and time-varying neural architecture of inhibition during a period of neurobehavioral fine-tuning (age 22-36 years). Younger individuals with superior inhibition showed distinguishable context-free and context-specific neural profiles, evidenced in both static and dynamic connectivity analyses. More mature individuals with superior inhibition evidenced only context-specific profiles, revealed in the static connectivity patterns linked to increased reward or cognitive load. Delayed expression of this profile predicted poorer life functioning. Our results underscore the importance of understanding the interplay among dispositional, developmental, and contextual factors in shaping behavior. Copyright © 2017 the authors 0270-6474/17/377711-16$15.00/0.

Monitoring the Photosynthetic Apparatus During Space Flight: Interspecific Variation in Chlorophyll Fluorescence Signatures Induced by Different Root Zone Stresses

NASA Technical Reports Server (NTRS)

Bubenheim, David L.; Patterson, Mark T.; Kliss, Mark H. (Technical Monitor)

1996-01-01

Chlorophyll fluorescence has been used extensively as a tool to indicate stress to the photosynthetic apparatus in green plants. A rise in fluorescence has been attributed to the blockage of photosystem II photochemistry, and patterns of fluorescence decay (quenching) from dark adapted leaves can be related to specific photochemical and non-photochemical deexcitation pathways of light trapped by the photosynthetic apparatus and thus result in characteristically different fluorescence signatures. Four distantly related plant species, Hypocharis radicata (Asteraceae), Brassica rapa (Brassicaceae), Spinacea oleracea (Chenopodiaceae) and Triticum aestivum (Poaceae), were grown hydroponically for three weeks before the initiation of three different root zone stresses (10 mM Cu, 100 mM NaCl and nitrogen deficient nutrition). After 10 days, characteristic fluorescence signatures for each stress could be noted although the degree varied between species. Fast kinetics analysis showed a reduction in plastoquinone pool size for copper and nitrogen stress for all species but a more species specific result with NaCl stress. Photochemical quenching kinetics varied between species and stress treatments from no quenching in S. oleracea in copper treatments to increased photochemical quenching in NaCl treatments. Non-photochemical quenching kinetics demonstrated a distinct pattern between stresses for all species. Copper treatments characteristically exhibited a shallow, flat non-photochemical quenching profile suggesting a general blockage of electron transport whereas NaCl treatments exhibited a slow rising profile that suggested damage to thylakoid acidification kinetics and nitrogen deficiency exhibited a fast rising and declining profile that suggested an altered state 1-state 2 transition regulated by the phosphorylation of LHCII. These results demonstrate characteristic fluorescence signatures for specific plant stresses that may be applied to different, unrelated plant species. In addition, the potential use of chlorophyll fluorescence for both basic research and diagnostic physiology in space biology is presented.

Recent progress in the design and clinical development of electronic-nose technologies

Treesearch

Dan Wilson

2016-01-01

Electronic-nose (e-nose) devices are instruments designed to detect and discriminate between precise complex gaseous mixtures of volatile organic compounds derived from specific organic sources, such as clinical test samples from patients, based on electronic aroma signature patterns (distinct digital sensor responses) resulting from the combined outputs of a...

The raf-like kinase ILK1 and the high affinity K+ transporter HAK5 are required for innate immunity and abiotic stress response

USDA-ARS?s Scientific Manuscript database

Plants combat bacterial infection by detecting conserved molecular signatures called pathogen-associated molecular patterns (PAMPs) and producing defensive compounds to restrict pathogen entry and reproduction. Numerous ion fluxes are activated within minutes of PAMP perception, including Ca2+ influ...

Sensing Surveillance & Navigation

DTIC Science & Technology

2012-03-07

Removing Atmospheric Turbulence Goal: to restore a single high quality image from the observed sequence Prof. Peyman...Computer Sciences – Higher wavelet studies , time-scale, time-frequency transformations, Reduced Signature Targets, Low Probability of Intercept...Range Dependent Beam -patterns •Electronic Steering with Frequency Offsets •Inherent Countermeasure Capability Why? W1(t) W2(t) W3

Pattern classifier for health monitoring of helicopter gearboxes

NASA Technical Reports Server (NTRS)

Chin, Hsinyung; Danai, Kourosh; Lewicki, David G.

1993-01-01

The application of a newly developed diagnostic method to a helicopter gearbox is demonstrated. This method is a pattern classifier which uses a multi-valued influence matrix (MVIM) as its diagnostic model. The method benefits from a fast learning algorithm, based on error feedback, that enables it to estimate gearbox health from a small set of measurement-fault data. The MVIM method can also assess the diagnosability of the system and variability of the fault signatures as the basis to improve fault signatures. This method was tested on vibration signals reflecting various faults in an OH-58A main rotor transmission gearbox. The vibration signals were then digitized and processed by a vibration signal analyzer to enhance and extract various features of the vibration data. The parameters obtained from this analyzer were utilized to train and test the performance of the MVIM method in both detection and diagnosis. The results indicate that the MVIM method provided excellent detection results when the full range of faults effects on the measurements were included in training, and it had a correct diagnostic rate of 95 percent when the faults were included in training.

Functional coordination of muscles underlying changes in behavioural dynamics.

PubMed

Vernooij, Carlijn A; Rao, Guillaume; Perdikis, Dionysios; Huys, Raoul; Jirsa, Viktor K; Temprado, Jean-Jacques

2016-06-10

The dynamical systems approach addresses Bernstein's degrees of freedom problem by assuming that the neuro-musculo-skeletal system transiently assembles and dismantles its components into functional units (or synergies) to meet task demands. Strikingly, little is known from a dynamical point of view about the functioning of the muscular sub-system in this process. To investigate the interaction between the dynamical organisation at muscular and behavioural levels, we searched for specific signatures of a phase transition in muscular coordination when a transition is displayed at the behavioural level. Our results provide evidence that, during Fitts' task when behaviour switches to a different dynamical regime, muscular activation displays typical signatures of a phase transition; a reorganisation in muscular coordination patterns accompanied by a peak in the variability of muscle activation. This suggests that consistent changes occur in coordination processes across the different levels of description (i.e., behaviour and muscles). Specifically, in Fitts' task, target size acts as a control parameter that induces a destabilisation and a reorganisation of coordination patterns at different levels of the neuro-musculo-skeletal system.

Agricultural trade networks and patterns of economic development.

PubMed

Shutters, Shade T; Muneepeerakul, Rachata

2012-01-01

International trade networks are manifestations of a complex combination of diverse underlying factors, both natural and social. Here we apply social network analytics to the international trade network of agricultural products to better understand the nature of this network and its relation to patterns of international development. Using a network tool known as triadic analysis we develop triad significance profiles for a series of agricultural commodities traded among countries. Results reveal a novel network "superfamily" combining properties of biological information processing networks and human social networks. To better understand this unique network signature, we examine in more detail the degree and triadic distributions within the trade network by country and commodity. Our results show that countries fall into two very distinct classes based on their triadic frequencies. Roughly 165 countries fall into one class while 18, all highly isolated with respect to international agricultural trade, fall into the other. Only Vietnam stands out as a unique case. Finally, we show that as a country becomes less isolated with respect to number of trading partners, the country's triadic signature follows a predictable trajectory that may correspond to a trajectory of development.

Partial bisulfite conversion for unique template sequencing.

PubMed

Kumar, Vijay; Rosenbaum, Julie; Wang, Zihua; Forcier, Talitha; Ronemus, Michael; Wigler, Michael; Levy, Dan

2018-01-25

We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Signatures of Fermi Arcs in the Quasiparticle Interferences of the Weyl Semimetals TaAs and NbP.

PubMed

Chang, Guoqing; Xu, Su-Yang; Zheng, Hao; Lee, Chi-Cheng; Huang, Shin-Ming; Belopolski, Ilya; Sanchez, Daniel S; Bian, Guang; Alidoust, Nasser; Chang, Tay-Rong; Hsu, Chuang-Han; Jeng, Horng-Tay; Bansil, Arun; Lin, Hsin; Hasan, M Zahid

2016-02-12

The recent discovery of the first Weyl semimetal in TaAs provides the first observation of a Weyl fermion in nature. Such a topological semimetal features a novel type of anomalous surface state, the Fermi arc, which connects a pair of Weyl nodes through the boundary of the crystal. Here, we present theoretical calculations of the quasiparticle interference (QPI) patterns that arise from the surface states including the topological Fermi arcs in the Weyl semimetals TaAs and NbP. Most importantly, we discover that the QPI exhibits termination points that are fingerprints of the Weyl nodes in the interference pattern. Our results, for the first time, propose a universal interference signature of the topological Fermi arcs in TaAs, which is fundamental for scanning tunneling microscope (STM) measurements on this prototypical Weyl semimetal compound. More generally, our work provides critical guideline and methodology for STM studies on new Weyl semimetals. Further, the scattering channels revealed by our QPIs are broadly relevant to surface transport and device applications based on Weyl semimetals.

CFD Predictions of Sonic-Boom Characteristics for Unmodified and Modified SR-71 Configurations

NASA Technical Reports Server (NTRS)

Fouladi, Kamran

1999-01-01

Shaped sonic-boom signatures refer to signatures that look something other than the typical N-waves. Shaped sonic-boom signatures such as "flat-top," "ramp-type," or "hybrid-type" waveforms have been shown to reduce the subjective loudness without requiring reductions in overpressure peaks. The shaping of sonic-boom signatures requires increasing the shock rise time and changes in frequency spectra. So far, a flat-top waveform was shown to be achievable in wind tunnels; however, the influence of long propagation distance and real atmosphere on shaped signatures should be addressed using flight tests. Two different approaches have been proposed for sonic-boom minimization flight tests. The first approach, proposed by Eagle Aerospace, is for a flight test using a modified BQM-34 "FIREBEE" remotely piloted vehicle. The 30-foot long FIREBEE has a steady state flight condition at the Mach number and altitude of interest, and it can be recovered by helicopter from the water. As an alternative approach, a modified SR-71 vehicle has been proposed by the McDonnell Douglas Corporation. Benefits of the SR-71 include its variable geometry supersonic inlets, small cockpit bulge, higher Mach number capabilities, slender design, and longer length (105 foot). The present investigation addresses the sonic-boom analysis for the second vehicle.The objective of the current investigation is to assess the feasibility of a modified SR-71 configuration, with McDonnell Douglas-designed fuselage modifications, intended to produce shaped sonic-boom signatures on the ground. The present study describes the use of a higher-order computational fluid dynamics (CFD) method to predict the sonic-boom characteristics for both unmodified and modified SR-71 configurations. An Euler unstructured grid methodology is used to predict the near-field, three-dimensional pressure patterns generated by both SR-71 models. The computed near-field pressure signatures are extrapolated to specified distances below the aircraft down to impingement on the ground using the code MDBOOM. Comparisons of the near-field pressure signatures with available flight-test data are presented in the current paper.

Evolution of PCDD/F-signatures during mechanochemical degradation in municipal solid waste incineration filter ash.

PubMed

Zhiliang, Chen; Minghui, Tang; Shengyong, Lu; Jiamin, Ding; Qili, Qiu; Yuting, Wang; Jianhua, Yan

2018-05-28

Mechanochemical degradation (MCD) is employed for the dechlorination of polychlorinated dibenzo-p-dioxins (PCDD) and -furans (PCDF) in filter ashes from municipal solid waste incinerators, respectively with the assist of six additive systems. The evolution of PCDD/F-signatures in all eleven samples are systematically monitored and studied at the level of individual congeners, and special attention is paid to CP-route congeners, 2,3,7,8-substitution, 1,9-substitution, and 4,6-PCDF. The PCDD/F-isomers distribution follows an analogous pattern, indicating the similar acting mechanism for all additives: additives transfer electrons to attack the CCl bond and then expulse chlorine. MC dechlorination is not favored for the chlorine on β-position (2,3,7,8-position). The oxygen with stronger electronegativity in PCDD/Fs negatively influences CCl bond to accept donated electrons, hindering the removal of chlorine on 1,9-position for PCDD, and chlroine on 4,6-position for PCDF. Finally, two fair dechlorination pathways for PCDD and PCDF are respectively proposed based on the detailed analysis of CP-route congeners. The evolution of PCDD-signatures is clear, yet obscure for PCDF-signatures, which still requires further investigations. Copyright © 2018 Elsevier Ltd. All rights reserved.

Hyperspectral imagery for observing spectral signature change in Aspergillus flavus

NASA Astrophysics Data System (ADS)

DiCrispino, Kevin; Yao, Haibo; Hruska, Zuzana; Brabham, Kori; Lewis, David; Beach, Jim; Brown, Robert L.; Cleveland, Thomas E.

2005-11-01

Aflatoxin contaminated corn is dangerous for domestic animals when used as feed and cause liver cancer when consumed by human beings. Therefore, the ability to detect A. flavus and its toxic metabolite, aflatoxin, is important. The objective of this study is to measure A. flavus growth using hyperspectral technology and develop spectral signatures for A. flavus. Based on the research group's previous experiments using hyperspectral imaging techniques, it has been confirmed that the spectral signature of A. flavus is unique and readily identifiable against any background or surrounding surface and among other fungal strains. This study focused on observing changes in the A. flavus spectral signature over an eight-day growth period. The study used a visible-near-infrared hyperspectral image system for data acquisition. This image system uses focal plane pushbroom scanning for high spatial and high spectral resolution imaging. Procedures previously developed by the research group were used for image calibration and image processing. The results showed that while A. flavus gradually progressed along the experiment timeline, the day-to-day surface reflectance of A. flavus displayed significant difference in discreet regions of the wavelength spectrum. External disturbance due to environmental changes also altered the growth and subsequently changed the reflectance patterns of A. flavus.

Lead isotope evolution across the Neoproterozoic boundary between craton and juvenile crust, Bayuda Desert, Sudan

NASA Astrophysics Data System (ADS)

Evuk, David; Lucassen, Friedrich; Franz, Gerhard

2017-11-01

Metaigneous mafic and ultramafic rocks from the juvenile Neoproterozoic Arabian Nubian Shield (ANS) and the Proterozoic, reworked Saharan Metacraton (SMC) have been analysed for major- and trace elements and Sr, Nd, and Pb isotopes. Most of the rocks are amphibolites metamorphosed at amphibolite facies conditions, some with relicts of a granulite facies stage. The other rocks are metapyroxenites, metagabbros, and some ultramafic rocks. Trace element compositions of the metabasaltic (dominantly tholeiitic) rocks resemble the patterns of island arcs and primitive lavas from continental arcs. Variable Sr and Nd isotope ratios indicate depleted mantle dominance for most of the samples. 207Pb/204Pb signatures distinguish between the influence of high 207Pb/204Pb old SMC crust and depleted mantle signatures of the juvenile ANS crust. The Pb isotope signatures for most metabasaltic rocks, metapyroxenites and metagabbros from SMC indicate an autochthonous formation. The interpretation of the new data together with published evidence from mafic xenoliths on SMC and ophiolite from ANS allows an extrapolation of mantle evolution in time. There are two lines of evolution in the regional mantle, one, which incorporates potential upper crust material during Neoproterozoic, and a second one with a depleted mantle signature since pre-Neoproterozoic that still is present in the Red Sea and Gulf of Aden spreading centres.

Proteomics goes forensic: Detection and mapping of blood signatures in fingermarks.

PubMed

Deininger, Lisa; Patel, Ekta; Clench, Malcolm R; Sears, Vaughn; Sammon, Chris; Francese, Simona

2016-06-01

A bottom up in situ proteomic method has been developed enabling the mapping of multiple blood signatures on the intact ridges of blood fingermarks by Matrix Assisted Laser Desorption Mass Spectrometry Imaging (MALDI-MSI). This method, at a proof of concept stage, builds upon recently published work demonstrating the opportunity to profile and identify multiple blood signatures in bloodstains via a bottom up proteomic approach. The present protocol addresses the limitation of the previously developed profiling method with respect to destructivity; destructivity should be avoided for evidence such as blood fingermarks, where the ridge detail must be preserved in order to provide the associative link between the biometric information and the events of bloodshed. Using a blood mark reference model, trypsin concentration and spraying conditions have been optimised within the technical constraints of the depositor eventually employed; the application of MALDI-MSI and Ion Mobility MS have enabled the detection, confirmation and visualisation of blood signatures directly onto the ridge pattern. These results are to be considered a first insight into a method eventually informing investigations (and judicial debates) of violent crimes in which the reliable and non-destructive detection and mapping of blood in fingermarks is paramount to reconstruct the events of bloodshed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Observable Signatures of Energy Release in Braided Coronal Loops

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

Pontin, D. I.; Janvier, M.; Tiwari, S. K.

We examine the turbulent relaxation of solar coronal loops containing non-trivial field line braiding. Such field line tangling in the corona has long been postulated in the context of coronal heating models. We focus on the observational signatures of energy release in such braided magnetic structures using MHD simulations and forward modeling tools. The aim is to answer the following question: if energy release occurs in a coronal loop containing braided magnetic flux, should we expect a clearly observable signature in emissions? We demonstrate that the presence of braided magnetic field lines does not guarantee a braided appearance to themore » observed intensities. Observed intensities may—but need not necessarily—reveal the underlying braided nature of the magnetic field, depending on the degree and pattern of the field line tangling within the loop. However, in all cases considered, the evolution of the braided loop is accompanied by localized heating regions as the loop relaxes. Factors that may influence the observational signatures are discussed. Recent high-resolution observations from Hi-C have claimed the first direct evidence of braided magnetic fields in the corona. Here we show that both the Hi-C data and some of our simulations give the appearance of braiding at a range of scales.« less

Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

PubMed

Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

2014-03-01

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg.

Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins

PubMed Central

Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

2014-01-01

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg. PMID:24603469

Genetic differences between blood- and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences.

PubMed Central

Korber, B T; Kunstman, K J; Patterson, B K; Furtado, M; McEvilly, M M; Levy, R; Wolinsky, S M

1994-01-01

Human immunodeficiency virus type 1 (HIV-1) sequences were generated from blood and from brain tissue obtained by stereotactic biopsy from six patients undergoing a diagnostic neurosurgical procedure. Proviral DNA was directly amplified by nested PCR, and 8 to 36 clones from each sample were sequenced. Phylogenetic analysis of intrapatient envelope V3-V5 region HIV-1 DNA sequence sets revealed that brain viral sequences were clustered relative to the blood viral sequences, suggestive of tissue-specific compartmentalization of the virus in four of the six cases. In the other two cases, the blood and brain virus sequences were intermingled in the phylogenetic analyses, suggesting trafficking of virus between the two tissues. Slide-based PCR-driven in situ hybridization of two of the patients' brain biopsy samples confirmed our interpretation of the intrapatient phylogenetic analyses. Interpatient V3 region brain-derived sequence distances were significantly less than blood-derived sequence distances. Relative to the tip of the loop, the set of brain-derived viral sequences had a tendency towards negative or neutral charge compared with the set of blood-derived viral sequences. Entropy calculations were used as a measure of the variability at each position in alignments of blood and brain viral sequences. A relatively conserved set of positions were found, with a significantly lower entropy in the brain-than in the blood-derived viral sequences. These sites constitute a brain "signature pattern," or a noncontiguous set of amino acids in the V3 region conserved in viral sequences derived from brain tissue. This brain-derived signature pattern was also well preserved among isolates previously characterized in vitro as macrophage tropic. Macrophage-monocyte tropism may be the biological constraint that results in the conservation of the viral brain signature pattern. Images PMID:7933130

Biological signatures of dynamic river networks from a coupled landscape evolution and neutral community model

NASA Astrophysics Data System (ADS)

Stokes, M.; Perron, J. T.

2017-12-01

Freshwater systems host exceptionally species-rich communities whose spatial structure is dictated by the topology of the river networks they inhabit. Over geologic time, river networks are dynamic; drainage basins shrink and grow, and river capture establishes new connections between previously separated regions. It has been hypothesized that these changes in river network structure influence the evolution of life by exchanging and isolating species, perhaps boosting biodiversity in the process. However, no general model exists to predict the evolutionary consequences of landscape change. We couple a neutral community model of freshwater organisms to a landscape evolution model in which the river network undergoes drainage divide migration and repeated river capture. Neutral community models are macro-ecological models that include stochastic speciation and dispersal to produce realistic patterns of biodiversity. We explore the consequences of three modes of speciation - point mutation, time-protracted, and vicariant (geographic) speciation - by tracking patterns of diversity in time and comparing the final result to an equilibrium solution of the neutral model on the final landscape. Under point mutation, a simple model of stochastic and instantaneous speciation, the results are identical to the equilibrium solution and indicate the dominance of the species-area relationship in forming patterns of diversity. The number of species in a basin is proportional to its area, and regional species richness reaches its maximum when drainage area is evenly distributed among sub-basins. Time-protracted speciation is also modeled as a stochastic process, but in order to produce more realistic rates of diversification, speciation is not assumed to be instantaneous. Rather, each new species must persist for a certain amount of time before it is considered to be established. When vicariance (geographic speciation) is included, there is a transient signature of increased regional diversity after river capture. The results indicate that the mode of speciation and the rate of speciation relative to the rate of divide migration determine the evolutionary signature of river capture.

Ten-year chemical signatures associated with long-range transport observed in the free troposphere over the central North Atlantic

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

Zhang, B.; Owen, R. C.; Perlinger, J. A.

Ten-year observations of trace gases at Pico Mountain Observatory (PMO), a free troposphere site in the central North Atlantic, were classified by transport patterns using the Lagrangian particle dispersion model, FLEXPART. The classification enabled identifying trace gas mixing ratios associated with background air and long- range transport of continental emissions, which were defined as chemical signatures. Comparison between the chemical signatures revealed the impacts of natural and anthropogenic sources, as well as chemical and physical processes during long transport, on air composition in the remote North Atlantic. Transport of North American anthropogenic emissions (NA-Anthro) and summertime wildfire plumes (Fire) significantlymore » enhanced CO and O 3 at PMO. Summertime CO enhancements caused by NA-Anthro were found to have been decreasing by a rate of 0.67 ± 0.60 ppbv/year in the ten-year period, due possibly to reduction of emissions in North America. Downward mixing from the upper troposphere and stratosphere due to the persistent Azores-Bermuda anticyclone causes enhanced O 3 and nitrogen oxides. The d [O 3]/d [CO] value was used to investigate O 3 sources and chemistry in different transport patterns. The transport pattern affected by Fire had the lowest d [O 3]/d [CO], which was likely due to intense CO production and depressed O 3 production in wildfire plumes. Slightly enhanced O 3 and d [O 3]/d [CO] were found in the background air, suggesting that weak downward mixing from the upper troposphere is common at PMO. Enhancements of both butane isomers were found during upslope flow periods, indicating contributions from local sources. The consistent ratio of butane isomers associated with the background air and NA-anthro implies no clear difference in the oxidation rates of the butane isomers during long transport. Based on observed relationships between non-methane hydrocarbons, the averaged photochemical age of the air masses at PMO was estimated to be 11 ± 4 days.« less

Ten-year chemical signatures associated with long-range transport observed in the free troposphere over the central North Atlantic

DOE PAGES

Zhang, B.; Owen, R. C.; Perlinger, J. A.; ...

2017-03-06

Ten-year observations of trace gases at Pico Mountain Observatory (PMO), a free troposphere site in the central North Atlantic, were classified by transport patterns using the Lagrangian particle dispersion model, FLEXPART. The classification enabled identifying trace gas mixing ratios associated with background air and long- range transport of continental emissions, which were defined as chemical signatures. Comparison between the chemical signatures revealed the impacts of natural and anthropogenic sources, as well as chemical and physical processes during long transport, on air composition in the remote North Atlantic. Transport of North American anthropogenic emissions (NA-Anthro) and summertime wildfire plumes (Fire) significantlymore » enhanced CO and O 3 at PMO. Summertime CO enhancements caused by NA-Anthro were found to have been decreasing by a rate of 0.67 ± 0.60 ppbv/year in the ten-year period, due possibly to reduction of emissions in North America. Downward mixing from the upper troposphere and stratosphere due to the persistent Azores-Bermuda anticyclone causes enhanced O 3 and nitrogen oxides. The d [O 3]/d [CO] value was used to investigate O 3 sources and chemistry in different transport patterns. The transport pattern affected by Fire had the lowest d [O 3]/d [CO], which was likely due to intense CO production and depressed O 3 production in wildfire plumes. Slightly enhanced O 3 and d [O 3]/d [CO] were found in the background air, suggesting that weak downward mixing from the upper troposphere is common at PMO. Enhancements of both butane isomers were found during upslope flow periods, indicating contributions from local sources. The consistent ratio of butane isomers associated with the background air and NA-anthro implies no clear difference in the oxidation rates of the butane isomers during long transport. Based on observed relationships between non-methane hydrocarbons, the averaged photochemical age of the air masses at PMO was estimated to be 11 ± 4 days.« less

The impact of transport processes on rare earth element patterns in marine authigenic and biogenic phosphates

NASA Astrophysics Data System (ADS)

Auer, Gerald; Reuter, Markus; Hauzenberger, Christoph A.; Piller, Werner E.

2017-04-01

Rare earth elements (REEs) are commonly used proxies to reconstruct water chemistry and oxygen saturation during the formation of authigenic and biogenic phosphates in marine environments. In the modern ocean REEs exhibit a distinct pattern with enrichment of heavy REEs and strong depletion in cerium (Ce). The wide range of REE enrichment patterns found in ancient marine phosphates lead to the proposition that water chemistry has been very different in the Earth's past. However, both early and late diagenesis are known to affect REE signatures in phosphates altering primary marine signals. Herein we present a dataset of REE signatures in 38 grain specific LA-ICP-MS measurements of isolated phosphate and carbonate grains in three discrete rock samples. The phosphates mainly consist of authigenic phosphates and phosphatized microfossils that formed in a microbially mediated micro-milieu. In addition, isolated biogenic and reworked phosphatic grains are also present. The phosphates are emplaced in bioclastic grain- to packstones deposited on a carbonate ramp setting in the central Mediterranean Sea during the middle Miocene Monterey event. The results reveal markedly different REE patterns (normalized to the Post Archean Australian Shale standard) in terms of total enrichment and pattern shape. Analyses of REE diagenesis proxies show that diagenetic alteration affected the samples only to a minor degree. Grain shape and REE patterns together indicate that authigenic, biogenic and reworked phosphates have distinct REE patterns irrespective of the sample. Our study shows that while REE patterns in phosphates do reflect water chemistry during authigenesis, they are often already heavily altered during reworking, a process, which can occur in geologically negligible timespans. REE patterns are therefore more likely to reflect complex enrichment processes after their formation. Similarities in the REE patterns of reworked and biogenic phosphate further suggest that the frequently observed hat-shaped pattern in biogenic phosphates can result from increased middle REE (Neodymium to Holmium) scavenging during taphonomic processes prior to final deposition. Cluster analysis coupled with sedimentological and previously published geochemical data (bulk carbon isotope and X-ray fluorescence spectrometry) allowed the characterization of REE patterns of phosphates in terms of their formation conditions and depositional history, such as the distinction of phosphates formed in situ from reworked and transported phosphate grains.

Induction of Chromosome Instability by Activation of Yes-Associated Protein and Forkhead Box M1 in Liver Cancer.

PubMed

Weiler, Sofia M E; Pinna, Federico; Wolf, Thomas; Lutz, Teresa; Geldiyev, Aman; Sticht, Carsten; Knaub, Maria; Thomann, Stefan; Bissinger, Michaela; Wan, Shan; Rössler, Stephanie; Becker, Diana; Gretz, Norbert; Lang, Hauke; Bergmann, Frank; Ustiyan, Vladimir; Kalin, Tatiana V; Singer, Stephan; Lee, Ju-Seog; Marquardt, Jens U; Schirmacher, Peter; Kalinichenko, Vladimir V; Breuhahn, Kai

2017-06-01

Many different types of cancer cells have chromosome instability. The hippo pathway leads to phosphorylation of the transcriptional activator yes-associated protein 1 (YAP1, YAP), which regulates proliferation and has been associated with the development of liver cancer. We investigated the effects of hippo signaling via YAP on chromosome stability and hepatocarcinogenesis in humans and mice. We analyzed transcriptome data from 242 patients with hepatocellular carcinoma (HCC) to search for gene signatures associated with chromosomal instability (CIN); we investigated associations with overall survival time and cancer recurrence using Kaplan-Meier curves. We analyzed changes in expression of these signature genes, at mRNA and protein levels, after small interfering RNA-mediated silencing of YAP in Sk-Hep1, SNU182, HepG2, or pancreatic cancer cells, as well as incubation with thiostrepton (an inhibitor of forkhead box M1 [FOXM1]) or verteporfin (inhibitor of the interaction between YAP and TEA domain transcription factor 4 [TEAD4]). We performed co-immunoprecipitation and chromatin immunoprecipitation experiments. We collected liver tissues from mice that express a constitutively active form of YAP (YAP S127A ) and analyzed gene expression signatures and histomorphologic parameters associated with chromosomal instability. Mice were given injections of thiostrepton and livers were collected and analyzed by immunoblotting, immunohistochemistry, histology, and real-time polymerase chain reaction. We performed immunohistochemical analyses on tissue microarrays of 105 HCCs and 7 nontumor liver tissues. Gene expression patterns associated with chromosome instability, called CIN25 and CIN70, were detected in HCCs from patients with shorter survival time or early cancer recurrence. TEAD4 and YAP were required for CIN25 and CIN70 signature expression via induction and binding of FOXM1. Disrupting the interaction between YAP and TEAD4 with verteporfin, or inhibiting FOXM1 with thiostrepton, reduced the chromosome instability gene expression patterns. Hyperplastic livers and tumors from YAP S127A mice had increased CIN25 and CIN70 gene expression patterns, aneuploidy, and defects in mitosis. Injection of YAP S127A mice with thiostrepton reduced liver overgrowth and signs of chromosomal instability. In human HCC tissues, high levels of nuclear YAP correlated with increased chromosome instability gene expression patterns and aneuploidy. By analyzing cell lines, genetically modified mice, and HCC tissues, we found that YAP cooperates with FOXM1 to contribute to chromosome instability. Agents that disrupt this pathway might be developed as treatments for liver cancer. Transcriptome data are available in the Gene Expression Omnibus public database (accession numbers: GSE32597 and GSE73396). Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

CYCLIC THERMAL SIGNATURE IN A GLOBAL MHD SIMULATION OF SOLAR CONVECTION

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

Cossette, Jean-Francois; Charbonneau, Paul; Smolarkiewicz, Piotr K.

Global magnetohydrodynamical simulations of the solar convection zone have recently achieved cyclic large-scale axisymmetric magnetic fields undergoing polarity reversals on a decadal time scale. In this Letter, we show that these simulations also display a thermal convective luminosity that varies in-phase with the magnetic cycle, and trace this modulation to deep-seated magnetically mediated changes in convective flow patterns. Within the context of the ongoing debate on the physical origin of the observed 11 yr variations in total solar irradiance, such a signature supports the thesis according to which all, or part, of the variations on decadal time scales and longermore » could be attributed to a global modulation of the Sun's internal thermal structure by magnetic activity.« less

Microwave responses of the western North Atlantic

NASA Technical Reports Server (NTRS)

Stacey, J. M.; Girard, M. A.

1985-01-01

Features and objects in the Western North Atlantic Ocean - the Eastern Seaboard of the United States - are observed from Earth orbit by passive microwaves. The intensities of their radiated flux signatures are measured and displayed in color as a microwave flux image. The features of flux emitting objects such as the course of the Gulf Stream and the occurrence of cold eddies near the Gulf Stream are identified by contoured patterns of relative flux intensities. The flux signatures of ships and their wakes are displayed and discussed. Metal data buoys and aircraft are detected. Signal to clutter ratios and probabilities of detection are computed from their measured irradiances. Theoretical models and the range equations that explain passive microwave detection using the irradiances of natural sources are summarized.

Strain Pattern in Supercooled Liquids

NASA Astrophysics Data System (ADS)

Illing, Bernd; Fritschi, Sebastian; Hajnal, David; Klix, Christian; Keim, Peter; Fuchs, Matthias

2016-11-01

Investigations of strain correlations at the glass transition reveal unexpected phenomena. The shear strain fluctuations show an Eshelby-strain pattern [˜cos (4 θ ) /r2 ], characteristic of elastic response, even in liquids, at long times. We address this using a mode-coupling theory for the strain fluctuations in supercooled liquids and data from both video microscopy of a two-dimensional colloidal glass former and simulations of Brownian hard disks. We show that the long-ranged and long-lived strain signatures follow a scaling law valid close to the glass transition. For large enough viscosities, the Eshelby-strain pattern is visible even on time scales longer than the structural relaxation time τ and after the shear modulus has relaxed to zero.

Recognition of surface lithologic and topographic patterns in southwest Colorado with ADP techniques

NASA Technical Reports Server (NTRS)

Melhorn, W. N.; Sinnock, S.

1973-01-01

Analysis of ERTS-1 multispectral data by automatic pattern recognition procedures is applicable toward grappling with current and future resource stresses by providing a means for refining existing geologic maps. The procedures used in the current analysis already yield encouraging results toward the eventual machine recognition of extensive surface lithologic and topographic patterns. Automatic mapping of a series of hogbacks, strike valleys, and alluvial surfaces along the northwest flank of the San Juan Basin in Colorado can be obtained by minimal man-machine interaction. The determination of causes for separable spectral signatures is dependent upon extensive correlation of micro- and macro field based ground truth observations and aircraft underflight data with the satellite data.

Arthropod food web restoration following removal of an invasive wetland plant.

PubMed

Gratton, Claudio; Denno, Robert F

2006-04-01

Restoration of habitats impacted by invasive plants is becoming an increasingly important tool in the management of native biodiversity, though most studies do not go beyond monitoring the abundance of particular taxonomic groups, such as the return of native vegetation. Yet, the reestablishment of trophic interactions among organisms in restored habitats is equally important if we are to monitor and understand how ecosystems recover. This study examined whether food web interactions among arthropods (as inferred by abundance of naturally occurring stable isotopes of C [delta13C] and N [delta15N]) were reestablished in the restoration of a coastal Spartina alterniflora salt marsh that had been invaded by Phragmites australis. From patterns of C and N stable isotopes we infer that trophic interactions among arthropods in the native salt marsh habitats are characterized by reliance on the dominant marsh plant Spartina as a basal resource. Herbivores such as delphacid planthoppers and mirid bugs have isotope signatures characteristic of Spartina, and predatory arthropods such as dolicopodid flies and spiders likewise have delta13C and delta15N signatures typical of Spartina-derived resources (approximately -13 per thousand and 10 per thousand, respectively). Stable isotope patterns also suggest that the invasion of Phragmites into salt marshes and displacement of Spartina significantly alter arthropod food web interactions. Arthropods in Phragmites-dominated sites have delta13C isotope values between -18 per thousand and -20 per thousand, suggesting reliance on detritus and/or benthic microalgae as basal resources and not on Phragmites, which has a delta13C approximately -26 per thousand. Since most Phragmites herbivores are either feeding internally or are rare transients from nearby Spartina, these resources do not provide significant prey resources for other arthropod consumers. Rather, predator isotope signatures in the invaded habitats indicate dependence on detritus/algae as basal resources instead of the dominant vegetation. The reestablishment of Spartina after removal of Phragmites, however, not only returned species assemblages typical of reference (uninvaded) Spartina, but stable isotope signatures suggest that the trophic interactions among the arthropods were also similar in reestablished habitats. Specifically, both herbivores and predators showed characteristic Spartina signatures, suggesting the return of the original grazer-based food web structure in the restored habitats.

Epigenetic changes in solid and hematopoietic tumors.

PubMed

Toyota, Minoru; Issa, Jean-Pierre J

2005-10-01

There are three connected molecular mechanisms of epigenetic cellular memory in mammalian cells: DNA methylation, histone modifications, and RNA interference. The first two have now been firmly linked to neoplastic transformation. Hypermethylation of CpG-rich promoters triggers local histone code modifications resulting in a cellular camouflage mechanism that sequesters gene promoters away from transcription factors and results in stable silencing. This normally restricted mechanism is ubiquitously used in cancer to silence hundreds of genes, among which some critically contribute to the neoplastic phenotype. Virtually every pathway important to cancer formation is affected by this process. Methylation profiling of human cancers reveals tissue-specific epigenetic signatures, as well as tumor-specific signatures, reflecting in particular the presence of epigenetic instability in a subset of cancers affected by the CpG island methylator phenotype. Generally, methylation patterns can be traced to a tissue-specific, proliferation-dependent accumulation of aberrant promoter methylation in aging tissues, a process that can be accelerated by chronic inflammation and less well-defined mechanisms including, possibly, diet and genetic predisposition. The epigenetic machinery can also be altered in cancer by specific lesions in epigenetic effector genes, or by aberrant recruitment of these genes by mutant transcription factors and coactivators. Epigenetic patterns are proving clinically useful in human oncology via risk assessment, early detection, and prognostic classification. Pharmacologic manipulation of these patterns-epigenetic therapy-is also poised to change the way we treat cancer in the clinic.

Presence of an epigenetic signature of prenatal cigarette smoke exposure in childhood☆

PubMed Central

Ladd-Acosta, Christine; Shu, Chang; Lee, Brian K.; Gidaya, Nicole; Singer, Alison; Schieve, Laura A.; Schendel, Diana E.; Jones, Nicole; Daniels, Julie L.; Windham, Gayle C.; Newschaffer, Craig J.; Croen, Lisa A.; Feinberg, Andrew P.; Fallin, M. Daniele

2016-01-01

Prenatal exposure to tobacco smoke has lifelong health consequences. Epigenetic signatures such as differences in DNA methylation (DNAm) may be a biomarker of exposure and, further, might have functional significance for how in utero tobacco exposure may influence disease risk. Differences in infant DNAm associated with maternal smoking during pregnancy have been identified. Here we assessed whether these infant DNAm patterns are detectible in early childhood, whether they are specific to smoking, and whether childhood DNAm can classify prenatal smoke exposure status. Using the Infinium 450 K array, we measured methylation at 26 CpG loci that were previously associated with prenatal smoking in infant cord blood from 572 children, aged 3–5, with differing prenatal exposure to cigarette smoke in the Study to Explore Early Development (SEED). Striking concordance was found between the pattern of prenatal smoking associated DNAm among preschool aged children in SEED and those observed at birth in other studies. These DNAm changes appear to be tobacco-specific. Support vector machine classification models and 10-fold cross-validation were applied to show classification accuracy for childhood DNAm at these 26 sites as a biomarker of prenatal smoking exposure. Classification models showed prenatal exposure to smoking can be assigned with 81% accuracy using childhood DNAm patterns at these 26 loci. These findings support the potential for blood-derived DNAm measurements to serve as biomarkers for prenatal exposure. PMID:26610292

A dehydration-inducible gene in the truffle Tuber borchii identifies a novel group of dehydrins

PubMed Central

Abba', Simona; Ghignone, Stefano; Bonfante, Paola

2006-01-01

Background The expressed sequence tag M6G10 was originally isolated from a screening for differentially expressed transcripts during the reproductive stage of the white truffle Tuber borchii. mRNA levels for M6G10 increased dramatically during fruiting body maturation compared to the vegetative mycelial stage. Results Bioinformatics tools, phylogenetic analysis and expression studies were used to support the hypothesis that this sequence, named TbDHN1, is the first dehydrin (DHN)-like coding gene isolated in fungi. Homologs of this gene, all defined as "coding for hypothetical proteins" in public databases, were exclusively found in ascomycetous fungi and in plants. Although complete (or almost complete) fungal genomes and EST collections of some Basidiomycota and Glomeromycota are already available, DHN-like proteins appear to be represented only in Ascomycota. A new and previously uncharacterized conserved signature pattern was identified and proposed to Uniprot database as the main distinguishing feature of this new group of DHNs. Expression studies provide experimental evidence of a transcript induction of TbDHN1 during cellular dehydration. Conclusion Expression pattern and sequence similarities to known plant DHNs indicate that TbDHN1 is the first characterized DHN-like protein in fungi. The high similarity of TbDHN1 with homolog coding sequences implies the existence of a novel fungal/plant group of LEA Class II proteins characterized by a previously undescribed signature pattern. PMID:16512918

Spectral singularities and Bragg scattering in complex crystals

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

Longhi, S.

2010-02-15

Spectral singularities that spoil the completeness of Bloch-Floquet states may occur in non-Hermitian Hamiltonians with complex periodic potentials. Here an equivalence is established between spectral singularities in complex crystals and secularities that arise in Bragg diffraction patterns. Signatures of spectral singularities in a scattering process with wave packets are elucidated for a PT-symmetric complex crystal.

Computational and Experimental Evaluation of a Complex Inlet Swirl Pattern Generation System (POSTPRINT)

DTIC Science & Technology

2016-08-01

Sanders, Chase A. Nessler, William W. Copenhaver, Michael G. List, and Timothy J. Janczewski Turbomachinery Branch Turbine Engine Division AUGUST...Branch Turbine Engine Division Turbine Engine Division Aerospace Systems Directorate //Signature// ROBERT D. HANCOCK Principal Scientist Turbine ...ORGANIZATION Turbomachinery Branch Turbine Engine Division Air Force Research Laboratory, Aerospace Systems Directorate Wright-Patterson Air Force

National Postsecondary Enrollment Trends: Before, during, and after the Great Recession. Signature[TM] Report 1

ERIC Educational Resources Information Center

Dunbar, Afet; Hossler, Don; Shapiro, Doug; Chen, Jin; Martin, Sarah; Torres, Vasti; Zerquera, Desiree; Ziskin, Mary

2011-01-01

This report, "National Postsecondary Enrollment Trends: Before, During, and After the Great Recession," brings to light emerging national and regional patterns among traditional-age, first-time students enrolling in colleges and universities during the fall term each year from 2006 through 2010--before, during, and after the recession.…

Late Influx: Evidence from Siderophile Elements in Terrestrial Peridotites and Lunar Breccias

NASA Technical Reports Server (NTRS)

Morgan, J. W.; Brandon, A. D.; Walker, R. J.; Horan, M. F.

2001-01-01

In terrestrial peridotites, Pd is sometimes enhanced relative to other PGE. This observation is taken to imply a "non-chondritic" HSE signature in the mantle. A similar pattern is seen in some Apollo 17 breccias suggesting it to be a primordial feature of late influx. Additional information is contained in the original extended abstract.

TOPICAL REVIEW: Biological and chemical sensors for cancer diagnosis

NASA Astrophysics Data System (ADS)

Simon, Elfriede

2010-11-01

The great challenge for sensor systems to be accepted as a relevant diagnostic and therapeutic tool for cancer detection is the ability to determine the presence of relevant biomarkers or biomarker patterns comparably to or even better than the traditional analytical systems. Biosensor and chemical sensor technologies are already used for several clinical applications such as blood glucose or blood gas measurements. However, up to now not many sensors have been developed for cancer-related tests because only a few of the biomarkers have shown clinical relevance and the performance of the sensor systems is not always satisfactory. New genomic and proteomic tools are used to detect new molecular signatures and identify which combinations of biomarkers may detect best the presence or risk of cancer or monitor cancer therapies. These molecular signatures include genetic and epigenetic signatures, changes in gene expressions, protein biomarker profiles and other metabolite profile changes. They provide new changes in using different sensor technologies for cancer detection especially when complex biomarker patterns have to be analyzed. To address requirements for this complex analysis, there have been recent efforts to develop sensor arrays and new solutions (e.g. lab on a chip) in which sampling, preparation, high-throughput analysis and reporting are integrated. The ability of parallelization, miniaturization and the degree of automation are the focus of new developments and will be supported by nanotechnology approaches. This review recaps some scientific considerations about cancer diagnosis and cancer-related biomarkers, relevant biosensor and chemical sensor technologies, their application as cancer sensors and consideration about future challenges.

Plant seed species identification from chemical fingerprints: a high-throughput application of direct analysis in real time mass spectrometry.

PubMed

Lesiak, Ashton D; Cody, Robert B; Dane, A John; Musah, Rabi A

2015-09-01

Plant species identification based on the morphological features of plant parts is a well-established science in botany. However, species identification from seeds has largely been unexplored, despite the fact that the seeds contain all of the genetic information that distinguishes one plant from another. Using seeds of genus Datura plants, we show here that the mass spectrum-derived chemical fingerprints for seeds of the same species are similar. On the other hand, seeds from different species within the same genus display distinct chemical signatures, even though they may contain similar characteristic biomarkers. The intraspecies chemical signature similarities on the one hand, and interspecies fingerprint differences on the other, can be processed by multivariate statistical analysis methods to enable rapid species-level identification and differentiation. The chemical fingerprints can be acquired rapidly and in a high-throughput manner by direct analysis in real time mass spectrometry (DART-MS) analysis of the seeds in their native form, without use of a solvent extract. Importantly, knowledge of the identity of the detected molecules is not required for species level identification. However, confirmation of the presence within the seeds of various characteristic tropane and other alkaloids, including atropine, scopolamine, scopoline, tropine, tropinone, and tyramine, was accomplished by comparison of the in-source collision-induced dissociation (CID) fragmentation patterns of authentic standards, to the fragmentation patterns observed in the seeds when analyzed under similar in-source CID conditions. The advantages, applications, and implications of the chemometric processing of DART-MS derived seed chemical signatures for species level identification and differentiation are discussed.

Aspergillus Cell Wall Chitin Induces Anti- and Proinflammatory Cytokines in Human PBMCs via the Fc-γ Receptor/Syk/PI3K Pathway

PubMed Central

Becker, K. L.; Aimanianda, V.; Wang, X.; Gresnigt, M. S.; Ammerdorffer, A.; Jacobs, C. W.; Gazendam, R. P.; Joosten, L. A. B.; Netea, M. G.

2016-01-01

ABSTRACT Chitin is an important cell wall component of Aspergillus fumigatus conidia, of which hundreds are inhaled on a daily basis. Previous studies have shown that chitin has both anti- and proinflammatory properties; however the exact mechanisms determining the inflammatory signature of chitin are poorly understood, especially in human immune cells. Human peripheral blood mononuclear cells were isolated from healthy volunteers and stimulated with chitin from Aspergillus fumigatus. Transcription and production of the proinflammatory cytokine interleukin-1β (IL-1β) and the anti-inflammatory cytokine IL-1 receptor antagonist (IL-1Ra) were measured from the cell culture supernatant by quantitative PCR (qPCR) or enzyme-linked immunosorbent assay (ELISA), respectively. Chitin induced an anti-inflammatory signature characterized by the production of IL-1Ra in the presence of human serum, which was abrogated in immunoglobulin-depleted serum. Fc-γ-receptor-dependent recognition and phagocytosis of IgG-opsonized chitin was identified as a novel IL-1Ra-inducing mechanism by chitin. IL-1Ra production induced by chitin was dependent on Syk kinase and phosphatidylinositol 3-kinase (PI3K) activation. In contrast, costimulation of chitin with the pattern recognition receptor (PRR) ligands lipopolysaccharide, Pam3Cys, or muramyl dipeptide, but not β-glucan, had synergistic effects on the induction of proinflammatory cytokines by human peripheral blood mononuclear cells (PBMCs). In conclusion, chitin can have both pro- and anti-inflammatory properties, depending on the presence of pathogen-associated molecular patterns and immunoglobulins, thus explaining the various inflammatory signatures reported for chitin. PMID:27247234

A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

PubMed Central

Farquhar, Iseabail L.; Young, Rachel; Lefevre, Lucas; Pridans, Clare; Tsang, Hiu G.; Afrasiabi, Cyrus; Watson, Mick; Whitelaw, C. Bruce; Freeman, Tom C.; Archibald, Alan L.; Hume, David A.

2017-01-01

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of ‘guilt by association’ was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages. PMID:28915238

A high resolution atlas of gene expression in the domestic sheep (Ovis aries).

PubMed

Clark, Emily L; Bush, Stephen J; McCulloch, Mary E B; Farquhar, Iseabail L; Young, Rachel; Lefevre, Lucas; Pridans, Clare; Tsang, Hiu G; Wu, Chunlei; Afrasiabi, Cyrus; Watson, Mick; Whitelaw, C Bruce; Freeman, Tom C; Summers, Kim M; Archibald, Alan L; Hume, David A

2017-09-01

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of 'guilt by association' was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.

Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells.

PubMed

Winterhoff, Boris J; Maile, Makayla; Mitra, Amit Kumar; Sebe, Attila; Bazzaro, Martina; Geller, Melissa A; Abrahante, Juan E; Klein, Molly; Hellweg, Raffaele; Mullany, Sally A; Beckman, Kenneth; Daniel, Jerry; Starr, Timothy K

2017-03-01

The purpose of this study was to determine the level of heterogeneity in high grade serous ovarian cancer (HGSOC) by analyzing RNA expression in single epithelial and cancer associated stromal cells. In addition, we explored the possibility of identifying subgroups based on pathway activation and pre-defined signatures from cancer stem cells and chemo-resistant cells. A fresh, HGSOC tumor specimen derived from ovary was enzymatically digested and depleted of immune infiltrating cells. RNA sequencing was performed on 92 single cells and 66 of these single cell datasets passed quality control checks. Sequences were analyzed using multiple bioinformatics tools, including clustering, principle components analysis, and geneset enrichment analysis to identify subgroups and activated pathways. Immunohistochemistry for ovarian cancer, stem cell and stromal markers was performed on adjacent tumor sections. Analysis of the gene expression patterns identified two major subsets of cells characterized by epithelial and stromal gene expression patterns. The epithelial group was characterized by proliferative genes including genes associated with oxidative phosphorylation and MYC activity, while the stromal group was characterized by increased expression of extracellular matrix (ECM) genes and genes associated with epithelial-to-mesenchymal transition (EMT). Neither group expressed a signature correlating with published chemo-resistant gene signatures, but many cells, predominantly in the stromal subgroup, expressed markers associated with cancer stem cells. Single cell sequencing provides a means of identifying subpopulations of cancer cells within a single patient. Single cell sequence analysis may prove to be critical for understanding the etiology, progression and drug resistance in ovarian cancer. Copyright © 2017 Elsevier Inc. All rights reserved.

Spatio-temporal dynamics of processing non-symbolic number: An ERP source localization study

PubMed Central

Hyde, Daniel C.; Spelke, Elizabeth S.

2013-01-01

Coordinated studies with adults, infants, and nonhuman animals provide evidence for two distinct systems of non-verbal number representation. The ‘parallel individuation’ system selects and retains information about 1–3 individual entities and the ‘numerical magnitude’ system establishes representations of the approximate cardinal value of a group. Recent ERP work has demonstrated that these systems reliably evoke functionally and temporally distinct patterns of brain response that correspond to established behavioral signatures. However, relatively little is known about the neural generators of these ERP signatures. To address this question, we targeted known ERP signatures of these systems, by contrasting processing of small versus large non-symbolic numbers, and used a source localization algorithm (LORETA) to identify their cortical origins. Early processing of small numbers, showing the signature effects of parallel individuation on the N1 (∼150 ms), was localized primarily to extrastriate visual regions. In contrast, qualitatively and temporally distinct processing of large numbers, showing the signatures of approximate number representation on the mid-latency P2p (∼200–250 ms), was localized primarily to right intraparietal regions. In comparison, mid-latency small number processing was localized to the right temporal-parietal junction and left-lateralized intraparietal regions. These results add spatial information to the emerging ERP literature documenting the process by which we represent number. Furthermore, these results substantiate recent claims that early attentional processes determine whether a collection of objects will be represented through parallel individuation or as an approximate numerical magnitude by providing evidence that downstream processing diverges to distinct cortical regions. PMID:21830257

Spatiotemporal dynamics of processing nonsymbolic number: an event-related potential source localization study.

PubMed

Hyde, Daniel C; Spelke, Elizabeth S

2012-09-01

Coordinated studies with adults, infants, and nonhuman animals provide evidence for two distinct systems of nonverbal number representation. The "parallel individuation" (PI) system selects and retains information about one to three individual entities and the "numerical magnitude" system establishes representations of the approximate cardinal value of a group. Recent event-related potential (ERP) work has demonstrated that these systems reliably evoke functionally and temporally distinct patterns of brain response that correspond to established behavioral signatures. However, relatively little is known about the neural generators of these ERP signatures. To address this question, we targeted known ERP signatures of these systems, by contrasting processing of small versus large nonsymbolic numbers, and used a source localization algorithm (LORETA) to identify their cortical origins. Early processing of small numbers, showing the signature effects of PI on the N1 (∼150 ms), was localized primarily to extrastriate visual regions. In contrast, qualitatively and temporally distinct processing of large numbers, showing the signatures of approximate number representation on the mid-latency P2p (∼200-250 ms), was localized primarily to right intraparietal regions. In comparison, mid-latency small number processing was localized to the right temporal-parietal junction and left-lateralized intraparietal regions. These results add spatial information to the emerging ERP literature documenting the process by which we represent number. Furthermore, these results substantiate recent claims that early attentional processes determine whether a collection of objects will be represented through PI or as an approximate numerical magnitude by providing evidence that downstream processing diverges to distinct cortical regions. Copyright © 2011 Wiley Periodicals, Inc.

Analysis of Human Plasma Metabolites across Different Liquid Chromatography - Mass Spectrometry Platforms: Cross-platform Transferable Chemical Signatures

PubMed Central

Telu, Kelly H.; Yan, Xinjian; Wallace, William E.; Stein, Stephen E.; Simón-Manso, Yamil

2016-01-01

RATIONALE The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different LC-MS platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. METHODS Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC-MS platforms using reversed phase chromatography and different chromatographic scales (nano, conventional and UHPLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). RESULTS Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (RSD < 2%); however, substantial differences were found in the LC-MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. CONLUSIONS Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. PMID:26842580

Muscle myeloid type I interferon gene expression may predict therapeutic responses to rituximab in myositis patients

PubMed Central

Nagaraju, Kanneboyina; Ghimbovschi, Svetlana; Rayavarapu, Sree; Phadke, Aditi; Rider, Lisa G.; Hoffman, Eric P.

2016-01-01

Abstract Objective. To identify muscle gene expression patterns that predict rituximab responses and assess the effects of rituximab on muscle gene expression in PM and DM. Methods. In an attempt to understand the molecular mechanism of response and non-response to rituximab therapy, we performed Affymetrix gene expression array analyses on muscle biopsy specimens taken before and after rituximab therapy from eight PM and two DM patients in the Rituximab in Myositis study. We also analysed selected muscle-infiltrating cell phenotypes in these biopsies by immunohistochemical staining. Partek and Ingenuity pathway analyses assessed the gene pathways and networks. Results. Myeloid type I IFN signature genes were expressed at higher levels at baseline in the skeletal muscle of rituximab responders than in non-responders, whereas classic non-myeloid IFN signature genes were expressed at higher levels in non-responders at baseline. Also, rituximab responders have a greater reduction of the myeloid and non-myeloid type I IFN signatures than non-responders. The decrease in the type I IFN signature following administration of rituximab may be associated with the decreases in muscle-infiltrating CD19 + B cells and CD68 + macrophages in responders. Conclusion. Our findings suggest that high levels of myeloid type I IFN gene expression in skeletal muscle predict responses to rituximab in PM/DM and that rituximab responders also have a greater decrease in the expression of these genes. These data add further evidence to recent studies defining the type I IFN signature as both a predictor of therapeutic responses and a biomarker of myositis disease activity. PMID:27215813

Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus).

PubMed

Marsden, Clare D; Woodroffe, Rosie; Mills, Michael G L; McNutt, J Weldon; Creel, Scott; Groom, Rosemary; Emmanuel, Masenga; Cleaveland, Sarah; Kat, Pieter; Rasmussen, Gregory S A; Ginsberg, Joshua; Lines, Robin; André, Jean-Marc; Begg, Colleen; Wayne, Robert K; Mable, Barbara K

2012-03-01

Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the major histocompatibility complex (MHC), are increasingly being incorporated into genetic studies. In this study, we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (N(e)  < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structuring of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations, we found that the spatial and temporal structure of microsatellite diversity and MHC diversity were correlated and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift. © 2012 Blackwell Publishing Ltd.

Inferring individual-level processes from population-level patterns in cultural evolution

PubMed Central

Wilder, Bryan

2017-01-01

Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data, we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution. PMID:28989786

GESearch: An Interactive GUI Tool for Identifying Gene Expression Signature.

PubMed

Ye, Ning; Yin, Hengfu; Liu, Jingjing; Dai, Xiaogang; Yin, Tongming

2015-01-01

The huge amount of gene expression data generated by microarray and next-generation sequencing technologies present challenges to exploit their biological meanings. When searching for the coexpression genes, the data mining process is largely affected by selection of algorithms. Thus, it is highly desirable to provide multiple options of algorithms in the user-friendly analytical toolkit to explore the gene expression signatures. For this purpose, we developed GESearch, an interactive graphical user interface (GUI) toolkit, which is written in MATLAB and supports a variety of gene expression data files. This analytical toolkit provides four models, including the mean, the regression, the delegate, and the ensemble models, to identify the coexpression genes, and enables the users to filter data and to select gene expression patterns by browsing the display window or by importing knowledge-based genes. Subsequently, the utility of this analytical toolkit is demonstrated by analyzing two sets of real-life microarray datasets from cell-cycle experiments. Overall, we have developed an interactive GUI toolkit that allows for choosing multiple algorithms for analyzing the gene expression signatures.

Molecular Aging of Human Liver: An Epigenetic/Transcriptomic Signature.

PubMed

Bacalini, Maria Giulia; Franceschi, Claudio; Gentilini, Davide; Ravaioli, Francesco; Zhou, Xiaoyuan; Remondini, Daniel; Pirazzini, Chiara; Giuliani, Cristina; Marasco, Elena; Gensous, Noémie; Di Blasio, Anna Maria; Ellis, Ewa; Gramignoli, Roberto; Castellani, Gastone; Capri, Miriam; Strom, Stephen; Nardini, Christine; Cescon, Matteo; Grazi, Gian Luca; Garagnani, Paolo

2018-03-15

The feasibility of liver transplantation from old healthy donors suggests that this organ is able to preserve its functionality during aging. To explore the biological basis of this phenomenon, we characterized the epigenetic profile of liver biopsies collected from 45 healthy liver donors ranging from 13 to 90 years old using the Infinium HumanMethylation450 BeadChip. The analysis indicates that a large remodeling in DNA methylation patterns occurs, with 8823 age-associated differentially methylated CpG probes. Notably, these age-associated changes tended to level off after the age of 60, as confirmed by Horvath's clock. Using stringent selection criteria we further identified a DNA methylation signature of aging liver including 75 genomic regions. We demonstrated that this signature is specific for liver compared to other tissues and that it is able to detect biological age-acceleration effects associated with obesity. Finally we combined DNA methylation measurements with available expression data. Although the intersection between the two omic characterizations was low, both approaches suggested a previously unappreciated role of epithelial-mesenchymal transition and Wnt signaling pathways in the aging of human liver.

Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

USGS Publications Warehouse

Limborg, Morten T.; Larson, Wesley; Seeb, Lisa W.; Seeb, James E.

2017-01-01

A whole-genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalysed adaptive radiation in some polyploid-origin lineages. However, little is known about general consequences of a WGD because gene duplicates (i.e., paralogs) are commonly filtered in genomic studies; such filtering may remove substantial portions of the genome in data sets from polyploid-origin species. We demonstrate a new method that enables genome-wide scans for signatures of selection at both nonduplicated and duplicated loci by taking locus-specific copy number into account. We apply this method to RAD sequence data from different ecotypes of a polyploid-origin salmonid (Oncorhynchus nerka) and reveal signatures of divergent selection that would have been missed if duplicated loci were filtered. We also find conserved signatures of elevated divergence at pairs of homeologous chromosomes with residual tetrasomic inheritance, suggesting that joint evolution of some nondiverged gene duplicates may affect the adaptive potential of these genes. These findings illustrate that including duplicated loci in genomic analyses enables novel insights into the evolutionary consequences of WGDs and local segmental gene duplications.

Persistence of social signatures in human communication.

PubMed

Saramäki, Jari; Leicht, E A; López, Eduardo; Roberts, Sam G B; Reed-Tsochas, Felix; Dunbar, Robin I M

2014-01-21

The social network maintained by a focal individual, or ego, is intrinsically dynamic and typically exhibits some turnover in membership over time as personal circumstances change. However, the consequences of such changes on the distribution of an ego's network ties are not well understood. Here we use a unique 18-mo dataset that combines mobile phone calls and survey data to track changes in the ego networks and communication patterns of students making the transition from school to university or work. Our analysis reveals that individuals display a distinctive and robust social signature, captured by how interactions are distributed across different alters. Notably, for a given ego, these social signatures tend to persist over time, despite considerable turnover in the identity of alters in the ego network. Thus, as new network members are added, some old network members either are replaced or receive fewer calls, preserving the overall distribution of calls across network members. This is likely to reflect the consequences of finite resources such as the time available for communication, the cognitive and emotional effort required to sustain close relationships, and the ability to make emotional investments.

Nature's chemical signatures in human olfaction: a foodborne perspective for future biotechnology.

PubMed

Dunkel, Andreas; Steinhaus, Martin; Kotthoff, Matthias; Nowak, Bettina; Krautwurst, Dietmar; Schieberle, Peter; Hofmann, Thomas

2014-07-07

The biocatalytic production of flavor naturals that determine chemosensory percepts of foods and beverages is an ever challenging target for academic and industrial research. Advances in chemical trace analysis and post-genomic progress at the chemistry-biology interface revealed odor qualities of nature's chemosensory entities to be defined by odorant-induced olfactory receptor activity patterns. Beyond traditional views, this review and meta-analysis now shows characteristic ratios of only about 3 to 40 genuine key odorants for each food, from a group of about 230 out of circa 10 000 food volatiles. This suggests the foodborn stimulus space has co-evolved with, and roughly match our circa 400 olfactory receptors as best natural agonists. This perspective gives insight into nature's chemical signatures of smell, provides the chemical odor codes of more than 220 food samples, and beyond addresses industrial implications for producing recombinants that fully reconstruct the natural odor signatures for use in flavors and fragrances, fully immersive interactive virtual environments, or humanoid bioelectronic noses. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Persistence of social signatures in human communication

PubMed Central

Saramäki, Jari; Leicht, E. A.; López, Eduardo; Roberts, Sam G. B.; Reed-Tsochas, Felix; Dunbar, Robin I. M.

2014-01-01

The social network maintained by a focal individual, or ego, is intrinsically dynamic and typically exhibits some turnover in membership over time as personal circumstances change. However, the consequences of such changes on the distribution of an ego’s network ties are not well understood. Here we use a unique 18-mo dataset that combines mobile phone calls and survey data to track changes in the ego networks and communication patterns of students making the transition from school to university or work. Our analysis reveals that individuals display a distinctive and robust social signature, captured by how interactions are distributed across different alters. Notably, for a given ego, these social signatures tend to persist over time, despite considerable turnover in the identity of alters in the ego network. Thus, as new network members are added, some old network members either are replaced or receive fewer calls, preserving the overall distribution of calls across network members. This is likely to reflect the consequences of finite resources such as the time available for communication, the cognitive and emotional effort required to sustain close relationships, and the ability to make emotional investments. PMID:24395777

Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA

NASA Astrophysics Data System (ADS)

Schmidt, Thomas P.; Perna, Anna M.; Fugmann, Tim; Böhm, Manja; Jan Hiss; Haller, Sarah; Götz, Camilla; Tegtmeyer, Nicole; Hoy, Benjamin; Rau, Tilman T.; Neri, Dario; Backert, Steffen; Schneider, Gisbert; Wessler, Silja

2016-03-01

The cell adhesion protein and tumour suppressor E-cadherin exhibits important functions in the prevention of gastric cancer. As a class-I carcinogen, Helicobacter pylori (H. pylori) has developed a unique strategy to interfere with E-cadherin functions. In previous studies, we have demonstrated that H. pylori secretes the protease high temperature requirement A (HtrA) which cleaves off the E-cadherin ectodomain (NTF) on epithelial cells. This opens cell-to-cell junctions, allowing bacterial transmigration across the polarised epithelium. Here, we investigated the molecular mechanism of the HtrA-E-cadherin interaction and identified E-cadherin cleavage sites for HtrA. Mass-spectrometry-based proteomics and Edman degradation revealed three signature motifs containing the [VITA]-[VITA]-x-x-D-[DN] sequence pattern, which were preferentially cleaved by HtrA. Based on these sites, we developed a substrate-derived peptide inhibitor that selectively bound and inhibited HtrA, thereby blocking transmigration of H. pylori. The discovery of HtrA-targeted signature sites might further explain why we detected a stable 90 kDa NTF fragment during H. pylori infection, but also additional E-cadherin fragments ranging from 105 kDa to 48 kDa in in vitro cleavage experiments. In conclusion, HtrA targets E-cadherin signature sites that are accessible in in vitro reactions, but might be partially masked on epithelial cells through functional homophilic E-cadherin interactions.

Distinguishing petroleum (crude oil and fuel) from smoke exposure within populations based on the relative levels of benzene, toluene, ethylbenzene, and xylenes (BTEX), styrene and 2,5-dimethylfuran by pattern recognition using artificial neural networks

PubMed Central

Chambers, D.M.; Reese, C.M.; Thornburg, L.G.; Sanchez, E.; Rafson, J.P.; Blount, B.C.; Ruhl, J.R.E.; De Jesús, V.R.

2017-01-01

Studies of human exposure to petroleum (crude oil and fuel) often involve monitoring volatile monoaromatic compounds because of their toxicity and prevalence. Monoaromatic compounds such as benzene, toluene, ethylbenzene, and xylenes (BTEX) associated with these sources have been well studied and have established reference concentrations (RfC) and reference doses (RfD). However, BTEX exposure levels for the general population are primarily from tobacco smoke, where smokers have blood levels up to 8 times higher on average than nonsmokers. Therefore, in assessing petroleum exposure, it is essential to identify exposure to tobacco smoke as well as other types of smoke exposure (e.g., cannabis, wood) because many smoke volatile organic compounds are also found in petroleum products such as crude oil, and fuel. This work describes a method using partition theory and artificial neural network (ANN) pattern recognition to accurately categorize exposure source based on BTEX and 2,5-dimethylfuran blood levels. For this evaluation three categories were created and include crude oil/fuel, other/nonsmoker, and smoker. A method for using surrogate signatures (i.e., relative VOC levels derived from the source material) to train the ANN was investigated where blood levels among cigarette smokers from the National Health and Nutrition Examination Survey (NHANES) were compared with signatures derived from machine-generated cigarette smoke. Use of surrogate signatures derived from machine-generated cigarette smoke did provide a sufficient means with which to train the ANN. As a result, surrogate signatures were used for assessing crude oil/fuel exposure because there is limited blood level data on individuals exposed to either crude oil or fuel. Classification agreement between using an ANN model trained with relative VOC levels and using the 2,5-dimethylfuran smoking biomarker cutpoint blood level of 0.014 ng/mL was up to 99.8 % for nonsmokers and 100.0% for smokers. For the NHANES 2007–08 data, the ANN model using a probability cutpoint above 0.5 assigned 7 samples out of 1998 (0.35%) to the crude oil/fuel signature category. For the NHANES 2013–14 data, 12 out of 2906 samples (0.41%) were assigned to the crude oil/fuel signature category. This approach using ANN makes it possible to quickly identify individuals with blood levels consistent with a crude oil/fuel surrogate among thousands of results while minimizing confounding from smoke. Use of an ANN fixed algorithm makes it possible to objectively compare across populations eliminating classification inconsistency that can result from relying on visual evaluation. PMID:29216422

Elastic Face, An Anatomy-Based Biometrics Beyond Visible Cue

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

Tsap, L V; Zhang, Y; Kundu, S J

2004-03-29

This paper describes a face recognition method that is designed based on the consideration of anatomical and biomechanical characteristics of facial tissues. Elastic strain pattern inferred from face expression can reveal an individual's biometric signature associated with the underlying anatomical structure, and thus has the potential for face recognition. A method based on the continuum mechanics in finite element formulation is employed to compute the strain pattern. Experiments show very promising results. The proposed method is quite different from other face recognition methods and both its advantages and limitations, as well as future research for improvement are discussed.

Brain transcriptome atlases: a computational perspective.

PubMed

Mahfouz, Ahmed; Huisman, Sjoerd M H; Lelieveldt, Boudewijn P F; Reinders, Marcel J T

2017-05-01

The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases allow researchers to probe the molecular mechanisms which define neuronal identities, neuroanatomy, and patterns of connectivity. Despite the immense effort put into generating such atlases, to answer fundamental questions in neuroscience, an even greater effort is needed to develop methods to probe the resulting high-dimensional multivariate data. We provide a comprehensive overview of the various computational methods used to analyze brain transcriptome atlases.

Linguistic Analysis of the Human Heartbeat Using Frequency and Rank Order Statistics

NASA Astrophysics Data System (ADS)

Yang, Albert C.-C.; Hseu, Shu-Shya; Yien, Huey-Wen; Goldberger, Ary L.; Peng, C.-K.

2003-03-01

Complex physiologic signals may carry unique dynamical signatures that are related to their underlying mechanisms. We present a method based on rank order statistics of symbolic sequences to investigate the profile of different types of physiologic dynamics. We apply this method to heart rate fluctuations, the output of a central physiologic control system. The method robustly discriminates patterns generated from healthy and pathologic states, as well as aging. Furthermore, we observe increased randomness in the heartbeat time series with physiologic aging and pathologic states and also uncover nonrandom patterns in the ventricular response to atrial fibrillation.

SELDI-TOF-based serum proteomic pattern diagnostics for early detection of cancer.

PubMed

Petricoin, Emanuel F; Liotta, Lance A

2004-02-01

Proteomics is more than just generating lists of proteins that increase or decrease in expression as a cause or consequence of pathology. The goal should be to characterize the information flow through the intercellular protein circuitry that communicates with the extracellular microenvironment and then ultimately to the serum/plasma macroenvironment. The nature of this information can be a cause, or a consequence, of disease and toxicity-based processes. Serum proteomic pattern diagnostics is a new type of proteomic platform in which patterns of proteomic signatures from high dimensional mass spectrometry data are used as a diagnostic classifier. This approach has recently shown tremendous promise in the detection of early-stage cancers. The biomarkers found by SELDI-TOF-based pattern recognition analysis are mostly low molecular weight fragments produced at the specific tumor microenvironment.

On mass transport in porosity waves

NASA Astrophysics Data System (ADS)

Jordan, Jacob S.; Hesse, Marc A.; Rudge, John F.

2018-03-01

Porosity waves arise naturally from the equations describing fluid migration in ductile rocks. Here, we show that higher-dimensional porosity waves can transport mass and therefore preserve geochemical signatures, at least partially. Fluid focusing into these high porosity waves leads to recirculation in their center. This recirculating fluid is separated from the background flow field by a circular dividing streamline and transported with the phase velocity of the porosity wave. Unlike models for one-dimensional chromatography in geological porous media, tracer transport in higher-dimensional porosity waves does not produce chromatographic separations between relatively incompatible elements due to the circular flow pattern. This may allow melt that originated from the partial melting of fertile heterogeneities or fluid produced during metamorphism to retain distinct geochemical signatures as they rise buoyantly towards the surface.

Phenotypic Checkpoints Regulate Neuronal Development

PubMed Central

Ben-Ari, Yehezkel; Spitzer, Nicholas C.

2010-01-01

Nervous system development proceeds by sequential gene expression mediated by cascades of transcription factors in parallel with sequences of patterned network activity driven by receptors and ion channels. These sequences are cell type- and developmental stage-dependent and modulated by paracrine actions of substances released by neurons and glia. How and to what extent these sequences interact to enable neuronal network development is not understood. Recent evidence demonstrates that CNS development requires intermediate stages of differentiation providing functional feedback that influences gene expression. We suggest that embryonic neuronal functions constitute a series of phenotypic checkpoint signatures; neurons failing to express these functions are delayed or developmentally arrested. Such checkpoints are likely to be a general feature of neuronal development and may constitute presymptomatic signatures of neurological disorders when they go awry. PMID:20864191

Spectral pattern recognition of controlled substances in street samples using artificial neural network system

NASA Astrophysics Data System (ADS)

Poryvkina, Larisa; Aleksejev, Valeri; Babichenko, Sergey M.; Ivkina, Tatjana

2011-04-01

The NarTest fluorescent technique is aimed at the detection of analyte of interest in street samples by recognition of its specific spectral patterns in 3-dimentional Spectral Fluorescent Signatures (SFS) measured with NTX2000 analyzer without chromatographic or other separation of controlled substances from a mixture with cutting agents. The illicit drugs have their own characteristic SFS features which can be used for detection and identification of narcotics, however typical street sample consists of a mixture with cutting agents: adulterants and diluents. Many of them interfere the spectral shape of SFS. The expert system based on Artificial Neural Networks (ANNs) has been developed and applied for such pattern recognition in SFS of street samples of illicit drugs.

Settlement patterns, GIS, remote sensing, and the late prehistory of the Black Prairie in east central Mississippi

NASA Technical Reports Server (NTRS)

Johnson, Jay K.

1991-01-01

Data recovered as the result of a recent field project designed to test a model of the distribution of protohistoric settlement in an unusual physiographic zone in eastern Mississippi are examined using GIS based techniques to manipulate soil and stream distance information. Significant patterning is derived. The generally thin soils and uniform substratum of the Black Prairie in combination with a distinctive settlement pattern offer a promising opportunity for the search for site specific characteristics within airborne imagery. Landsat TM data provide information on modern ground cover which is used as a mask to select areas in which a multivariate search for archaeological site signatures within a TIMS image is most likely to prove fruitful.

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery

PubMed Central

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-01-01

Background DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. Results GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. Conclusion GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at . PMID:19728865

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.

PubMed

Feng, Chunlai; Araki, Michihiro; Kunimoto, Ryo; Tamon, Akiko; Makiguchi, Hiroki; Niijima, Satoshi; Tsujimoto, Gozoh; Okuno, Yasushi

2009-09-03

DNA microarray technology provides us with a first step toward the goal of uncovering gene functions on a genomic scale. In recent years, vast amounts of gene expression data have been collected, much of which are available in public databases, such as the Gene Expression Omnibus (GEO). To date, most researchers have been manually retrieving data from databases through web browsers using accession numbers (IDs) or keywords, but gene-expression patterns are not considered when retrieving such data. The Connectivity Map was recently introduced to compare gene expression data by introducing gene-expression signatures (represented by a set of genes with up- or down-regulated labels according to their biological states) and is available as a web tool for detecting similar gene-expression signatures from a limited data set (approximately 7,000 expression profiles representing 1,309 compounds). In order to support researchers to utilize the public gene expression data more effectively, we developed a web tool for finding similar gene expression data and generating its co-expression networks from a publicly available database. GEM-TREND, a web tool for searching gene expression data, allows users to search data from GEO using gene-expression signatures or gene expression ratio data as a query and retrieve gene expression data by comparing gene-expression pattern between the query and GEO gene expression data. The comparison methods are based on the nonparametric, rank-based pattern matching approach of Lamb et al. (Science 2006) with the additional calculation of statistical significance. The web tool was tested using gene expression ratio data randomly extracted from the GEO and with in-house microarray data, respectively. The results validated the ability of GEM-TREND to retrieve gene expression entries biologically related to a query from GEO. For further analysis, a network visualization interface is also provided, whereby genes and gene annotations are dynamically linked to external data repositories. GEM-TREND was developed to retrieve gene expression data by comparing query gene-expression pattern with those of GEO gene expression data. It could be a very useful resource for finding similar gene expression profiles and constructing its gene co-expression networks from a publicly available database. GEM-TREND was designed to be user-friendly and is expected to support knowledge discovery. GEM-TREND is freely available at http://cgs.pharm.kyoto-u.ac.jp/services/network.

Stable isotope fingerprinting: a novel method for identifying plant, fungal, or bacterial origins of amino acids

Treesearch

Thomas Larsen; D. Lee Taylor; Mary Beth Leigh; Diane M. O' Brien

2009-01-01

Amino acids play an important role in ecology as essential nutrients for animals and as currencies in symbiotic associations. Here we present a new approach to tracing the origins of amino acids by identifying unique patterns of carbon isotope signatures generated by amino acid synthesis in plants, fungi, and bacteria ("13C fingerprints...

Secondary School Curriculum Guide. Music, Grades 7-9. Draft Copy.

ERIC Educational Resources Information Center

Rogers, Arnold R., Ed.; And Others

This draft curriculum guide is for use in grades 7-9 and covers six levels of musical competence. The levels included for study in this 3 year program are: 1) general music, in which the student learns about rythm, tempo, and beat patterns, note and rest values, time signatures, and some musical terms; 2) musical forms, elements of music, score…

Major Sources of Organic Matter in a Complex Coral Reef Lagoon: Identification from Isotopic Signatures (δ13C and δ15N)

PubMed Central

Briand, Marine J.; Bonnet, Xavier; Goiran, Claire; Guillou, Gaël; Letourneur, Yves

2015-01-01

A wide investigation was conducted into the main organic matter (OM) sources supporting coral reef trophic networks in the lagoon of New Caledonia. Sampling included different reef locations (fringing, intermediate and barrier reef), different associated ecosystems (mangroves and seagrass beds) and rivers. In total, 30 taxa of macrophytes, plus pools of particulate and sedimentary OM (POM and SOM) were sampled. Isotopic signatures (C and N) of each OM sources was characterized and the composition of OM pools assessed. In addition, spatial and seasonal variations of reef OM sources were examined. Mangroves isotopic signatures were the most C-depleted (-30.17 ± 0.41 ‰) and seagrass signatures were the most C-enriched (-4.36 ± 0.72 ‰). Trichodesmium spp. had the most N-depleted signatures (-0.14 ± 0.03 ‰) whereas mangroves had the most N-enriched signatures (6.47 ± 0.41 ‰). The composition of POM and SOM varied along a coast-to-barrier reef gradient. River POM and marine POM contributed equally to coastal POM, whereas marine POM represented 90% of the POM on barrier reefs, compared to 10% river POM. The relative importance of river POM, marine POM and mangroves to the SOM pool decreased from fringing to barrier reefs. Conversely, the relative importance of seagrass, Trichodesmium spp. and macroalgae increased along this gradient. Overall, spatial fluctuations in POM and SOM were much greater than in primary producers. Seasonal fluctuations were low for all OM sources. Our results demonstrated that a large variety of OM sources sustain coral reefs, varying in their origin, composition and role and suggest that δ13C was a more useful fingerprint than δ15N in this endeavour. This study also suggested substantial OM exchanges and trophic connections between coral reefs and surrounding ecosystems. Finally, the importance of accounting for environmental characteristics at small temporal and spatial scales before drawing general patterns is highlighted. PMID:26134985

IAR signatures in the ionosphere: Modeling and observations at the Chibis-M microsatellite

NASA Astrophysics Data System (ADS)

Pilipenko, V.; Dudkin, D.; Fedorov, E.; Korepanov, V.; Klimov, S.

2017-02-01

A peculiar feature of geomagnetic variations at middle/low latitudes in the ULF band, just below the fundamental tone of the Schumann resonance, is the occurrence of a multi-band spectral resonant structure, observed by high-sensitivity induction magnetometers during nighttime. The occurrence of such spectral structure was commonly attributed to the Ionospheric Alfvén Resonator (IAR) in the upper ionosphere. Rather surprisingly, while ground observations of the IAR are ubiquitous, there are practically no reports on the IAR signatures from space missions. According to the new paradigm, the multi-band spectral structure excited by a lightning discharge is in fact produced by a regular sequence of an original pulse from a stroke and echo-pulses reflected from the IAR upper boundary. Upon the interaction of initial lightning-generated pulse with the anisotropic lower ionosphere, it partially penetrates into the ionosphere, travels up the ionosphere as an Alfvén pulse, and reflects back from the upper IAR boundary. The superposition of the initial pulse and echo-pulses produces spectra with multiple spectral peaks. Our modeling of Alfvénic pulse propagation in a system with the altitude profile of Alfven velocity modeling the realistic ionosphere has shown that IAR spectral signatures are to be evident only on the ground and above the IAR. Inside the IAR, the superposition of upward and downward propagating pulses produces a more complicated spectral pattern and the IAR spectral signatures deteriorate. We have used electric field data from the low-orbit Chibis-M microsatellite to search for IAR signatures in the ionosphere. We found evidence that the multi-band structure revealed by spectral analysis in the frequency range of interest is indeed the result of a sequence of lightning-produced pulses. According to the proposed conception it seems possible to comprehend why the IAR signatures are less evident in the ionosphere than on the ground.

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures.

PubMed

Vazquez, Miguel; Nogales-Cadenas, Ruben; Arroyo, Javier; Botías, Pedro; García, Raul; Carazo, Jose M; Tirado, Francisco; Pascual-Montano, Alberto; Carmona-Saez, Pedro

2010-07-01

The enormous amount of data available in public gene expression repositories such as Gene Expression Omnibus (GEO) offers an inestimable resource to explore gene expression programs across several organisms and conditions. This information can be used to discover experiments that induce similar or opposite gene expression patterns to a given query, which in turn may lead to the discovery of new relationships among diseases, drugs or pathways, as well as the generation of new hypotheses. In this work, we present MARQ, a web-based application that allows researchers to compare a query set of genes, e.g. a set of over- and under-expressed genes, against a signature database built from GEO datasets for different organisms and platforms. MARQ offers an easy-to-use and integrated environment to mine GEO, in order to identify conditions that induce similar or opposite gene expression patterns to a given experimental condition. MARQ also includes additional functionalities for the exploration of the results, including a meta-analysis pipeline to find genes that are differentially expressed across different experiments. The application is freely available at http://marq.dacya.ucm.es.

Medieval Warm Period and Little Ice Age Signatures in the Distribution of Modern Ocean Temperatures

NASA Astrophysics Data System (ADS)

Gebbie, G.; Huybers, P. J.

2017-12-01

It is well established both that global temperatures have varied overthe last millenium and that the interior ocean reflects surfaceproperties inherited over these timescales. Signatures of theMedieval Warm Period and Little Ice Age are thus to be expected in themodern ocean state, though the magnitude of these effects and whetherthey are detectable is unclear. Analysis of changes in temperatureacross those obtained in the 1870s as part of the theH.M.S. Challenger expedition, the 1990s World Ocean CirculationExperiment, and recent Argo observations shows a consistent pattern:the upper ocean and Atlantic have warmed, but the oldest waters inthe deep Pacific appear to have cooled. The implications of pressureeffects on the H.M.S. Challenger thermometers and uncertainties indepth of observations are non-negligible but do not appear tofundamentally alter this pattern. Inversion of the modern hydrographyusing ocean transport estimates derived from passive tracer andradiocarbon observations indicates that deep Pacific cooling could bea vestige of the Medieval Warm Period, and that warming elsewhere reflects thecombined effects of emergence from the Little Ice Age and modernanthropogenic warming. Implications for longterm variations in oceanheat uptake and separating natural and anthropogenic contributions to themodern energy imbalance are discussed.

A Resource for Discovering Specific and Universal Biomarkers for Distributed Stem Cells

PubMed Central

Noh, Minsoo; Smith, Janet L.; Huh, Yang Hoon; Sherley, James L.

2011-01-01

Specific and universal biomarkers for distributed stem cells (DSCs) have been elusive. A major barrier to discovery of such ideal DSC biomarkers is difficulty in obtaining DSCs in sufficient quantity and purity. To solve this problem, we used cell lines genetically engineered for conditional asymmetric self-renewal, the defining DSC property. In gene microarray analyses, we identified 85 genes whose expression is tightly asymmetric self-renewal associated (ASRA). The ASRA gene signature prescribed DSCs to undergo asymmetric self-renewal to a greater extent than committed progenitor cells, embryonic stem cells, or induced pluripotent stem cells. This delineation has several significant implications. These include: 1) providing experimental evidence that DSCs in vivo undergo asymmetric self-renewal as individual cells; 2) providing an explanation why earlier attempts to define a common gene expression signature for DSCs were unsuccessful; and 3) predicting that some ASRA proteins may be ideal biomarkers for DSCs. Indeed, two ASRA proteins, CXCR6 and BTG2, and two other related self-renewal pattern associated (SRPA) proteins identified in this gene resource, LGR5 and H2A.Z, display unique asymmetric patterns of expression that have a high potential for universal and specific DSC identification. PMID:21818293

Neurons as sensors: individual and cascaded chemical sensing.

PubMed

Prasad, Shalini; Zhang, Xuan; Yang, Mo; Ozkan, Cengiz S; Ozkan, Mihrimah

2004-07-15

A single neuron sensor has been developed based on the interaction of gradient electric fields and the cell membrane. Single neurons are rapidly positioned over individual microelectrodes using positive dielectrophoretic traps. This enables the continuous extracellular electrophysiological measurements from individual neurons. The sensor developed using this technique provides the first experimental method for determining single cell sensitivity; the speed of response and the associated physiological changes to a broad spectrum of chemical agents. Binding of specific chemical agents to a specific combination of receptors induces changes to the extracellular membrane potential of a single neuron, which can be translated into unique "signature patterns" (SP), which function as identification tags. Signature patterns are derived using Fast Fourier Transformation (FFT) analysis and Wavelet Transformation (WT) analysis of the modified extracellular action potential. The validity and the sensitivity of the system are demonstrated for a variety of chemical agents ranging from behavior altering chemicals (ethanol), environmentally hazardous agents (hydrogen peroxide, EDTA) to physiologically harmful agents (pyrethroids) at pico- and femto-molar concentrations. The ability of a single neuron to selectively identify specific chemical agents when injected in a serial manner is demonstrated in "cascaded sensing".

Agricultural Trade Networks and Patterns of Economic Development

PubMed Central

Shutters, Shade T.; Muneepeerakul, Rachata

2012-01-01

International trade networks are manifestations of a complex combination of diverse underlying factors, both natural and social. Here we apply social network analytics to the international trade network of agricultural products to better understand the nature of this network and its relation to patterns of international development. Using a network tool known as triadic analysis we develop triad significance profiles for a series of agricultural commodities traded among countries. Results reveal a novel network “superfamily” combining properties of biological information processing networks and human social networks. To better understand this unique network signature, we examine in more detail the degree and triadic distributions within the trade network by country and commodity. Our results show that countries fall into two very distinct classes based on their triadic frequencies. Roughly 165 countries fall into one class while 18, all highly isolated with respect to international agricultural trade, fall into the other. Only Vietnam stands out as a unique case. Finally, we show that as a country becomes less isolated with respect to number of trading partners, the country's triadic signature follows a predictable trajectory that may correspond to a trajectory of development. PMID:22768310

DNA methylation profiling reveals the presence of population-specific signatures correlating with phenotypic characteristics.

PubMed

Giri, Anil K; Bharadwaj, Soham; Banerjee, Priyanka; Chakraborty, Shraddha; Parekatt, Vaisak; Rajashekar, Donaka; Tomar, Abhishek; Ravindran, Aarthi; Basu, Analabha; Tandon, Nikhil; Bharadwaj, Dwaipayan

2017-06-01

Phenotypic characteristics are known to vary substantially among different ethnicities around the globe. These variations are mediated by number of stochastic events and cannot be attributed to genetic architecture alone. DNA methylation is a well-established mechanism that sculpts our epigenome influencing phenotypic variation including disease manifestation. Since DNA methylation is an important determinant for health issues of a population, it demands a thorough investigation of the natural differences in genome wide DNA methylation patterns across different ethnic groups. This study is based on comparative analyses of methylome from five different ethnicities with major focus on Indian subjects. The current study uses hierarchical clustering approaches, principal component analysis and locus specific differential methylation analysis on Illumina 450K methylation data to compare methylome of different ethnic subjects. Our data indicates that the variations in DNA methylation patterns of Indians are less among themselves compared to other global population. It empirically correlated with dietary, cultural and demographical divergences across different ethnic groups. Our work further suggests that Indians included in this study, despite their genetic similarity with the Caucasian population, are in close proximity with Japanese in terms of their methylation signatures.

Early Whole Blood Transcriptional Signatures Are Associated with Severity of Lung Inflammation in Cynomolgus Macaques with Mycobacterium tuberculosis Infection.

PubMed

Gideon, Hannah P; Skinner, Jason A; Baldwin, Nicole; Flynn, JoAnne L; Lin, Philana Ling

2016-12-15

Whole blood transcriptional profiling offers great diagnostic and prognostic potential. Although studies identified signatures for pulmonary tuberculosis (TB) and transcripts that predict the risk for developing active TB in humans, the early transcriptional changes immediately following Mycobacterium tuberculosis infection have not been evaluated. We evaluated the gene expression changes in the cynomolgus macaque model of TB, which recapitulates all clinical aspects of human M. tuberculosis infection, using a human microarray and analytics platform. We performed genome-wide blood transcriptional analysis on 38 macaques at 11 postinfection time points during the first 6 mo of M. tuberculosis infection. Of 6371 differentially expressed transcripts between preinfection and postinfection, the greatest change in transcriptional activity occurred 20-56 d postinfection, during which fluctuation of innate and adaptive immune response-related transcripts was observed. Modest transcriptional differences between active TB and latent infection were observed over the time course with substantial overlap. The pattern of module activity previously published for human active TB was similar in macaques with active disease. Blood transcript activity was highly correlated with lung inflammation (lung [ 18 F]fluorodeoxyglucose [FDG] avidity) measured by positron emission tomography and computed tomography at early time points postinfection. The differential signatures between animals with high and low lung FDG were stronger than between clinical outcomes. Analysis of preinfection signatures of macaques revealed that IFN signatures could influence eventual clinical outcomes and lung FDG avidity, even before infection. Our data support that transcriptional changes in the macaque model are translatable to human M. tuberculosis infection and offer important insights into early events of M. tuberculosis infection. Copyright © 2016 by The American Association of Immunologists, Inc.

Muscle myeloid type I interferon gene expression may predict therapeutic responses to rituximab in myositis patients.

PubMed

Nagaraju, Kanneboyina; Ghimbovschi, Svetlana; Rayavarapu, Sree; Phadke, Aditi; Rider, Lisa G; Hoffman, Eric P; Miller, Frederick W

2016-09-01

To identify muscle gene expression patterns that predict rituximab responses and assess the effects of rituximab on muscle gene expression in PM and DM. In an attempt to understand the molecular mechanism of response and non-response to rituximab therapy, we performed Affymetrix gene expression array analyses on muscle biopsy specimens taken before and after rituximab therapy from eight PM and two DM patients in the Rituximab in Myositis study. We also analysed selected muscle-infiltrating cell phenotypes in these biopsies by immunohistochemical staining. Partek and Ingenuity pathway analyses assessed the gene pathways and networks. Myeloid type I IFN signature genes were expressed at higher levels at baseline in the skeletal muscle of rituximab responders than in non-responders, whereas classic non-myeloid IFN signature genes were expressed at higher levels in non-responders at baseline. Also, rituximab responders have a greater reduction of the myeloid and non-myeloid type I IFN signatures than non-responders. The decrease in the type I IFN signature following administration of rituximab may be associated with the decreases in muscle-infiltrating CD19(+) B cells and CD68(+) macrophages in responders. Our findings suggest that high levels of myeloid type I IFN gene expression in skeletal muscle predict responses to rituximab in PM/DM and that rituximab responders also have a greater decrease in the expression of these genes. These data add further evidence to recent studies defining the type I IFN signature as both a predictor of therapeutic responses and a biomarker of myositis disease activity. Published by Oxford University Press on behalf British Society for Rheumatology 2016. This work is written by US Government employees and is in the public domain in the US.

Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures.

PubMed

Telu, Kelly H; Yan, Xinjian; Wallace, William E; Stein, Stephen E; Simón-Manso, Yamil

2016-03-15

The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different liquid chromatography/mass spectrometry (LC/MS) platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC/MS platforms using reversed-phase chromatography and different chromatographic scales (conventional HPLC, UHPLC and nanoLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (relative standard deviation (RSD) <2%); however, substantial differences were found in the LC/MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.

Gene Expression Signatures Characterized by Longitudinal Stability and Interindividual Variability Delineate Baseline Phenotypic Groups with Distinct Responses to Immune Stimulation.

PubMed

Scheid, Adam D; Van Keulen, Virginia P; Felts, Sara J; Neier, Steven C; Middha, Sumit; Nair, Asha A; Techentin, Robert W; Gilbert, Barry K; Jen, Jin; Neuhauser, Claudia; Zhang, Yuji; Pease, Larry R

2018-03-01

Human immunity exhibits remarkable heterogeneity among individuals, which engenders variable responses to immune perturbations in human populations. Population studies reveal that, in addition to interindividual heterogeneity, systemic immune signatures display longitudinal stability within individuals, and these signatures may reliably dictate how given individuals respond to immune perturbations. We hypothesize that analyzing relationships among these signatures at the population level may uncover baseline immune phenotypes that correspond with response outcomes to immune stimuli. To test this, we quantified global gene expression in peripheral blood CD4 + cells from healthy individuals at baseline and following CD3/CD28 stimulation at two time points 1 mo apart. Systemic CD4 + cell baseline and poststimulation molecular immune response signatures (MIRS) were defined by identifying genes expressed at levels that were stable between time points within individuals and differential among individuals in each state. Iterative differential gene expression analyses between all possible phenotypic groupings of at least three individuals using the baseline and stimulated MIRS gene sets revealed shared baseline and response phenotypic groupings, indicating the baseline MIRS contained determinants of immune responsiveness. Furthermore, significant numbers of shared phenotype-defining sets of determinants were identified in baseline data across independent healthy cohorts. Combining the cohorts and repeating the analyses resulted in identification of over 6000 baseline immune phenotypic groups, implying that the MIRS concept may be useful in many immune perturbation contexts. These findings demonstrate that patterns in complex gene expression variability can be used to define immune phenotypes and discover determinants of immune responsiveness. Copyright © 2018 by The American Association of Immunologists, Inc.

Global modeling of flux transfer events: generation mechanism and spacecraft signatures

NASA Astrophysics Data System (ADS)

Raeder, J.

2003-04-01

Magnetic reconnection is a fundamental mode of energy and momentum transfer from the solar wind to the magnetosphere. It is known to occur in different forms depending on solar wind and magnetospheric conditions. In particular, steady reconnection can be distinguished from pulse-like reconnection events which are also known as Flux Transfer Events (FTEs). The formation mechanism of FTEs and their contolling factors remain controversial. We use global MHD simulations of Earth's magnetosphere to show that for southward IMF conditions: a) steady reconnection preferentially occurs without FTEs when the stagnation flow line nearly coincides with the X-line location, which requires small dipole tilt and nearly due southward IMF, b) FTEs occur when the flow/field symmetry is broken, which requires either a large dipole tilt and/or a substantial east-west component of the IMF, c) the predicted spacecraft signature and the repetition frequency of FTEs in the simulations agrees very well with typical observations, lending credibility to the the model, d) the fundamental process that leads to FTE formation is multiple X-line formation caused by the flow and field patterns in the magnetosheath and requires no intrinsic plasma property variations like variable resistivity, e) if the dipole tilt breaks the symmetry FTEs occur only in the winter hemisphere whereas the reconnection signatures in the summer hemisphere are steady with no bipolar FTE-like signatures, f) if the IMF east-west field component breaks the symmetry FTEs occur in both hemispheres, and g) FTE formation depends on sufficient resolution and low diffusion in the model -- coarse resolution and/or high diffusivity lead to flow-through reconnection signatures that appear unphysical given the frequent observation of FTEs.

LA-ICP-MS analysis of isolated phosphatic grains indicates selective rare earth element enrichment during reworking and transport processes

NASA Astrophysics Data System (ADS)

Auer, Gerald; Reuter, Markus; Hauzenberger, Christoph A.; Piller, Werner E.

2016-04-01

Rare earth elements (REE) are a commonly used proxy to reconstruct water chemistry and oxygen saturation during the formation history of authigenic and biogenic phosphates in marine environments. In the modern ocean REE exhibit a distinct pattern with enrichment of heavy REE and strong depletion in Cerium. Studies of ancient phosphates and carbonates, however, showed that this 'modern' pattern is only rarely present in the geological past. Consequently, the wide range of REE enrichment patterns found in ancient marine phosphates lead to the proposition that water chemistry had to have been radically different in the earth's past. A wealth of studies has already shown that both early and late diagenesis can strongly affect REE signatures in phosphates and severely alter primary marine signals. However, no previous research was conducted on how alteration processes occurring prior to final deposition affect marine phosphates. Herein we present a dataset of multiple LA-ICP-MS measurements of REE signatures in isolated phosphate and carbonate grains deposited in a carbonate ramp setting in the central Mediterranean Sea during the middle Miocene "Monterey event". The phosphates are represented by authigenic, biogenic and detrital grains emplaced in bioclastic grain- to packstones dominated by bryozoan and echinoderm fragments, as well as abundant benthic and planktic foraminifers. The results of 39 grain specific LA-ICP-MS measurements in three discrete rock samples reveals four markedly different REE patterns (normalized to the Post Archean Australian Shale standard) in terms of total enrichment and pattern shape. Analyses of REE diagenesis proxies show that diagenetic alteration affected the samples only to a minor degree. Considering grain shape and REE patterns together indicate that authigenic, detrital and biogenic phosphates have distinct REE patterns irrespective of the sample. Our results show that the observed REE patterns in phosphates only broadly reflect water chemistry under certain well constrained circumstances of primary authigenesis. Are these conditions not met, REE patterns are more likely to reflect complex enrichment processes that likely already started to occur during reworking over geologically relatively short time frames. Similarities in the REE patterns of clearly detrital and biogenic phosphate further suggest that the often observed 'hat-shaped' pattern in biogenic phosphates can easily result from increased middle REE (Neodymium to Holmium) scavenging during taphonomic processes prior to final deposition. Finally, cluster analysis coupled with sedimentological considerations proved a valuable tool for the characterization of REE patterns of phosphates in terms of their formation conditions and depositional history, such as the distinction of phosphates formed in situ from reworked and transported phosphate grains.

Catchment-Scale Sampling Reveals the Consistent Function of the Sediment-Water Interface to Remove Landscape Scale Dissolved Organic Carbon Properties

NASA Astrophysics Data System (ADS)

Lee-Cullin, J. A.; Zarnetske, J. P.; Wiewiora, E.; Ruhala, S.; Hampton, T. B.

2016-12-01

Dissolved organic carbon (DOC) is a critical component to biogeochemical cycling and water quality in surface waters. As DOC moves through stream networks, from headwaters to higher order streams, the sediment-water interface (SWI), where streams and groundwater readily interact, exerts a strong influence on DOC concentrations and compositional characteristics (i.e., molecular properties). Few studies examine SWI patterns at larger spatial scales, instead focusing primarily on site-level studies because sampling in the SWI is methodologically time and labor intensive. It is presently unknown how land use and landcover influence the fate of DOC in the SWI and therefore the function of the SWI on catchment-scale DOC conditions. Here, we performed a catchment-scale, high spatial-resolution SWI sampling campaign to test how landscape pattern DOC signatures are propagated into the stream and groundwater, and to assess the fate of these signatures when DOC travels through the SWI. We sampled across 39 sites composed of first-, second-, and third-order locations in a lowland, third-order catchment composed of diverse landscape units and properties, including wetland, upland forest, and agriculture. At each of these locations, surface water, groundwater, and SWI water were collected, including six discrete depths across the SWI. The major land use and landcover properties were also determined for each of these locations. We developed two simple generalized linear models to identify the landscape properties with greatest explanatory power for DOC conditions - one for stream water and one for groundwater. The correlation between landscape properties and surface water DOC characteristics was stronger than between landscape properties and groundwater DOC characteristics. To test if the DOC properties from surface and groundwater were preserved or removed by the SWI, the resulting best-fit models for each water source were used to predict the DOC conditions across the SWI. The models were unable to predict SWI DOC conditions, indicating that the landscape signature present in both the surface water and groundwater is removed by processes occurring in the SWI. Overall, this suggests that the SWI functions as and effective zone for processing the landscape-derived DOC signatures.

Catchment-Scale Sampling Reveals the Consistent Function of the Sediment-Water Interface to Remove Landscape Scale Dissolved Organic Carbon Properties

NASA Astrophysics Data System (ADS)

Lee-Cullin, J. A.; Zarnetske, J. P.; Wiewiora, E.; Ruhala, S.; Hampton, T. B.

2017-12-01

Dissolved organic carbon (DOC) is a critical component to biogeochemical cycling and water quality in surface waters. As DOC moves through stream networks, from headwaters to higher order streams, the sediment-water interface (SWI), where streams and groundwater readily interact, exerts a strong influence on DOC concentrations and compositional characteristics (i.e., molecular properties). Few studies examine SWI patterns at larger spatial scales, instead focusing primarily on site-level studies because sampling in the SWI is methodologically time and labor intensive. It is presently unknown how land use and landcover influence the fate of DOC in the SWI and therefore the function of the SWI on catchment-scale DOC conditions. Here, we performed a catchment-scale, high spatial-resolution SWI sampling campaign to test how landscape pattern DOC signatures are propagated into the stream and groundwater, and to assess the fate of these signatures when DOC travels through the SWI. We sampled across 39 sites composed of first-, second-, and third-order locations in a lowland, third-order catchment composed of diverse landscape units and properties, including wetland, upland forest, and agriculture. At each of these locations, surface water, groundwater, and SWI water were collected, including six discrete depths across the SWI. The major land use and landcover properties were also determined for each of these locations. We developed two simple generalized linear models to identify the landscape properties with greatest explanatory power for DOC conditions - one for stream water and one for groundwater. The correlation between landscape properties and surface water DOC characteristics was stronger than between landscape properties and groundwater DOC characteristics. To test if the DOC properties from surface and groundwater were preserved or removed by the SWI, the resulting best-fit models for each water source were used to predict the DOC conditions across the SWI. The models were unable to predict SWI DOC conditions, indicating that the landscape signature present in both the surface water and groundwater is removed by processes occurring in the SWI. Overall, this suggests that the SWI functions as and effective zone for processing the landscape-derived DOC signatures.

Tectonic Origin of Serpentinites on Syros, Greece: Geochemical Signatures of Seafloor Serpentinization Preserved in the HP/LT Subduction Complex

NASA Astrophysics Data System (ADS)

Raia, N. H.; Cooperdock, E. H. G.; Barnes, J.; Stockli, D. F.; Schwarzenbach, E. M.

2016-12-01

Serpentinized ultramafic rocks are commonly found in exhumed HP/LT subduction complexes, but their tectonic origins (i.e., setting of serpentinization) are difficult to decipher due to extensive alteration. Growing literature and geochemical datasets demonstrate that immobile elements (REE, HFSE) in serpentinites can retain magmatic signatures indicative of the tectonic setting of parent peridotite, while fluid-mobile elements and stable isotopic signatures shed light on the fluids causing serpentinization. This study combines whole-rock trace and major element geochemistry, stable isotope (δD and δO) analyses with petrographic observation to determine the tectonic origin of ultramafic rocks in the HP/LT Aegean subduction complex. The best-preserved HP rocks of the Cycladic Blueschist Unit (CBU) are found on Syros, Greece, where serpentinized ultramafic rocks within the CBU are closely associated with metamorphosed remnants of subducted oceanic crust. All samples are completely serpentinized, lacking relict pyroxene or spinel grains, with typical assemblages consisting of serpentine, talc, chlorite, magnetite, and minor carbonate. The serpentinizing fluid was characterized using stable isotopes. δD and δO values of bulk-rock serpentinite powders and chips, respectively, suggest seafloor serpentinites hydrated by seawater at low T, typical of alteration at mid-ocean ridges and hyper-extended margins (δD = -64 to -33‰ and δO = 5.2 to 9.0‰). To fingerprint a tectonic origin, whole rock serpentinite REE patterns are compared to a global database of whole rock serpentinite analyses from fore-arc mantle wedge, mid-ocean ridge, and hyper-extended margin tectonic settings. Whole rock major element, trace element, and REE analyses are consistent with limited melt extraction, flat REE patterns (LaN/SmN = 0.2-2.6, SmN/YbN = 0.3-3.5; N= C1 normalized), and do not show pronounced Eu anomalies. These data are consistent with abyssal peridotites derived from hyper-extended margin settings, although some overlap with mid-ocean ridge serpentinites makes it difficult to rule out. In any case, the geochemical signatures retained in these serpentinites indicate they are unlikely sourced from the mantle wedge, as has been historically speculated.

Oceans Apart: Using Stable Isotopes to Assess the Role of Fog in Two Semi-Arid Island Ecosystems

NASA Astrophysics Data System (ADS)

Schmitt, S.; Riveros-Iregui, D.; Hu, J.

2017-12-01

Fog is a significant hydrologic input in many tropical island systems, and is a water source particularly susceptible to the effects of global climate change. To better understand the role of fog as a hydrological input in two oceanic islands, we address two principal questions: 1) Do seasonal or extreme precipitation events lead to distinguishable differences in stable isotopic signatures of water inputs within and between sites and islands? 2) Does microclimatic zonation lead to distinguishable differences in isotopic signatures of meteoric inputs between different sites on a given island? To perform this analysis, meteoric water samples (fog, rain and throughfall) were collected over three sites (one windward and two leeward) and three field seasons in San Cristobal, Galapagos to ascertain the isotopic signature of each water balance input during different times of year. An additional field season of data in Ascension Island, UK, was also used to perform a comparative analysis between islands. A stable isotope mixing model was used to determine the relative proportion of surface water and groundwater that is composed of fog, and to demonstrate spatiotemporal patterns of recharge dynamics in each island system. Local meteoric water lines were generated for each site and over each field season to determine the source of hydrologic inputs (trade wind-generated orographic precipitation versus storm precipitation) and the role of locally recycled water in the overall water balance of each site. Our results will approximate potential changes in water inputs to San Cristobal and Ascension, respectively, that could be impacted by an increase in cloud base height or a change in weather patterns brought about by climate change.

Mapping hydrological signatures in the tropical Andes using a network of paired catchments

NASA Astrophysics Data System (ADS)

Ochoa-Tocachi, B. F.; Buytaert, W.; De Bièvre, B.

2016-12-01

The complexity and data scarcity of tropical Andean catchments make regional hydrological predictions very challenging. The strong spatiotemporal patterns of the local climate contrast with the inadequate coverage, especially of remote areas, by the national monitoring networks. We present an approach to regionalize the hydrological impacts of land-use and land-cover (LUC) using a network of 24 headwater catchments in a pairwise comparison approach. We monitored precipitation and streamflow through an informal partnership of stakeholders in the Andes, known as iMHEA. Using a `trading-space-for-time' approach, our design aims at strengthening the statistical significance of LUC signals. To test our hypothesis, we summarized the hydrological responses using a set of indices, which are then regionalized against catchment properties including land-use. Lastly, the regionalization model is then used to generate distributed maps of hydrological signatures in ungauged areas. Our results clearly reflect the dominant regional climate patterns of the tropical Andes and the associated wide spectrum of hydrological responses. Although the hydrological impacts of LUC are equally diverse, we find consistent trends within different biomes. Contrary to earlier studies, we find that incorporating LUC variables in the regionalization increases significantly the performance of the regression model and its predictive capacity, which makes it possible to generate regional maps that predict the dynamics and propagation of streamflow signatures in complex regions with an explicit report of uncertainty. We attribute the robust regionalization results to the regional pairwise setup that covers diverse physiographic characteristics, contrasting LUC types, and degrees of conservation/alteration. As such, it may be a useful strategy to optimize data collection, leverage commonly available geographical information, and understand the major controls of hydrological response in data-scarce regions.

Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen

PubMed Central

2018-01-01

The cereal pathogen Fusarium graminearum is the primary cause of Fusarium head blight (FHB) and a significant threat to food safety and crop production. To elucidate population structure and identify genomic targets of selection within major FHB pathogen populations in North America we sequenced the genomes of 60 diverse F. graminearum isolates. We also assembled the first pan-genome for F. graminearum to clarify population-level differences in gene content potentially contributing to pathogen diversity. Bayesian and phylogenomic analyses revealed genetic structure associated with isolates that produce the novel NX-2 mycotoxin, suggesting a North American population that has remained genetically distinct from other endemic and introduced cereal-infecting populations. Genome scans uncovered distinct signatures of selection within populations, focused in high diversity, frequently recombining regions. These patterns suggested selection for genomic divergence at the trichothecene toxin gene cluster and thirteen additional regions containing genes potentially involved in pathogen specialization. Gene content differences further distinguished populations, in that 121 genes showed population-specific patterns of conservation. Genes that differentiated populations had predicted functions related to pathogenesis, secondary metabolism and antagonistic interactions, though a subset had unique roles in temperature and light sensitivity. Our results indicated that F. graminearum populations are distinguished by dozens of genes with signatures of selection and an array of dispensable accessory genes, suggesting that FHB pathogen populations may be equipped with different traits to exploit the agroecosystem. These findings provide insights into the evolutionary processes and genomic features contributing to population divergence in plant pathogens, and highlight candidate genes for future functional studies of pathogen specialization across evolutionarily and ecologically diverse fungi. PMID:29584736

Base changes in tumour DNA have the power to reveal the causes and evolution of cancer

DOE PAGES

Hollstein, M.; Alexandrov, L. B.; Wild, C. P.; ...

2016-06-06

Next-generation sequencing (NGS) technology has demonstrated that the cancer genomes are peppered with mutations. Although most somatic tumour mutations are unlikely to have any role in the cancer process per se, the spectra of DNA sequence changes in tumour mutation catalogues have the potential to identify the mutagens, and to reveal the mutagenic processes responsible for human cancer. Very recently, a novel approach for data mining of the vast compilations of tumour NGS data succeeded in separating and precisely defining at least 30 distinct patterns of sequence change hidden in mutation databases. At least half of these mutational signatures canmore » be readily assigned to known human carcinogenic exposures or endogenous mechanisms of mutagenesis. A quantum leap in our knowledge of mutagenesis in human cancers has resulted, stimulating a flurry of research activity. We trace here the major findings leading first to the hypothesis that carcinogenic insults leave characteristic imprints on the DNA sequence of tumours, and culminating in empirical evidence from NGS data that well-defined carcinogen mutational signatures are indeed present in tumour genomic DNA from a variety of cancer types. The notion that tumour DNAs can divulge environmental sources of mutation is now a well-accepted fact. This approach to cancer aetiology has also incriminated various endogenous, enzyme-driven processes that increase the somatic mutation load in sporadic cancers. The tasks now confronting the field of molecular epidemiology are to assign mutagenic processes to orphan and newly discovered tumour mutation patterns, and to determine whether avoidable cancer risk factors influence signatures produced by endogenous enzymatic mechanisms. As a result, innovative research with experimental models and exploitation of the geographical heterogeneity in cancer incidence can address these challenges.« less

Genetic signatures in choline and 1-carbon metabolism are associated with the severity of hepatic steatosis

PubMed Central

Corbin, Karen D.; Abdelmalek, Manal F.; Spencer, Melanie D.; da Costa, Kerry-Ann; Galanko, Joseph A.; Sha, Wei; Suzuki, Ayako; Guy, Cynthia D.; Cardona, Diana M.; Torquati, Alfonso; Diehl, Anna Mae; Zeisel, Steven H.

2013-01-01

Choline metabolism is important for very low-density lipoprotein secretion, making this nutritional pathway an important contributor to hepatic lipid balance. The purpose of this study was to assess whether the cumulative effects of multiple single nucleotide polymorphisms (SNPs) across genes of choline/1-carbon metabolism and functionally related pathways increase susceptibility to developing hepatic steatosis. In biopsy-characterized cases of nonalcoholic fatty liver disease and controls, we assessed 260 SNPs across 21 genes in choline/1-carbon metabolism. When SNPs were examined individually, using logistic regression, we only identified a single SNP (PNPLA3 rs738409) that was significantly associated with severity of hepatic steatosis after adjusting for confounders and multiple comparisons (P=0.02). However, when groupings of SNPs in similar metabolic pathways were defined using unsupervised hierarchical clustering, we identified groups of subjects with shared SNP signatures that were significantly correlated with steatosis burden (P=0.0002). The lowest and highest steatosis clusters could also be differentiated by ethnicity. However, unique SNP patterns defined steatosis burden irrespective of ethnicity. Our results suggest that analysis of SNP patterns in genes of choline/1-carbon metabolism may be useful for prediction of severity of steatosis in specific subsets of people, and the metabolic inefficiencies caused by these SNPs should be examined further.—Corbin, K. D., Abdelmalek, M. F., Spencer, M. D., da Costa, K.-A., Galanko, J. A., Sha, W., Suzuki, A., Guy, C. D., Cardona, D. M., Torquati, A., Diehl, A. M., Zeisel, S. H. Genetic signatures in choline and 1-carbon metabolism are associated with the severity of hepatic steatosis. PMID:23292069

Radiomic signature of infiltration in peritumoral edema predicts subsequent recurrence in glioblastoma: implications for personalized radiotherapy planning.

PubMed

Rathore, Saima; Akbari, Hamed; Doshi, Jimit; Shukla, Gaurav; Rozycki, Martin; Bilello, Michel; Lustig, Robert; Davatzikos, Christos

2018-04-01

Standard surgical resection of glioblastoma, mainly guided by the enhancement on postcontrast T1-weighted magnetic resonance imaging (MRI), disregards infiltrating tumor within the peritumoral edema region (ED). Subsequent radiotherapy typically delivers uniform radiation to peritumoral FLAIR-hyperintense regions, without attempting to target areas likely to be infiltrated more heavily. Noninvasive in vivo delineation of the areas of tumor infiltration and prediction of early recurrence in peritumoral ED could assist in targeted intensification of local therapies, thereby potentially delaying recurrence and prolonging survival. This paper presents a method for estimating peritumoral edema infiltration using radiomic signatures determined via machine learning methods, and tests it on 90 patients with de novo glioblastoma. The generalizability of the proposed predictive model was evaluated via cross-validation in a discovery cohort ([Formula: see text]) and was subsequently evaluated in a replication cohort ([Formula: see text]). Spatial maps representing the likelihood of tumor infiltration and future early recurrence were compared with regions of recurrence on postresection follow-up studies with pathology confirmation. The cross-validated accuracy of our predictive infiltration model on the discovery and replication cohorts was 87.51% (odds ratio = 10.22, sensitivity = 80.65, and specificity = 87.63) and 89.54% (odds ratio = 13.66, sensitivity = 97.06, and specificity = 76.73), respectively. The radiomic signature of the recurrent tumor region revealed higher vascularity and cellularity when compared with the nonrecurrent region. The proposed model shows evidence that multiparametric pattern analysis from clinical MRI sequences can assist in in vivo estimation of the spatial extent and pattern of tumor recurrence in peritumoral edema, which may guide supratotal resection and/or intensification of postoperative radiation therapy.

Discrimination of prey species of juvenile swordfish Xiphias gladius (Linnaeus, 1758) using signature fatty acid analyses

NASA Astrophysics Data System (ADS)

Young, Jock W.; Guest, Michaela A.; Lansdell, Matt; Phleger, Charles F.; Nichols, Peter D.

2010-07-01

Signature lipid and fatty acid analysis were used to discriminate the diet of swordfish ( Xiphias gladius, orbital fork length: 60-203 cm) from waters off eastern Australia. The fatty acid (FA) composition of a range of known prey (squid, myctophids, and other fishes) of swordfish, taken from stomach samples and from net tows, was compared with that of the white muscle tissue (WMT) of swordfish from the same region. Swordfish muscle was lipid rich (average 24-42% dry weight), as was the skeleton (28-41%). The robustness of the approach was also tested by comparison against a key squid prey species that was collected and stored using different protocols: (i) fresh frozen, (ii) fresh frozen, then thawed, and (iii) stomach content collection. The FA profiles were generally similar, with the ratio of docosahexaenoic acid (DHA) and palmitic acid (16:0) in particular showing no significant difference. Major fatty acids in swordfish WMT were 18:1ω9c, 16:0, 22:6ω3, and 18:0. Multidimensional scaling showed that the swordfish WMT grouped closely with small fish prey including myctophids, and not with squid. Squid contained markedly higher 22:6ω3 than swordfish. Individual prey species of the myctophidae could also be separated by the same technique. These results were supported by traditional stomach content analyses (SCA) that showed fish were the dominant prey for small swordfish sampled from southern waters whereas squid were the main prey in more northern waters, matching the FA patterns we found for the two regions. We propose that where general diet patterns are established, signature FA analysis has good potential to compliment or in some cases, replace temporal and spatial monitoring of trophic pathways for swordfish and other marine species.

Base changes in tumour DNA have the power to reveal the causes and evolution of cancer

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

Hollstein, M.; Alexandrov, L. B.; Wild, C. P.

Next-generation sequencing (NGS) technology has demonstrated that the cancer genomes are peppered with mutations. Although most somatic tumour mutations are unlikely to have any role in the cancer process per se, the spectra of DNA sequence changes in tumour mutation catalogues have the potential to identify the mutagens, and to reveal the mutagenic processes responsible for human cancer. Very recently, a novel approach for data mining of the vast compilations of tumour NGS data succeeded in separating and precisely defining at least 30 distinct patterns of sequence change hidden in mutation databases. At least half of these mutational signatures canmore » be readily assigned to known human carcinogenic exposures or endogenous mechanisms of mutagenesis. A quantum leap in our knowledge of mutagenesis in human cancers has resulted, stimulating a flurry of research activity. We trace here the major findings leading first to the hypothesis that carcinogenic insults leave characteristic imprints on the DNA sequence of tumours, and culminating in empirical evidence from NGS data that well-defined carcinogen mutational signatures are indeed present in tumour genomic DNA from a variety of cancer types. The notion that tumour DNAs can divulge environmental sources of mutation is now a well-accepted fact. This approach to cancer aetiology has also incriminated various endogenous, enzyme-driven processes that increase the somatic mutation load in sporadic cancers. The tasks now confronting the field of molecular epidemiology are to assign mutagenic processes to orphan and newly discovered tumour mutation patterns, and to determine whether avoidable cancer risk factors influence signatures produced by endogenous enzymatic mechanisms. As a result, innovative research with experimental models and exploitation of the geographical heterogeneity in cancer incidence can address these challenges.« less

A true real-time, on-line security system for waterborne pathogen surveillance

NASA Astrophysics Data System (ADS)

Adams, John A.; McCarty, David L.

2008-04-01

Over the past several years many advances have been made to monitor potable water systems for toxic threats. However, the need for real-time, on-line systems to detect the malicious introduction of deadly pathogens still exists. Municipal water distribution systems, government facilities and buildings, and high profile public events remain vulnerable to terrorist-related biological contamination. After years of research and development, an instrument using multi-angle light scattering (MALS) technology has been introduced to achieve on-line, real-time detection and classification of a waterborne pathogen event. The MALS system utilizes a continuous slip stream of water passing through a flow cell in the instrument. A laser beam, focused perpendicular to the water flow, strikes particles as they pass through the beam generating unique light scattering patterns that are captured by photodetectors. Microorganisms produce patterns termed 'bio-optical signatures' which are comparable to fingerprints. By comparing these bio-optical signatures to an on-board database of microorganism patterns, detection and classification occurs within minutes. If a pattern is not recognized, it is classified as an 'unknown' and the unidentified contaminant is registered as a potential threat. In either case, if the contaminant exceeds a customer's threshold, the system will immediately alert personnel to the contamination event while extracting a sample for confirmation. The system, BioSentry TM, developed by JMAR Technologies is now field-tested and commercially available. BioSentry is cost effective, uses no reagents, operates remotely, and can be used for continuous microbial surveillance in many water treatment environments. Examples of HLS installations will be presented along with data from the US EPA NHSRC Testing and Evaluation Facility.

Imaging Surrogates of Infiltration Obtained Via Multiparametric Imaging Pattern Analysis Predict Subsequent Location of Recurrence of Glioblastoma

PubMed Central

Akbari, Hamed; Macyszyn, Luke; Da, Xiao; Bilello, Michel; Wolf, Ronald L.; Martinez-Lage, Maria; Biros, George; Alonso-Basanta, Michelle; O’Rourke, Donald M.; Davatzikos, Christos

2016-01-01

Background Glioblastoma is an aggressive and highly infiltrative brain cancer. Standard surgical resection is guided by enhancement on postcontrast T1-weighted (T1) magnetic resonance imaging (MRI), which is insufficient for delineating surrounding infiltrating tumor. Objective To develop imaging biomarkers that delineate areas of tumor infiltration and predict early recurrence in peritumoral tissue. Such markers would enable intensive, yet targeted, surgery and radiotherapy, thereby potentially delaying recurrence and prolonging survival. Methods Preoperative multiparametric MRIs (T1, T1-Gad, T2-weighted [T2], T2-fluid-attenuated inversion recovery [FLAIR], diffusion tensor imaging (DTI), and dynamic susceptibility contrast-enhanced [DSC]-MRI) from 31 patients were combined using machine learning methods, thereby creating predictive spatial maps of infiltrated peritumoral tissue. Cross validation was used in the retrospective cohort to achieve generalizable biomarkers. Subsequently, the imaging signatures learned from the retrospective study were used in a replication cohort of 34 new patients. Spatial maps representing likelihood of tumor infiltration and future early recurrence were compared to regions of recurrence on postresection follow-up studies with pathology confirmation. Results This technique produced predictions of early recurrence with a mean area under the curve (AUC) of 0.84, sensitivity of 91%, specificity of 93%, and odds ratio estimates of 9.29 (99% CI, 8.95–9.65) for tissue predicted to be heavily infiltrated in the replication study. Regions of tumor recurrence were found to have subtle, yet fairly distinctive multiparametric imaging signatures when analyzed quantitatively by pattern analysis and machine learning. Conclusion Visually imperceptible imaging patterns discovered via multiparametric pattern analysis methods were found to estimate the extent of infiltration and location of future tumor recurrence, paving the way for improved targeted treatment. PMID:26813856

Virus-like attachment sites as structural landmarks of plants retrotransposons.

PubMed

Ochoa Cruz, Edgar Andres; Cruz, Guilherme Marcello Queiroga; Vieira, Andréia Prata; Van Sluys, Marie-Anne

2016-01-01

The genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. Among them, long terminal repeat retrotransposons (LTR-RTs) are the largest component of most plant genomes, the Gypsy and Copia superfamilies being the most common. Recently it has been found that Del lineage, an LTR-RT of Gypsy superfamily, has putative virus-like attachment (vl-att) sites. This signature, originally described for retroviruses, is recognized by retroviral integrase conferring specificity to the integration process. Here we retrieved 26,092 putative complete LTR-RTs from 10 lineages found in 10 fully sequenced angiosperm genomes and found putative vl-att sites that are a conserved structural landmark across these genomes. Furthermore, we reveal that each plant genome has a distinguishable LTR-RT lineage amplification pattern that could be related to the vl-att sites diversity. We used these patterns to generate a specific quick-response (QR) code for each genome that could be used as a barcode of identification of plants in the future. The universal distribution of vl-att sites represents a new structural feature common to plant LTR-RTs and retroviruses. This is an important finding that expands the information about the structural similarity between LTR-RT and retroviruses. We speculate that the sequence diversity of vl-att sites could be important for the life cycle of retrotransposons, as it was shown for retroviruses. All the structural vl-att site signatures are strong candidates for further functional studies. Moreover, this is the first identification of specific LTR-RT content and their amplification patterns in a large dataset of LTR-RT lineages and angiosperm genomes. These distribution patterns could be used in the future with biotechnological identification purposes.

Quantifying the scale- and process- dependent reorganization of landscape under climatic change: inferences from an experimental landscape

NASA Astrophysics Data System (ADS)

Singh, A.; Tejedor, A.; Grimaud, J. L.; Zaliapin, I. V.; Foufoula-Georgiou, E.

2016-12-01

Knowledge of the dynamics of evolving landscapes in terms of their geomorphic and topologic re-organization in response to changing climatic or tectonic forcing is of scientific and practical interest. Although several studies have addressed the large-scale response (e.g., change in mean relief), studies on the smaller-scale drainage pattern re-organization and quantification of landscape vulnerability to the timing, magnitude, and frequency of changing forcing are lacking. The reason is the absence of data for such an analysis. To that goal, a series of controlled laboratory experiments were conducted at the St. Anthony Falls laboratory of the University of Minnesota to study the effect of changing precipitation patterns on landscape evolution at the short and long-time scales. High resolution digital elevation (DEM) both in space and time were measured for a range of rainfall patterns and uplift rates. Results from our study show a distinct signature of the precipitation increase on the probabilistic and geometrical structure of landscape features, evident in widening and deepening of channels and valleys, change in drainage patterns within sub-basins and change in the space-time structure of erosional and depositional events. A spatially explicit analysis of the locus of these erosional and depositional events suggests a regime shift, during the onset of the transient state, from supply-limited to transport-limited fluvial channels. We document a characteristic scale-dependent signature of erosion at steady state (which we term the "E50-area curve") and show that during reorganization, its evolving shape reflects process and scales of geomorphic change. Finally, we document changes in the longitudinal river profiles, in response to increased precipitation rate, with the formation of abrupt gradient (knickpoints) that migrate upstream as time proceeds.

Using Recombinant Lactococci as an Approach to Dissect the Immunomodulating Capacity of Surface Piliation in Probiotic Lactobacillus rhamnosus GG

PubMed Central

Nummenmaa, Elina; Mäkinen, Veli-Matti; Reunanen, Justus; Satokari, Reetta; de Vos, Willem M.; Palva, Ilkka; Palva, Airi

2013-01-01

Primarily arising from their well understood beneficial health effects, many lactobacilli strains are considered good candidates for use as probiotics in humans and animals. Lactobacillar probiosis can itself be best typified by the Lactobacillus rhamnosus GG strain, which, with its well-documented clinical benefits, has emerged as one of the most widely used probiotics in the food and health-supplement industries. Even so, many facets of its molecular mechanisms and limitations as a beneficial commensal bacterium still remain to be thoroughly explored and dissected. Because L. rhamnosus GG is one of only a few such strains exhibiting surface piliation (called SpaCBA), we sought to examine whether this particular type of cell-surface appendage has a discernible immunomodulating capacity and is able to trigger targeted responses in human immune-related cells. Thus, presented herein for this study, we recombinantly engineered Lactococcus lactis to produce native (and pilin-deleted) SpaCBA pili that were assembled in a structurally authentic form and anchored to the cell surface, and which had retained mucus-binding functionality. By using these recombinant lactococcal constructs, we were able to demonstrate that the SpaCBA pilus can be a contributory factor in the activation of Toll-like receptor 2-dependent signaling in HEK cells as well as in the modulation of pro- and anti-inflammatory cytokine (TNF-α, IL-6, IL-10, and IL-12) production in human monocyte-derived dendritic cells. From these data, we suggest that the recombinant-expressed and surface-anchored SpaCBA pilus, given its projected functioning in the gut environment, might be viewed as a new microbe-associated molecular pattern (MAMP)-like modulator of innate immunity. Accordingly, our study has brought some new insight to the molecular immunogenicity of the SpaCBA pilus, thus opening the way to a better understanding of its possible role in the multifaceted nature of L. rhamnosus GG probiosis within the human gut. PMID:23691212

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota.

PubMed

Bulgarelli, Davide; Rott, Matthias; Schlaeppi, Klaus; Ver Loren van Themaat, Emiel; Ahmadinejad, Nahal; Assenza, Federica; Rauf, Philipp; Huettel, Bruno; Reinhardt, Richard; Schmelzer, Elmon; Peplies, Joerg; Gloeckner, Frank Oliver; Amann, Rudolf; Eickhorst, Thilo; Schulze-Lefert, Paul

2012-08-02

The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication. Several studies attempted to describe the structure of bacterial root endophytes; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells.

Correlating chemical sensitivity and basal gene expression reveals mechanism of action | Office of Cancer Genomics

Cancer.gov

Changes in cellular gene expression in response to small-molecule or genetic perturbations have yielded signatures that can connect unknown mechanisms of action (MoA) to ones previously established. We hypothesized that differential basal gene expression could be correlated with patterns of small-molecule sensitivity across many cell lines to illuminate the actions of compounds whose MoA are unknown.

Nanoflare vs Footpoint Heating : Observational Signatures

NASA Technical Reports Server (NTRS)

Winebarger, Amy; Alexander, Caroline; Lionello, Roberto; Linker, Jon; Mikic, Zoran; Downs, Cooper

2015-01-01

Time lag analysis shows very long time lags between all channel pairs. Impulsive heating cannot address these long time lags. 3D Simulations of footpoint heating shows a similar pattern of time lags (magnitude and distribution) to observations. Time lags and relative peak intensities may be able to differentiate between TNE and impulsive heating solutions. Adding a high temperature channel (like XRT Be-­thin) may improve diagnostics.

Non-Linear Acoustic Concealed Weapons Detector

DTIC Science & Technology

2006-05-01

signature analysis 8 the interactions of the beams with concealed objects. The Khokhlov- Zabolotskaya-Kuznetsov ( KZK ) equation is the most widely used...Hamilton developed a finite difference method based on the KZK equation to model pulsed acoustic emissions from axial symmetric sources. Using a...College of William & Mary, we have developed a simulation code using the KZK equation to model non-linear acoustic beams and visualize beam patterns

Hunting for the Signatures of Cancer

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

Giorgi, Elena Edi

2016-04-26

This prompts the ambitious question: can we find common mutations across individuals with the same cancer? And how many of these mutational patterns that are common across individuals can we attribute to particular exposures or biological processes? Distinguished postdoctoral researcher Ludmil Alexandrov, from the Los Alamos National Laboratory, has been working on this problem since his he was a PhD student at the Wellcome Trust Sanger Institute.

A Generalized Mechanism for Perception of Pitch Patterns

PubMed Central

Loui, Psyche; Wu, Elaine H.; Wessel, David L.; Knight, Robert T.

2009-01-01

Surviving in a complex and changeable environment relies upon the ability to extract probable recurring patterns. Here we report a neurophysiological mechanism for rapid probabilistic learning of a new system of music. Participants listened to different combinations of tones from a previously-unheard system of pitches based on the Bohlen-Pierce scale, with chord progressions that form 3:1 ratios in frequency, notably different from 2:1 frequency ratios in existing musical systems. Event-related brain potentials elicited by improbable sounds in the new music system showed emergence over a one-hour period of physiological signatures known to index sound expectation in standard Western music. These indices of expectation learning were eliminated when sound patterns were played equiprobably, and co-varied with individual behavioral differences in learning. These results demonstrate that humans utilize a generalized probability-based perceptual learning mechanism to process novel sound patterns in music. PMID:19144845

DNA methylation as a predictor of fetal alcohol spectrum disorder.

PubMed

Lussier, Alexandre A; Morin, Alexander M; MacIsaac, Julia L; Salmon, Jenny; Weinberg, Joanne; Reynolds, James N; Pavlidis, Paul; Chudley, Albert E; Kobor, Michael S

2018-01-01

Fetal alcohol spectrum disorder (FASD) is a developmental disorder that manifests through a range of cognitive, adaptive, physiological, and neurobiological deficits resulting from prenatal alcohol exposure. Although the North American prevalence is currently estimated at 2-5%, FASD has proven difficult to identify in the absence of the overt physical features characteristic of fetal alcohol syndrome. As interventions may have the greatest impact at an early age, accurate biomarkers are needed to identify children at risk for FASD. Building on our previous work identifying distinct DNA methylation patterns in children and adolescents with FASD, we have attempted to validate these associations in a different clinical cohort and to use our DNA methylation signature to develop a possible epigenetic predictor of FASD. Genome-wide DNA methylation patterns were analyzed using the Illumina HumanMethylation450 array in the buccal epithelial cells of a cohort of 48 individuals aged 3.5-18 (24 FASD cases, 24 controls). The DNA methylation predictor of FASD was built using a stochastic gradient boosting model on our previously published dataset FASD cases and controls (GSE80261). The predictor was tested on the current dataset and an independent dataset of 48 autism spectrum disorder cases and 48 controls (GSE50759). We validated findings from our previous study that identified a DNA methylation signature of FASD, replicating the altered DNA methylation levels of 161/648 CpGs in this independent cohort, which may represent a robust signature of FASD in the epigenome. We also generated a predictive model of FASD using machine learning in a subset of our previously published cohort of 179 samples (83 FASD cases, 96 controls), which was tested in this novel cohort of 48 samples and resulted in a moderately accurate predictor of FASD status. Upon testing the algorithm in an independent cohort of individuals with autism spectrum disorder, we did not detect any bias towards autism, sex, age, or ethnicity. These findings further support the association of FASD with distinct DNA methylation patterns, while providing a possible entry point towards the development of epigenetic biomarkers of FASD.

Optimizing of MALDI-ToF-based low-molecular-weight serum proteome pattern analysis in detection of breast cancer patients; the effect of albumin removal on classification performance.

PubMed

Pietrowska, M; Marczak, L; Polanska, J; Nowicka, E; Behrent, K; Tarnawski, R; Stobiecki, M; Polanski, A; Widlak, P

2010-01-01

Mass spectrometry-based analysis of the serum proteome allows identifying multi-peptide patterns/signatures specific for blood of cancer patients, thus having high potential value for cancer diagnostics. However, because of problems with optimization and standardization of experimental and computational design, none of identified proteome patterns/signatures was approved for diagnostics in clinical practice as yet. Here we compared two methods of serum sample preparation for mass spectrometry-based proteome pattern analysis aimed to identify biomarkers that could be used in early detection of breast cancer patients. Blood samples were collected in a group of 92 patients diagnosed at early (I and II) stages of the disease before the start of therapy, and in a group of age-matched healthy controls (104 women). Serum specimens were purified and analyzed using MALDI-ToF spectrometry, either directly or after membrane filtration (50 kDa cut-off) to remove albumin and other large serum proteins. Mass spectra of the low-molecular-weight fraction (2-10 kDa) of the serum proteome were resolved using the Gaussian mixture decomposition, and identified spectral components were used to build classifiers that differentiated samples from breast cancer patients and healthy persons. Mass spectra of complete serum and membrane-filtered albumin-depleted samples have apparently different structure and peaks specific for both types of samples could be identified. The optimal classifier built for the complete serum specimens consisted of 8 spectral components, and had 81% specificity and 72% sensitivity, while that built for the membrane-filtered samples consisted of 4 components, and had 80% specificity and 81% sensitivity. We concluded that pre-processing of samples to remove albumin might be recommended before MALDI-ToF mass spectrometric analysis of the low-molecular-weight components of human serum Keywords: albumin removal; breast cancer; clinical proteomics; mass spectrometry; pattern analysis; serum proteome.

Using linear algebra for protein structural comparison and classification

PubMed Central

2009-01-01

In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in. PMID:21637532

Using linear algebra for protein structural comparison and classification.

PubMed

Gomide, Janaína; Melo-Minardi, Raquel; Dos Santos, Marcos Augusto; Neshich, Goran; Meira, Wagner; Lopes, Júlio César; Santoro, Marcelo

2009-07-01

In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.

Revisiting demographic processes in cattle with genome-wide population genetic analysis

PubMed Central

Orozco-terWengel, Pablo; Barbato, Mario; Nicolazzi, Ezequiel; Biscarini, Filippo; Milanesi, Marco; Davies, Wyn; Williams, Don; Stella, Alessandra; Ajmone-Marsan, Paolo; Bruford, Michael W.

2015-01-01

The domestication of the aurochs took place approximately 10,000 years ago giving rise to the two main types of domestic cattle known today, taurine (Bos taurus) domesticated somewhere on or near the Fertile Crescent, and indicine (Bos indicus) domesticated in the Indus Valley. However, although cattle have historically played a prominent role in human society the exact origin of many extant breeds is not well known. Here we used a combination of medium and high-density Illumina Bovine SNP arrays (i.e., ~54,000 and ~770,000 SNPs, respectively), genotyped for over 1300 animals representing 56 cattle breeds, to describe the relationships among major European cattle breeds and detect patterns of admixture among them. Our results suggest modern cross-breeding and ancient hybridisation events have both played an important role, including with animals of indicine origin. We use these data to identify signatures of selection reflecting both domestication (hypothesized to produce a common signature across breeds) and local adaptation (predicted to exhibit a signature of selection unique to a single breed or group of related breeds with a common history) to uncover additional demographic complexity of modern European cattle. PMID:26082794

Encountering bird alarms in full-stare IRSTs

NASA Astrophysics Data System (ADS)

de Jong, Arie N.; Winkel, Hans; Kemp, Rob A. W.

2000-12-01

Birds are a potential source of frequent false alarms in Infrared Search and Track (IRST) systems. One reason is that the signals, generated by birds at short ranges (1-2 km) in IR sensors may be of the same magnitude as the signals generated by real targets (missiles) at long ranges (10-20 km). Another reason is that new generations of IRSTs have more sensitivity which brings more birds within the detection range. Furthermore military operations tend to be held more and more in coastal zones, where the frequency of occurrence of birds is greater than in the open ocean. Finally, the variety in type of birds and their flight characteristics and signature is larger. In the paper attention is spent on the IR signatures of birds in various backgrounds, including rapid variations in signature due to wing motions. Basically, these fluctuations and the flight pattern of a bird provide opportunities to encounter bird alarms in next generation IRSTs, using multiple Focal Plan Array cameras with high frame rates. One has to take into account in this process the difference between signal variations due to wing motions and scintillation for long range targets above the horizon.

Characterising private and shared signatures of positive selection in 37 Asian populations.

PubMed

Liu, Xuanyao; Lu, Dongsheng; Saw, Woei-Yuh; Shaw, Philip J; Wangkumhang, Pongsakorn; Ngamphiw, Chumpol; Fucharoen, Suthat; Lert-Itthiporn, Worachart; Chin-Inmanu, Kwanrutai; Chau, Tran Nguyen Bich; Anders, Katie; Kasturiratne, Anuradhani; de Silva, H Janaka; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Ohkubo, Takayoshi; Tabara, Yasuharu; Takeuchi, Fumihiko; Yamamoto, Ken; Yokota, Mitsuhiro; Mamatyusupu, Dolikun; Yang, Wenjun; Chung, Yeun-Jun; Jin, Li; Hoh, Boon-Peng; Wickremasinghe, Ananda R; Ong, RickTwee-Hee; Khor, Chiea-Chuen; Dunstan, Sarah J; Simmons, Cameron; Tongsima, Sissades; Suriyaphol, Prapat; Kato, Norihiro; Xu, Shuhua; Teo, Yik-Ying

2017-04-01

The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.

Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures.

PubMed

Lee, Jongkeun; Lee, Andy Jinseok; Lee, June-Koo; Park, Jongkeun; Kwon, Youngoh; Park, Seongyeol; Chun, Hyonho; Ju, Young Seok; Hong, Dongwan

2018-05-22

Somatic genome mutations occur due to combinations of various intrinsic/extrinsic mutational processes and DNA repair mechanisms. Different molecular processes frequently generate different signatures of somatic mutations in their own favored contexts. As a result, the regional somatic mutation rate is dependent on the local DNA sequence, the DNA replication/RNA transcription dynamics and epigenomic chromatin organization landscape in the genome. Here, we propose an online computational framework, termed Mutalisk, which correlates somatic mutations with various genomic, transcriptional and epigenomic features in order to understand mutational processes that contribute to the generation of the mutations. This user-friendly tool explores the presence of localized hypermutations (kataegis), dissects the spectrum of mutations into the maximum likelihood combination of known mutational signatures and associates the mutation density with numerous regulatory elements in the genome. As a result, global patterns of somatic mutations in any query sample can be efficiently screened, thus enabling a deeper understanding of various mutagenic factors. This tool will facilitate more effective downstream analyses of cancer genome sequences to elucidate the diversity of mutational processes underlying the development and clonal evolution of cancer cells. Mutalisk is freely available at http://mutalisk.org.

Neural Signatures of Stimulus Features in Visual Working Memory—A Spatiotemporal Approach

PubMed Central

Jackson, Margaret C.; Klein, Christoph; Mohr, Harald; Shapiro, Kimron L.; Linden, David E. J.

2010-01-01

We examined the neural signatures of stimulus features in visual working memory (WM) by integrating functional magnetic resonance imaging (fMRI) and event-related potential data recorded during mental manipulation of colors, rotation angles, and color–angle conjunctions. The N200, negative slow wave, and P3b were modulated by the information content of WM, and an fMRI-constrained source model revealed a progression in neural activity from posterior visual areas to higher order areas in the ventral and dorsal processing streams. Color processing was associated with activity in inferior frontal gyrus during encoding and retrieval, whereas angle processing involved right parietal regions during the delay interval. WM for color–angle conjunctions did not involve any additional neural processes. The finding that different patterns of brain activity underlie WM for color and spatial information is consistent with ideas that the ventral/dorsal “what/where” segregation of perceptual processing influences WM organization. The absence of characteristic signatures of conjunction-related brain activity, which was generally intermediate between the 2 single conditions, suggests that conjunction judgments are based on the coordinated activity of these 2 streams. PMID:19429863

Characterising private and shared signatures of positive selection in 37 Asian populations

PubMed Central

Liu, Xuanyao; Lu, Dongsheng; Saw, Woei-Yuh; Shaw, Philip J; Wangkumhang, Pongsakorn; Ngamphiw, Chumpol; Fucharoen, Suthat; Lert-itthiporn, Worachart; Chin-inmanu, Kwanrutai; Chau, Tran Nguyen Bich; Anders, Katie; Kasturiratne, Anuradhani; de Silva, H Janaka; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Ohkubo, Takayoshi; Tabara, Yasuharu; Takeuchi, Fumihiko; Yamamoto, Ken; Yokota, Mitsuhiro; Mamatyusupu, Dolikun; Yang, Wenjun; Chung, Yeun-Jun; Jin, Li; Hoh, Boon-Peng; Wickremasinghe, Ananda R; Ong, RickTwee-Hee; Khor, Chiea-Chuen; Dunstan, Sarah J; Simmons, Cameron; Tongsima, Sissades; Suriyaphol, Prapat; Kato, Norihiro; Xu, Shuhua; Teo, Yik-Ying

2017-01-01

The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events. PMID:28098149

Biometric verification in dynamic writing

NASA Astrophysics Data System (ADS)

George, Susan E.

2002-03-01

Pen-tablet devices capable of capturing the dynamics of writing record temporal and pressure information as well as the spatial pattern. This paper explores biometric verification based upon the dynamics of writing where writers are distinguished not on the basis of what they write (ie the signature), but how they write. We have collected samples of dynamic writing from 38 Chinese writers. Each writer was asked to provide 10 copies of a paragraph of text and the same number of signature samples. From the data we have extracted stroke-based primitives from the sentence data utilizing pen-up/down information and heuristic rules about the shape of the character. The x, y and pressure values of each primitive were interpolated into an even temporal range based upon a 20 msec sampling rate. We applied the Daubechies 1 wavelet transform to the x signal, y signal and pressure signal using the coefficients as inputs to a multi-layer perceptron trained with back-propagation on the sentence data. We found a sensitivity of 0.977 and specificity of 0.990 recognizing writers based on test primitives extracted from sentence data and measures of 0.916 and 0.961 respectively, from test primitives extracted from signature data.

Isotope investigation on groundwater recharge and dynamics in shallow and deep alluvial aquifers of southwest Punjab.

PubMed

Keesari, Tirumalesh; Sharma, Diana A; Rishi, Madhuri S; Pant, Diksha; Mohokar, Hemant V; Jaryal, Ajay Kumar; Sinha, U K

2017-11-01

Groundwater samples collected from the alluvial aquifers of southwest Punjab, both shallow and deep zones were measured for environmental tritium ( 3 H) and stable isotopes ( 2 H and 18 O) to evaluate the source of recharge and aquifer dynamics. The shallow groundwater shows wide variation in isotopic signature (δ 18 O: -11.3 to -5.0‰) reflecting multiple sources of recharge. The average isotopic signature of shallow groundwaters (δ 18 O: -6.73 ± 1.03‰) is similar to that of local precipitation (-6.98 ± 1.66‰) indicating local precipitation contributes to a large extent compared to other sources. Other sources have isotopically distinct signatures due to either high altitude recharge (canal sources) or evaporative enrichment (irrigation return flow). Deep groundwater shows relatively depleted isotopic signature (δ 18 O: -8.6‰) and doesn't show any evaporation effect as compared to shallow zone indicating recharge from precipitation occurring at relatively higher altitudes. Environmental tritium indicates that both shallow ( 3 H: 5 - 10 T.U.) and deeper zone ( 3 H: 1.5 - 2.5 T.U.) groundwaters are modern. In general the inter-aquifer connections seem to be unlikely except a few places. Environmental isotope data suggests that shallow groundwater is dynamic, local and prone to changes in land use patterns while deep zone water is derived from distant sources, less dynamic and not impacted by surface manifestations. A conceptual groundwater flow diagram is presented. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of StrengthsQuest Signature Themes in Student Pharmacists and Other Health Care Profession Students.

PubMed

Bloom, Timothy J

2018-02-01

Objective. To determine whether there is a distinctive pattern of StrengthsQuest Signature Themes or leadership domains for Doctor of Pharmacy students compared to students in other health care professional programs. Methods. Students in Doctor of Pharmacy (PharmD), Master of Physician Assistant (PA), Doctor of Physical Therapy (DPT), and Doctor of Osteopathic Medicine (DO) programs at Campbell University completed the online Clifton StrengthsQuest assessment and received their Signature Themes. The frequency of individual themes and the leadership domains into which they are sorted by Gallup was analyzed for each program. Results were compared between programs and with national frequencies among undergraduate students. Results. The most common themes in the total population were Learner, Relator, Responsibility, Harmony, and Achiever. Learner and Relator were among the five most frequent themes for all four individual programs while Responsibility and Harmony were among the top five for three programs. The most frequently reported themes in PharmD and PA students (39% and 38% of all themes, respectively) are grouped by Gallup into the executing domain, and into the relationship-building domain for DO and DPT students (35% and 33% of all themes, respectively). The least frequent themes in PharmD, DO and PA students were those grouped into the influencing domain, reported by 10% or fewer students. Conclusion. Numerous similarities were found in theme frequencies among students in four different health care professions, suggesting there is not a distinctive Doctor of Pharmacy Signature Theme profile.

Genome-wide scans between two honeybee populations reveal putative signatures of human-mediated selection.

PubMed

Parejo, M; Wragg, D; Henriques, D; Vignal, A; Neuditschko, M

2017-12-01

Human-mediated selection has left signatures in the genomes of many domesticated animals, including the European dark honeybee, Apis mellifera mellifera, which has been selected by apiculturists for centuries. Using whole-genome sequence information, we investigated selection signatures in spatially separated honeybee subpopulations (Switzerland, n = 39 and France, n = 17). Three different test statistics were calculated in windows of 2 kb (fixation index, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio) and combined into a recently developed composite selection score. Applying a stringent false discovery rate of 0.01, we identified six significant selective sweeps distributed across five chromosomes covering eight genes. These genes are associated with multiple molecular and biological functions, including regulation of transcription, receptor binding and signal transduction. Of particular interest is a selection signature on chromosome 1, which corresponds to the WNT4 gene, the family of which is conserved across the animal kingdom with a variety of functions. In Drosophila melanogaster, WNT4 alleles have been associated with differential wing, cross vein and abdominal phenotypes. Defining phenotypic characteristics of different Apis mellifera ssp., which are typically used as selection criteria, include colour and wing venation pattern. This signal is therefore likely to be a good candidate for human mediated-selection arising from different applied breeding practices in the two managed populations. © 2017 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

Separation of Doppler radar-based respiratory signatures.

PubMed

Lee, Yee Siong; Pathirana, Pubudu N; Evans, Robin J; Steinfort, Christopher L

2016-08-01

Respiration detection using microwave Doppler radar has attracted significant interest primarily due to its unobtrusive form of measurement. With less preparation in comparison with attaching physical sensors on the body or wearing special clothing, Doppler radar for respiration detection and monitoring is particularly useful for long-term monitoring applications such as sleep studies (i.e. sleep apnoea, SIDS). However, motion artefacts and interference from multiple sources limit the widespread use and the scope of potential applications of this technique. Utilising the recent advances in independent component analysis (ICA) and multiple antenna configuration schemes, this work investigates the feasibility of decomposing respiratory signatures into each subject from the Doppler-based measurements. Experimental results demonstrated that FastICA is capable of separating two distinct respiratory signatures from two subjects adjacent to each other even in the presence of apnoea. In each test scenario, the separated respiratory patterns correlate closely to the reference respiration strap readings. The effectiveness of FastICA in dealing with the mixed Doppler radar respiration signals confirms its applicability in healthcare applications, especially in long-term home-based monitoring as it usually involves at least two people in the same environment (i.e. two people sleeping next to each other). Further, the use of FastICA to separate involuntary movements such as the arm swing from the respiratory signatures of a single subject was explored in a multiple antenna environment. The separated respiratory signal indeed demonstrated a high correlation with the measurements made by a respiratory strap used currently in clinical settings.

Global patterns of synchronization in human communications.

PubMed

Morales, Alfredo J; Vavilala, Vaibhav; Benito, Rosa M; Bar-Yam, Yaneer

2017-03-01

Social media are transforming global communication and coordination and provide unprecedented opportunities for studying socio-technical domains. Here we study global dynamical patterns of communication on Twitter across many scales. Underlying the observed patterns is both the diurnal rotation of the Earth, day and night, and the synchrony required for contingency of actions between individuals. We find that urban areas show a cyclic contraction and expansion that resembles heartbeats linked to social rather than natural cycles. Different urban areas have characteristic signatures of daily collective activities. We show that the differences detected are consistent with a new emergent global synchrony that couples behaviour in distant regions across the world. Although local synchrony is the major force that shapes the collective behaviour in cities, a larger-scale synchronization is beginning to occur. © 2017 The Author(s).

Optical and microwave detection using Bi-Sr-Ca-Cu-O thin films

NASA Technical Reports Server (NTRS)

Grabow, B. E.; Sova, R. M.; Boone, B. G.; Moorjani, K.; Kim, B. F.; Bohandy, J.; Adrian, F.; Green, W. J.

1990-01-01

Recent progress at the Johns Hopkins University Applied Physics Laboratory (JHU/APL) in the development of optical and microwave detectors using high temperature superconducting thin films is described. Several objectives of this work have been accomplished, including: deposition of Bi-Sr-Ca-Cu-O thin films by laser abation processing (LAP); development of thin film patterning techniques, including in situ masking, wet chemical etching and laser patterning; measurements of bolometric and non-bolometric signatures in patterned Bi-Sr-Ca-Cu-O films using optical and microwave sources, respectively; analysis and design of an optimized bolometer through computer simulation, and investigation of its use in a Fourier transform spectrometer. The focus here is primarily on results from the measurement of the bolometric and non-bolometric response.

Optical and microwave detection using Bi-Sr-Ca-Cu-O thin films

NASA Technical Reports Server (NTRS)

Grabow, B. E.; Sova, R. M.; Boone, B. G.; Moorjani, K.; Kim, B. F.; Bohandy, J.; Adrian, F.; Green, W. J.

1991-01-01

Recent progress at the Johns Hopkins University Applied Physics Laboratory (JHU/APL) in the development of optical and microwave detectors using high temperature superconducting thin films is described. Several objectives of this work have been accomplished, including: deposition of Bi-Sr-Ca-Cu-O thin films by laser abation processing (LAP); development of thin film patterning techniques, including in situ masking, wet chemical etching, and laser patterning; measurements of bolometric and non-bolometric signatures in patterned Bi-Sr-Ca-Cu-O films using optical and microwave sources, respectively; analysis and design of an optimized bolometer through computer simulation; and investigation of its use in a Fourier transform spectrometer. The focus here is primarily on results from the measurement of the bolometric and non-bolometric response.

Cell-of-Origin DNA Methylation Signatures Are Maintained during Colorectal Carcinogenesis.

PubMed

Bormann, Felix; Rodríguez-Paredes, Manuel; Lasitschka, Felix; Edelmann, Dominic; Musch, Tanja; Benner, Axel; Bergman, Yehudit; Dieter, Sebastian M; Ball, Claudia R; Glimm, Hanno; Linhart, Heinz G; Lyko, Frank

2018-06-12

Colorectal adenomas are precursor lesions of colorectal cancers and represent clonal amplifications of single cells from colonic crypts. DNA methylation patterns specify cell-type identity during cellular differentiation and, therefore, provide opportunities for the molecular analysis of tumors. We have now analyzed DNA methylation patterns in colorectal adenomas and identified three biologically defined subclasses that describe different intestinal crypt differentiation stages. Importantly, colorectal carcinomas could be classified into the same methylation subtypes, reflecting their shared cell types of origin with adenomas. Further data analysis also revealed significantly reduced overall survival for one of the subtypes. Our results provide a concept for understanding the methylation patterns observed in colorectal cancer and provide opportunities for tumor subclassification and patient stratification. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Temporal patterns of diversity: Assessing the biotic and abiotic controls on ant assemblages

USGS Publications Warehouse

Dunn, R.R.; Parker, C.R.; Sanders, N.J.

2007-01-01

In this study, we use 12 months of data from 11 ant assemblages to test whether seasonal variation in ant diversity is governed by either the structuring influences of interspecific competition or environmental conditions. Because the importance of competition might vary along environmental gradients, we also test whether the signature of competition depends on elevation. We find little evidence that competition structures the seasonal patterns of activity in the ant assemblages considered, but find support for the effects of temperature on seasonal patterns of diversity, especially at low-elevation sites. Although, in general, both competition and the environment interact to structure ant assemblages, our results suggest that environmental conditions are the primary force structuring the seasonal activity of the ant assemblages studied here. ?? 2007 The Linnean Society of London.

Global patterns of synchronization in human communications

PubMed Central

Vavilala, Vaibhav; Benito, Rosa M.; Bar-Yam, Yaneer

2017-01-01

Social media are transforming global communication and coordination and provide unprecedented opportunities for studying socio-technical domains. Here we study global dynamical patterns of communication on Twitter across many scales. Underlying the observed patterns is both the diurnal rotation of the Earth, day and night, and the synchrony required for contingency of actions between individuals. We find that urban areas show a cyclic contraction and expansion that resembles heartbeats linked to social rather than natural cycles. Different urban areas have characteristic signatures of daily collective activities. We show that the differences detected are consistent with a new emergent global synchrony that couples behaviour in distant regions across the world. Although local synchrony is the major force that shapes the collective behaviour in cities, a larger-scale synchronization is beginning to occur. PMID:28250100

Identification of Malicious Web Pages by Inductive Learning

NASA Astrophysics Data System (ADS)

Liu, Peishun; Wang, Xuefang

Malicious web pages are an increasing threat to current computer systems in recent years. Traditional anti-virus techniques focus typically on detection of the static signatures of Malware and are ineffective against these new threats because they cannot deal with zero-day attacks. In this paper, a novel classification method for detecting malicious web pages is presented. This method is generalization and specialization of attack pattern based on inductive learning, which can be used for updating and expanding knowledge database. The attack pattern is established from an example and generalized by inductive learning, which can be used to detect unknown attacks whose behavior is similar to the example.

Seasat radar geomorphic applications in coastal and wetland environments, southeastern U.S

NASA Technical Reports Server (NTRS)

Macdonald, H. C.

1981-01-01

The application of Seasat Synthetic Aperture Radar (SAR) to the assessment of terrain conditions in coastal environments is considered. Drainage patterns and plant community spatial relationships can be adequately mapped as is shown by Seasat L-band imagery of the southeastern Gulf Coast and Atlantic Coastal Plain. Anomalously bright radar signatures are identified as characteristic of mangrove and cypress swamps. Marshes have a low radar return, less than that from non-marsh areas and open water in tidal channels. Drainage patterns for coastal plain transition zones can also be determined. Spaceborne imaging radar provides information which complements geomorphic analyses presently obtained with optical sensors.

Rare earth patterns in shergottite phosphates and residues

NASA Technical Reports Server (NTRS)

Laul, J. C.

1987-01-01

Leaching experiments with 1M HCl on ALHA 77005 powder show that rare earth elements (REE) are concentrated in accessory phosphate phases (whitlockite, apatite) that govern the REE patterns of bulk shergottites. The REE patterns of whitlockite are typically light REE-depleted with a negative Eu anomaly and show a hump at the heavy REE side, while the REE pattern of apatite (in Shergotty) is light REE-enriched. Parent magmas are calculated from the modal compositions of residues of ALHA 77005, Shergotty, and EETA 79001. The parent magmas lack a Eu anomaly, indicating that plagioclase was a late-stage crystallizing phase and that it probably crystallized before the phosphates. The parent magmas of ALHA 77005 and Shergotty have similar REE patterns, with a subchondritic Nd/Sm ratio. However, the Sm/Nd isotopoics require a light REE-depleted source for ALHA 77005 (if the crystallization age is less than 600 Myr) and a light REE-enriched source for Shergotty. Distant Nd and Sr isotopic signatures may suggest different source regions for shergottites.

Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data

PubMed Central

2010-01-01

Background In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.). Although many methodological approaches allow practitioners to compute the distribution of a pattern count in a random sequence generated by a Markov source, no specific developments have taken into account the counting of occurrences in a set of independent sequences. We aim to address this problem by deriving efficient approaches and algorithms to perform these computations both for low and high complexity patterns in the framework of homogeneous or heterogeneous Markov models. Results The latest advances in the field allowed us to use a technique of optimal Markov chain embedding based on deterministic finite automata to introduce three innovative algorithms. Algorithm 1 is the only one able to deal with heterogeneous models. It also permits to avoid any product of convolution of the pattern distribution in individual sequences. When working with homogeneous models, Algorithm 2 yields a dramatic reduction in the complexity by taking advantage of previous computations to obtain moment generating functions efficiently. In the particular case of low or moderate complexity patterns, Algorithm 3 exploits power computation and binary decomposition to further reduce the time complexity to a logarithmic scale. All these algorithms and their relative interest in comparison with existing ones were then tested and discussed on a toy-example and three biological data sets: structural patterns in protein loop structures, PROSITE signatures in a bacterial proteome, and transcription factors in upstream gene regions. On these data sets, we also compared our exact approaches to the tempting approximation that consists in concatenating the sequences in the data set into a single sequence. Conclusions Our algorithms prove to be effective and able to handle real data sets with multiple sequences, as well as biological patterns of interest, even when the latter display a high complexity (PROSITE signatures for example). In addition, these exact algorithms allow us to avoid the edge effect observed under the single sequence approximation, which leads to erroneous results, especially when the marginal distribution of the model displays a slow convergence toward the stationary distribution. We end up with a discussion on our method and on its potential improvements. PMID:20205909

Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data.

PubMed

Nuel, Gregory; Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

2010-01-26

In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.). Although many methodological approaches allow practitioners to compute the distribution of a pattern count in a random sequence generated by a Markov source, no specific developments have taken into account the counting of occurrences in a set of independent sequences. We aim to address this problem by deriving efficient approaches and algorithms to perform these computations both for low and high complexity patterns in the framework of homogeneous or heterogeneous Markov models. The latest advances in the field allowed us to use a technique of optimal Markov chain embedding based on deterministic finite automata to introduce three innovative algorithms. Algorithm 1 is the only one able to deal with heterogeneous models. It also permits to avoid any product of convolution of the pattern distribution in individual sequences. When working with homogeneous models, Algorithm 2 yields a dramatic reduction in the complexity by taking advantage of previous computations to obtain moment generating functions efficiently. In the particular case of low or moderate complexity patterns, Algorithm 3 exploits power computation and binary decomposition to further reduce the time complexity to a logarithmic scale. All these algorithms and their relative interest in comparison with existing ones were then tested and discussed on a toy-example and three biological data sets: structural patterns in protein loop structures, PROSITE signatures in a bacterial proteome, and transcription factors in upstream gene regions. On these data sets, we also compared our exact approaches to the tempting approximation that consists in concatenating the sequences in the data set into a single sequence. Our algorithms prove to be effective and able to handle real data sets with multiple sequences, as well as biological patterns of interest, even when the latter display a high complexity (PROSITE signatures for example). In addition, these exact algorithms allow us to avoid the edge effect observed under the single sequence approximation, which leads to erroneous results, especially when the marginal distribution of the model displays a slow convergence toward the stationary distribution. We end up with a discussion on our method and on its potential improvements.

Sodium Chloride Crystal-Induced SERS Platform for Controlled Highly Sensitive Detection of Illicit Drugs.

PubMed

Yu, Borong; Li, Pan; Zhou, Binbin; Tang, Xianghu; Li, Shaofei; Yang, Liangbao

2018-04-03

A sodium chloride crystal-driven spontaneous 'hot spot' structure was demonstrated as a SERS-active platform, to get reproducible SERS signals, and eliminate the need for mapping large areas, in comparison with solution phase testing. During the process of solvent evaporation, the crystals produced induced silver aggregates to assemble around themselves. The micro-scale crystals can also act as a template to obtain an optical position, such that the assembled hot area is conveniently located during SERS measurements. More importantly, the chloride ions added in colloids can also replace the citrate and on the surface of the silver sol, and further decrease the background interference. High quality SERS spectra from heroin, methamphetamine (MAMP), and cocaine have been obtained on the crystal-driven hot spot structure with high sensitivity and credible reproducibility. This approach can not only bring the nanoparticles to form plasmonic hot spots in a controlled way, and thus provide high sensitivity, but also potentially be explored as an active substrate for label-free detection of other illicit drugs or additives. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fluvial signatures of modern and paleo orographic rainfall gradients

NASA Astrophysics Data System (ADS)

Schildgen, Taylor; Strecker, Manfred

2016-04-01

The morphology of river profiles is intimately linked to both climate and tectonic forcing. While much interest recently has focused on how river profiles can be inverted to derive uplift histories, here we show how in regions of strong orographic rainfall gradients, rivers may primarily record spatial patterns of precipitation. As a case study, we examine the eastern margin of the Andean plateau in NW Argentina, where the outward (eastward) growth of a broken foreland has led to a eastward shift in the main orographic rainfall gradient over the last several million years. Rivers influenced by the modern rainfall gradient are characterized by normalized river steepness values in tributary valleys that closely track spatial variations in rainfall, with higher steepness values in drier areas and lower steepness values in wetter areas. The same river steepness pattern has been predicted in landscape evolution models that apply a spatial gradient in rainfall to a region of uniform erosivity and uplift rate (e.g., Han et al., 2015). Also, chi plots from river networks on individual ranges affected by the modern orographic rainfall reveal patterns consistent with assymmetric precipitation across the range: the largest channels on the windward slopes are characterized by capture, while the longest channels on the leeward slopes are dominated by beheadings. Because basins on the windward side both lengthen and widen, tributary channels in the lengthening basins are characterized by capture, while tributary channels from neighboring basins on the windward side are dominated by beheadings. These patterns from the rivers influenced by the modern orographic rainfall gradient provide a guide for identifying river morphometric signatures of paleo orographic rainfall gradients. Mountain ranges to the west of the modern orographic rainfall have been interpreted to mark the location of orographic rainfall in the past, but these ranges are now in spatially near-uniform semi-arid to arid precipitation regimes. Indeed, despite uniform lithology and uplift history, we see patterns in river steepness values and in chi plots that are consistest a rainfall gradient on the (former) windward side of the range and asymmetric precipitation across the range. We suggest that morphological aspects of the river networks in such regions are dominated by their history of changing climate. These morphologic signatures appear to persist for millions of years in NW Argentina, most likely because the transition from a wetter to a drier climate has prevented a rapid readjustment to new forcing conditions. Reference: Han, J., Gasparini, N.M., and Johnson, J.P., 2015, Measuring the imprint of orographic rainfall gradients on the morphology of steady-state numerical fluvial landscapes. Earth Surf. Process. Landforms, 40(10), 1334-1350.

Hill slope and erosional controls on soil organic geochemistry in intensely managed landscapes

NASA Astrophysics Data System (ADS)

Filley, T. R.; Hou, T.; Hughes, M.; Tong, Y.; Papanicolaou, T.; Wacha, K.; Abban, B. K.; Boys, J.; Wilson, C. G.

2015-12-01

Like many regions of North America, the last 100 years of agriculture in the glaciated upper Midwest has lead to a major redistribution of soil carbon and nitrogen on the landscape. Through the natural coevolution of geomorphic, pedogenic, and ecological processes in the critical zone or by punctual changes in these processes as a result of intensive management, landscapes established characteristic hierarchies of physicochemical controls on organic matter stability. In the Intensively-Managed Landscapes - Critical Zone Observatory (IML-CZO) in Iowa and Illinois these processes are being studied with a combination of surface soil geochemical surveys and simulated rainfall/erosion experiments to document how the organic geochemistry of hill slopes, under land management ranging from row crop to restored prairie, are currently evolving, and how they evolved during early management and pre settlement. Using a combination of soil analyses including elemental, stable isotope, textural, and soil biopolymers (lignin and cutin/suberin fatty acids (SFA)) we investigated the spatial patterns of static surface soil properties and time course rainfall-erosional experiments along the same slopes to gain insight into soil carbon and biopolymer enrichment patterns in east-central Iowa within the Clear Creek Watershed. Both lignin and substituted fatty acid concentration and their molecular ratios highlighted differences in C3/C4 (soy/corn) management activities in surface soils while over 40 years of prairie restoration dramatically altered surface soil profiles. For example, a general pattern in static baseline samples was an enrichment of 15N in soils down slope and an opposite pattern of accumulation/loss of lignin and SFA in topographic highs and lows. Transport of soil particles, associated biopolymers, and elemental and isotope signatures, exhibited distinct patterns based upon both position of the hill slope and directionality of flow with respect to rill/gully direction created by tillage activity. This indicates that particle/chemistry transport and enrichment of organic chemical signatures down slope and into associated flood plains and streams in modern intensively managed systems should be distinct from pre-settlement patterns and help interpret pre- and post settlement alluvium sediment.

A Framework for Network Visualisation: Progress Report

DTIC Science & Technology

2006-12-01

time; secondly a simple oscillation, in which traffic changes, but those changes repeat periodically; or thirdly, a “ strange attractor ”, a pattern of...changes that never repeats exactly, though it may appear to repeat approximately. The strange attractor is the signature of a chaotic system, which...IST-063 3 - 1 Taylor, M.M. (2006) A Framework for Network Visualisation: Progress Report. In Visualising Network Information (pp. 3-1 – 3-22

Photomorphic analysis techniques: An interim spatial analysis using satellite remote sensor imagery and historical data

NASA Technical Reports Server (NTRS)

Keuper, H. R.; Peplies, R. W.; Gillooly, R. P.

1977-01-01

The use of machine scanning and/or computer-based techniques to provide greater objectivity in the photomorphic approach was investigated. Photomorphic analysis and its application in regional planning are discussed. Topics included: delineation of photomorphic regions; inadequacies of existing classification systems; tonal and textural characteristics and signature analysis techniques; pattern recognition and Fourier transform analysis; and optical experiments. A bibliography is included.

Using MODIS NDVI phenoclasses and phenoclusters to characterize wildlife habitat: Mexican spotted owl as a case study

Treesearch

Serra J. Hoagland; Paul Beier; Danny Lee

2018-01-01

Most uses of remotely sensed satellite data to characterize wildlife habitat have used metrics such as mean NDVI (Normalized Difference Vegetation Index) in a year or season. These simple metrics do not take advantage of the temporal patterns in NDVI within and across years and the spatial arrangement of cells with various temporal NDVI signatures. Here we use 13 years...

Ecosystem Composition Controls the Fate of Rare Earth Elements during Incipient Soil Genesis

NASA Astrophysics Data System (ADS)

Zaharescu, Dragos G.; Burghelea, Carmen I.; Dontsova, Katerina; Presler, Jennifer K.; Maier, Raina M.; Huxman, Travis; Domanik, Kenneth J.; Hunt, Edward A.; Amistadi, Mary K.; Gaddis, Emily E.; Palacios-Menendez, Maria A.; Vaquera-Ibarra, Maria O.; Chorover, Jon

2017-02-01

The rare earth elements (REE) are increasingly important in a variety of science and economic fields, including (bio)geosciences, paleoecology, astrobiology, and mining. However, REE distribution in early rock-microbe-plant systems has remained elusive. We tested the hypothesis that REE mass-partitioning during incipient weathering of basalt, rhyolite, granite and schist depends on the activity of microbes, vascular plants (Buffalo grass), and arbuscular mycorrhiza. Pore-water element abundances revealed a rapid transition from abiotic to biotic signatures of weathering, the latter associated with smaller aqueous loss and larger plant uptake. Abiotic dissolution was 39% of total denudation in plant-microbes-mycorrhiza treatment. Microbes incremented denudation, particularly in rhyolite, and this resulted in decreased bioavailable solid pools in this rock. Total mobilization (aqueous + uptake) was ten times greater in planted compared to abiotic treatments, REE masses in plant generally exceeding those in water. Larger plants increased bioavailable solid pools, consistent with enhanced soil genesis. Mycorrhiza generally had a positive effect on total mobilization. The main mechanism behind incipient REE weathering was carbonation enhanced by biotic respiration, the denudation patterns being largely dictated by mineralogy. A consistent biotic signature was observed in La:phosphate and mobilization: solid pool ratios, and in the pattern of denudation and uptake.

Keystroke dynamics in the pre-touchscreen era

PubMed Central

Ahmad, Nasir; Szymkowiak, Andrea; Campbell, Paul A.

2013-01-01

Biometric authentication seeks to measure an individual’s unique physiological attributes for the purpose of identity verification. Conventionally, this task has been realized via analyses of fingerprints or signature iris patterns. However, whilst such methods effectively offer a superior security protocol compared with password-based approaches for example, their substantial infrastructure costs, and intrusive nature, make them undesirable and indeed impractical for many scenarios. An alternative approach seeks to develop similarly robust screening protocols through analysis of typing patterns, formally known as keystroke dynamics. Here, keystroke analysis methodologies can utilize multiple variables, and a range of mathematical techniques, in order to extract individuals’ typing signatures. Such variables may include measurement of the period between key presses, and/or releases, or even key-strike pressures. Statistical methods, neural networks, and fuzzy logic have often formed the basis for quantitative analysis on the data gathered, typically from conventional computer keyboards. Extension to more recent technologies such as numerical keypads and touch-screen devices is in its infancy, but obviously important as such devices grow in popularity. Here, we review the state of knowledge pertaining to authentication via conventional keyboards with a view toward indicating how this platform of knowledge can be exploited and extended into the newly emergent type-based technological contexts. PMID:24391568

MicroRNA profiling of human kidney cancer subtypes.

PubMed

Petillo, David; Kort, Eric J; Anema, John; Furge, Kyle A; Yang, Ximing J; Teh, Bin Tean

2009-07-01

Although the functions of most of the identified microRNAs (miRNAs) have yet to be determined, their use as potential biomarkers has been considered in several human diseases and cancers. In order to understand their role in renal tumorigenesis, we screened the expression levels of miRNAs in four subtypes of human renal neoplasms: clear cell, papillary, and chromophobe renal cell carcinomas (RCC) as well as benign renal oncocytomas. We found a unique miRNA signature for each subtype of renal tumor. Furthermore, we identified unique patterns of miRNA expression distinguishing clear cell RCC cases with favorable vs. unfavorable outcome. Specifically, we documented the overexpression of miRs 424 and 203 in clear cell RCC relative to papillary RCC, as well as the inversion of expression of miR-203 in the benign oncocytomas (where it is underexpressed relative to normal kidney) as compared to the malignant chromophobe RCC (where it is overexpressed relative to normal kidney). Our results further suggest that overexpression of S-has-miR-32 is associated with poor outcome. While previous studies have identified unique miRNA expression pattern distinguishing tumors from different anatomical locations, here we extend this principle to demonstrate the utility of miRNA expression profiling to identify a signature unique to various tumor subtypes at a single anatomic locus.

A single-trace dual-process model of episodic memory: a novel computational account of familiarity and recollection.

PubMed

Greve, Andrea; Donaldson, David I; van Rossum, Mark C W

2010-02-01

Dual-process theories of episodic memory state that retrieval is contingent on two independent processes: familiarity (providing a sense of oldness) and recollection (recovering events and their context). A variety of studies have reported distinct neural signatures for familiarity and recollection, supporting dual-process theory. One outstanding question is whether these signatures reflect the activation of distinct memory traces or the operation of different retrieval mechanisms on a single memory trace. We present a computational model that uses a single neuronal network to store memory traces, but two distinct and independent retrieval processes access the memory. The model is capable of performing familiarity and recollection-based discrimination between old and new patterns, demonstrating that dual-process models need not to rely on multiple independent memory traces, but can use a single trace. Importantly, our putative familiarity and recollection processes exhibit distinct characteristics analogous to those found in empirical data; they diverge in capacity and sensitivity to sparse and correlated patterns, exhibit distinct ROC curves, and account for performance on both item and associative recognition tests. The demonstration that a single-trace, dual-process model can account for a range of empirical findings highlights the importance of distinguishing between neuronal processes and the neuronal representations on which they operate.

Neural dynamics based on the recognition of neural fingerprints

PubMed Central

Carrillo-Medina, José Luis; Latorre, Roberto

2015-01-01

Experimental evidence has revealed the existence of characteristic spiking features in different neural signals, e.g., individual neural signatures identifying the emitter or functional signatures characterizing specific tasks. These neural fingerprints may play a critical role in neural information processing, since they allow receptors to discriminate or contextualize incoming stimuli. This could be a powerful strategy for neural systems that greatly enhances the encoding and processing capacity of these networks. Nevertheless, the study of information processing based on the identification of specific neural fingerprints has attracted little attention. In this work, we study (i) the emerging collective dynamics of a network of neurons that communicate with each other by exchange of neural fingerprints and (ii) the influence of the network topology on the self-organizing properties within the network. Complex collective dynamics emerge in the network in the presence of stimuli. Predefined inputs, i.e., specific neural fingerprints, are detected and encoded into coexisting patterns of activity that propagate throughout the network with different spatial organization. The patterns evoked by a stimulus can survive after the stimulation is over, which provides memory mechanisms to the network. The results presented in this paper suggest that neural information processing based on neural fingerprints can be a plausible, flexible, and powerful strategy. PMID:25852531

Remote optical configuration of pigmented lesion detection and diagnosis of bone fractures

NASA Astrophysics Data System (ADS)

Ozana, Nisan; Bishitz, Yael; Beiderman, Yevgeny; Garcia, Javier; Zalevsky, Zeev; Schwarz, Ariel

2016-02-01

In this paper we present a novel approach of realizing a safe, simple, and inexpensive sensor applicable to bone fractures and pigmented lesions detection. The approach is based on temporal tracking of back-reflected secondary speckle pattern generated while illuminating the affected area with a laser and applying periodic pressure to the surface via a controlled vibration. The use of such a concept was already demonstrated for non-contact monitoring of various bio-medical parameters such as heart rate, blood pulse pressure, concentration of alcohol and glucose in the blood stream and intraocular pressure. The presented technique is a safe and effective method of detecting bone fractures in populations at risk. When applied to pigmented lesions, the technique is superior to visual examination in avoiding many false positives and resultant unnecessary biopsies. Applying a series of different vibration frequencies at the examined tissue and analyzing the 2-D speckle pattern trajectory in response to the applied periodic pressure creates a unique signature for each and different pigmented lesion. Analyzing these signatures is the first step toward detection of malignant melanoma. In this paper we present preliminary experiments that show the validity of the developed sensor for both applications: the detection of damaged bones as well as the classification of pigmented lesions.

Ecosystem Composition Controls the Fate of Rare Earth Elements during Incipient Soil Genesis

PubMed Central

Zaharescu, Dragos G.; Burghelea, Carmen I.; Dontsova, Katerina; Presler, Jennifer K.; Maier, Raina M.; Huxman, Travis; Domanik, Kenneth J.; Hunt, Edward A.; Amistadi, Mary K.; Gaddis, Emily E.; Palacios-Menendez, Maria A.; Vaquera-Ibarra, Maria O.; Chorover, Jon

2017-01-01

The rare earth elements (REE) are increasingly important in a variety of science and economic fields, including (bio)geosciences, paleoecology, astrobiology, and mining. However, REE distribution in early rock-microbe-plant systems has remained elusive. We tested the hypothesis that REE mass-partitioning during incipient weathering of basalt, rhyolite, granite and schist depends on the activity of microbes, vascular plants (Buffalo grass), and arbuscular mycorrhiza. Pore-water element abundances revealed a rapid transition from abiotic to biotic signatures of weathering, the latter associated with smaller aqueous loss and larger plant uptake. Abiotic dissolution was 39% of total denudation in plant-microbes-mycorrhiza treatment. Microbes incremented denudation, particularly in rhyolite, and this resulted in decreased bioavailable solid pools in this rock. Total mobilization (aqueous + uptake) was ten times greater in planted compared to abiotic treatments, REE masses in plant generally exceeding those in water. Larger plants increased bioavailable solid pools, consistent with enhanced soil genesis. Mycorrhiza generally had a positive effect on total mobilization. The main mechanism behind incipient REE weathering was carbonation enhanced by biotic respiration, the denudation patterns being largely dictated by mineralogy. A consistent biotic signature was observed in La:phosphate and mobilization: solid pool ratios, and in the pattern of denudation and uptake. PMID:28230202

A cytoarchitecture-driven myelin model reveals area-specific signatures in human primary and secondary areas using ultra-high resolution in-vivo brain MRI.

PubMed

Dinse, J; Härtwich, N; Waehnert, M D; Tardif, C L; Schäfer, A; Geyer, S; Preim, B; Turner, R; Bazin, P-L

2015-07-01

This work presents a novel approach for modelling laminar myelin patterns in the human cortex in brain MR images on the basis of known cytoarchitecture. For the first time, it is possible to estimate intracortical contrast visible in quantitative ultra-high resolution MR images in specific primary and secondary cytoarchitectonic areas. The presented technique reveals different area-specific signatures which may help to study the spatial distribution of cortical T1 values and the distribution of cortical myelin in general. It may lead to a new discussion on the concordance of cyto- and myeloarchitectonic boundaries, given the absence of such concordance atlases. The modelled myelin patterns are quantitatively compared with data from human ultra-high resolution in-vivo 7T brain MR images (9 subjects). In the validation, the results are compared to one post-mortem brain sample and its ex-vivo MRI and histological data. Details of the analysis pipeline are provided. In the context of the increasing interest in advanced methods in brain segmentation and cortical architectural studies, the presented model helps to bridge the gap between the microanatomy revealed by classical histology and the macroanatomy visible in MRI. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Chemical and Sr isotopic characterization of North America uranium ores: Nuclear forensic applications

DOE PAGES

Balboni, Enrica; Jones, Nina; Spano, Tyler; ...

2016-08-31

This study reports major, minor, and trace element data and Sr isotope ratios for 11 uranium ore (uraninite, UO 2+x) samples and one processed uranium ore concentrate (UOC) from various U.S. deposits. The uraninite investigated represent ores formed via different modes of mineralization (e.g., high- and low-temperature) and within various geological contexts, which include magmatic pegmatites, metamorphic rocks, sandstone-hosted, and roll front deposits. In situ trace element data obtained by laser ablation-ICP-MS and bulk sample Sr isotopic ratios for uraninite samples investigated here indicate distinct signatures that are highly dependent on the mode of mineralization and host rock geology. Relativemore » to their high-temperature counterparts, low-temperature uranium ores record high U/Th ratios (>1000), low total rare earth element (REE) abundances (<1 wt%), high contents (>300 ppm) of first row transition metals (Sc, Ti, V, Cr, Mn, Co, Ni), and radiogenic 87Sr/ 86Sr ratios (>0.7200). Comparison of chondrite normalized REE patterns between uraninite and corresponding processed UOC from the same locality indicates identical patterns at different absolute concentrations. Lastly, this result ultimately confirms the importance of establishing geochemical signatures of raw, uranium ore materials for attribution purposes in the forensic analysis of intercepted nuclear materials.« less

Chemical and Sr isotopic characterization of North America uranium ores: Nuclear forensic applications

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

Balboni, Enrica; Jones, Nina; Spano, Tyler

This study reports major, minor, and trace element data and Sr isotope ratios for 11 uranium ore (uraninite, UO 2+x) samples and one processed uranium ore concentrate (UOC) from various U.S. deposits. The uraninite investigated represent ores formed via different modes of mineralization (e.g., high- and low-temperature) and within various geological contexts, which include magmatic pegmatites, metamorphic rocks, sandstone-hosted, and roll front deposits. In situ trace element data obtained by laser ablation-ICP-MS and bulk sample Sr isotopic ratios for uraninite samples investigated here indicate distinct signatures that are highly dependent on the mode of mineralization and host rock geology. Relativemore » to their high-temperature counterparts, low-temperature uranium ores record high U/Th ratios (>1000), low total rare earth element (REE) abundances (<1 wt%), high contents (>300 ppm) of first row transition metals (Sc, Ti, V, Cr, Mn, Co, Ni), and radiogenic 87Sr/ 86Sr ratios (>0.7200). Comparison of chondrite normalized REE patterns between uraninite and corresponding processed UOC from the same locality indicates identical patterns at different absolute concentrations. Lastly, this result ultimately confirms the importance of establishing geochemical signatures of raw, uranium ore materials for attribution purposes in the forensic analysis of intercepted nuclear materials.« less

Establishment of quantitative hydrological indexes for studies of hydro-biogeochemical interactions at the subsurface.

NASA Astrophysics Data System (ADS)

Alves Meira Neto, A.; Sengupta, A.; Wang, Y.; Volkmann, T.; Chorover, J.; Troch, P. A. A.

2017-12-01

Advances in the understanding of processes in the critical zone (CZ) are dependent on studies coupling the fields of hydrology, microbiology, geochemistry and soil development. At the same time, better insights are needed to integrate hydrologic information into biogeochemical analysis of subsurface environments. This study investigated potential hydrological indexes that help explaining spatiotemporal biogeochemical patterns. The miniLEO is a 2 m3, 10 degree sloping lysimeter located at Biosphere 2 - University of Arizona. The lysimeter was initially filled with pristine basaltic soil and subject to intermittent rainfall applications throughout the period of 18 months followed by its excavation, resulting in a grid-based sample collection at 324 locations. As a result, spatially distributed microbiological and geochemical patterns as well as soil physical properties were obtained. A hydrologic model was then developed in order to simulate the history of the system until the excavation. After being calibrated against sensor data to match its observed input-state-output behavior, the resulting distributed fields of flow velocities and moisture states were retrieved. These results were translated into several hydrological indexes to be used in with distributed microbiological and geochemical signatures. Our study attempts at conciliating sound hydrological modelling with an investigation of the subsurface biological signatures, thus providing a unique opportunity for understanding of fine-scale hydro-biological interactions.

Keystroke dynamics in the pre-touchscreen era.

PubMed

Ahmad, Nasir; Szymkowiak, Andrea; Campbell, Paul A

2013-12-19

Biometric authentication seeks to measure an individual's unique physiological attributes for the purpose of identity verification. Conventionally, this task has been realized via analyses of fingerprints or signature iris patterns. However, whilst such methods effectively offer a superior security protocol compared with password-based approaches for example, their substantial infrastructure costs, and intrusive nature, make them undesirable and indeed impractical for many scenarios. An alternative approach seeks to develop similarly robust screening protocols through analysis of typing patterns, formally known as keystroke dynamics. Here, keystroke analysis methodologies can utilize multiple variables, and a range of mathematical techniques, in order to extract individuals' typing signatures. Such variables may include measurement of the period between key presses, and/or releases, or even key-strike pressures. Statistical methods, neural networks, and fuzzy logic have often formed the basis for quantitative analysis on the data gathered, typically from conventional computer keyboards. Extension to more recent technologies such as numerical keypads and touch-screen devices is in its infancy, but obviously important as such devices grow in popularity. Here, we review the state of knowledge pertaining to authentication via conventional keyboards with a view toward indicating how this platform of knowledge can be exploited and extended into the newly emergent type-based technological contexts.

Scenario drafting to anticipate future developments in technology assessment.

PubMed

Retèl, Valesca P; Joore, Manuela A; Linn, Sabine C; Rutgers, Emiel J T; van Harten, Wim H

2012-08-16

Health Technology Assessment (HTA) information, and in particular cost-effectiveness data is needed to guide decisions, preferably already in early stages of technological development. However, at that moment there is usually a high degree of uncertainty, because evidence is limited and different development paths are still possible. We developed a multi-parameter framework to assess dynamic aspects of a technology -still in development-, by means of scenario drafting to determine the effects, costs and cost-effectiveness of possible future diffusion patterns. Secondly, we explored the value of this method on the case of the clinical implementation of the 70-gene signature for breast cancer, a gene expression profile for selecting patients who will benefit most from chemotherapy. To incorporate process-uncertainty, ten possible scenarios regarding the introduction of the 70-gene signature were drafted with European experts. Out of 5 most likely scenarios, 3 drivers of diffusion (non-compliance, technical failure, and uptake) were quantitatively integrated in a decision-analytical model. For these scenarios, the cost-effectiveness of the 70-gene signature expressed in Incremental Cost-Effectiveness Ratios (ICERs) was compared to clinical guidelines, calculated from the past (2005) until the future (2020). In 2005 the ICER was €1,9 million/quality-adjusted-life-year (QALY), meaning that the 70-gene signature was not yet cost-effective compared to the current clinical guideline. The ICER for the 70-gene signature improved over time with a range of €1,9 million to €26,145 in 2010 and €1,9 million to €11,123/QALY in 2020 depending on the separate scenario used. From 2010, the 70-gene signature should be cost-effective, based on the combined scenario. The uptake-scenario had strongest influence on the cost-effectiveness. When optimal diffusion of a technology is sought, incorporating process-uncertainty by means of scenario drafting into a decision model may reveal unanticipated developments and can demonstrate a range of possible cost-effectiveness outcomes. The effect of scenarios give additional information on the speed with cost effectiveness might be reached and thus provide a more realistic picture for policy makers, opinion leaders and manufacturers.

Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy.

PubMed

Honeyborne, Isobella; McHugh, Timothy D; Kuittinen, Iitu; Cichonska, Anna; Evangelopoulos, Dimitrios; Ronacher, Katharina; van Helden, Paul D; Gillespie, Stephen H; Fernandez-Reyes, Delmiro; Walzl, Gerhard; Rousu, Juho; Butcher, Philip D; Waddell, Simon J

2016-04-07

New treatment options are needed to maintain and improve therapy for tuberculosis, which caused the death of 1.5 million people in 2013 despite potential for an 86 % treatment success rate. A greater understanding of Mycobacterium tuberculosis (M.tb) bacilli that persist through drug therapy will aid drug development programs. Predictive biomarkers for treatment efficacy are also a research priority. Genome-wide transcriptional profiling was used to map the mRNA signatures of M.tb from the sputa of 15 patients before and 3, 7 and 14 days after the start of standard regimen drug treatment. The mRNA profiles of bacilli through the first 2 weeks of therapy reflected drug activity at 3 days with transcriptional signatures at days 7 and 14 consistent with reduced M.tb metabolic activity similar to the profile of pre-chemotherapy bacilli. These results suggest that a pre-existing drug-tolerant M.tb population dominates sputum before and after early drug treatment, and that the mRNA signature at day 3 marks the killing of a drug-sensitive sub-population of bacilli. Modelling patient indices of disease severity with bacterial gene expression patterns demonstrated that both microbiological and clinical parameters were reflected in the divergent M.tb responses and provided evidence that factors such as bacterial load and disease pathology influence the host-pathogen interplay and the phenotypic state of bacilli. Transcriptional signatures were also defined that predicted measures of early treatment success (rate of decline in bacterial load over 3 days, TB test positivity at 2 months, and bacterial load at 2 months). This study defines the transcriptional signature of M.tb bacilli that have been expectorated in sputum after two weeks of drug therapy, characterizing the phenotypic state of bacilli that persist through treatment. We demonstrate that variability in clinical manifestations of disease are detectable in bacterial sputa signatures, and that the changing M.tb mRNA profiles 0-2 weeks into chemotherapy predict the efficacy of treatment 6 weeks later. These observations advocate assaying dynamic bacterial phenotypes through drug therapy as biomarkers for treatment success.

Scenario drafting to anticipate future developments in technology assessment

PubMed Central

2012-01-01

Background Health Technology Assessment (HTA) information, and in particular cost-effectiveness data is needed to guide decisions, preferably already in early stages of technological development. However, at that moment there is usually a high degree of uncertainty, because evidence is limited and different development paths are still possible. We developed a multi-parameter framework to assess dynamic aspects of a technology -still in development-, by means of scenario drafting to determine the effects, costs and cost-effectiveness of possible future diffusion patterns. Secondly, we explored the value of this method on the case of the clinical implementation of the 70-gene signature for breast cancer, a gene expression profile for selecting patients who will benefit most from chemotherapy. Methods To incorporate process-uncertainty, ten possible scenarios regarding the introduction of the 70-gene signature were drafted with European experts. Out of 5 most likely scenarios, 3 drivers of diffusion (non-compliance, technical failure, and uptake) were quantitatively integrated in a decision-analytical model. For these scenarios, the cost-effectiveness of the 70-gene signature expressed in Incremental Cost-Effectiveness Ratios (ICERs) was compared to clinical guidelines, calculated from the past (2005) until the future (2020). Results In 2005 the ICER was €1,9 million/quality-adjusted-life-year (QALY), meaning that the 70-gene signature was not yet cost-effective compared to the current clinical guideline. The ICER for the 70-gene signature improved over time with a range of €1,9 million to €26,145 in 2010 and €1,9 million to €11,123/QALY in 2020 depending on the separate scenario used. From 2010, the 70-gene signature should be cost-effective, based on the combined scenario. The uptake-scenario had strongest influence on the cost-effectiveness. Conclusions When optimal diffusion of a technology is sought, incorporating process-uncertainty by means of scenario drafting into a decision model may reveal unanticipated developments and can demonstrate a range of possible cost-effectiveness outcomes. The effect of scenarios give additional information on the speed with cost effectiveness might be reached and thus provide a more realistic picture for policy makers, opinion leaders and manufacturers. PMID:22894140

Low-angle X-ray scattering properties of irradiated spices

NASA Astrophysics Data System (ADS)

Almeida, A. P. G.; Braz, D.; Barroso, R. C.; Lopes, R. T.

2007-09-01

The scattering of X-rays at low angles (LAXS) is a technique dominated by the coherent scattering process. One characteristic observation of low-angle coherent scattering is the so-called molecular interference effect, being characterized by the presence of one or more peaks in the forward direction of scattering. In the present study, LAXS profiles from five different spices are carefully measured in order to establish characteristic scattering signatures. Samples of Ceylon cinnamon, cumin, nutmeg, paprika and black pepper were bought in local market in Rio de Janeiro, Brazil. The LAXS patterns were obtained using a Shimadzu DRX 6000 diffractometer in reflection geometry. Coherent scattering patterns are measured for the samples for θ=5-35°. The data were collected in 0.05° increments every 3 s. In order to evaluate the possible molecular structure changes caused to the irradiation procedure, the signatures obtained for control (non-irradiated) spices were compared with spice samples irradiated with different doses varying from 3 to 40 kGy. The LAXS patterns of all samples were obtained after 30, 60, 90, 120 days to evaluate the effect of storage period. Scattering profiles from spices irradiated with different irradiation doses were obtained and the results compared. For each spice, there is no considerable deviation in shape in function of the irradiation dose. It indicates that the molecular structure of each analyzed spices is preserved considering the dose range chosen. The results show that the molecular structure was found to be stable during storage at the ambient temperature for up to 4 months.

Characterization of Mycobacterium tuberculosis Complex DNAs from Egyptian Mummies by Spoligotyping

PubMed Central

Zink, Albert R.; Sola, Christophe; Reischl, Udo; Grabner, Waltraud; Rastogi, Nalin; Wolf, Hans; Nerlich, Andreas G.

2003-01-01

Bone and soft tissue samples from 85 ancient Egyptian mummies were analyzed for the presence of ancient Mycobacterium tuberculosis complex DNA (aDNA) and further characterized by spoligotyping. The specimens were obtained from individuals from different tomb complexes in Thebes West, Upper Egypt, which were used for upper social class burials between the Middle Kingdom (since ca. 2050 BC) and the Late Period (until ca. 500 BC). A total of 25 samples provided a specific positive signal for the amplification of a 123-bp fragment of the repetitive element IS6110, indicating the presence of M. tuberculosis DNA. Further PCR-based tests for the identification of subspecies failed due to lack of specific amplification products in the historic tissue samples. Of these 25 positive specimens, 12 could be successfully characterized by spoligotyping. The spoligotyping signatures were compared to those in an international database. They all show either an M. tuberculosis or an M. africanum pattern, but none revealed an M. bovis-specific pattern. The results from a Middle Kingdom tomb (used exclusively between ca. 2050 and 1650 BC) suggest that these samples bear an M. africanum-type specific spoligotyping signature. The samples from later periods provided patterns typical for M. tuberculosis. This study clearly demonstrates that spoligotyping can be applied to historic tissue samples. In addition, our results do not support the theory that M. tuberculosis originated from the M. bovis type but, rather, suggest that human M. tuberculosis may have originated from a precursor complex probably related to M. africanum. PMID:12517873

Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma.

PubMed

Tremblay, Marie-Pier; Armero, Victoria E S; Allaire, Andréa; Boudreault, Simon; Martenon-Brodeur, Camille; Durand, Mathieu; Lapointe, Elvy; Thibault, Philippe; Tremblay-Létourneau, Maude; Perreault, Jean-Pierre; Scott, Michelle S; Bisaillon, Martin

2016-08-26

Dysregulations in alternative splicing (AS) patterns have been associated with many human diseases including cancer. In the present study, alterations to the global RNA splicing landscape of cellular genes were investigated in a large-scale screen from 377 liver tissue samples using high-throughput RNA sequencing data. Our study identifies modifications in the AS patterns of transcripts encoded by more than 2500 genes such as tumor suppressor genes, transcription factors, and kinases. These findings provide insights into the molecular differences between various types of hepatocellular carcinoma (HCC). Our analysis allowed the identification of 761 unique transcripts for which AS is misregulated in HBV-associated HCC, while 68 are unique to HCV-associated HCC, 54 to HBV&HCV-associated HCC, and 299 to virus-free HCC. Moreover, we demonstrate that the expression pattern of the RNA splicing factor hnRNPC in HCC tissues significantly correlates with patient survival. We also show that the expression of the HBx protein from HBV leads to modifications in the AS profiles of cellular genes. Finally, using RNA interference and a reverse transcription-PCR screening platform, we examined the implications of cellular proteins involved in the splicing of transcripts involved in apoptosis and demonstrate the potential contribution of these proteins in AS control. This study provides the first comprehensive portrait of global changes in the RNA splicing signatures that occur in hepatocellular carcinoma. Moreover, these data allowed us to identify unique signatures of genes for which AS is misregulated in the different types of HCC.

Noble gas signatures in the Island of Maui, Hawaii: Characterizing groundwater sources in fractured systems

USGS Publications Warehouse

Niu, Yi; Castro, M. Clara; Hall, Chris M.; Gingerich, Stephen B.; Scholl, Martha A.; Warrier, Rohit B.

2017-01-01

Uneven distribution of rainfall and freshwater scarcity in populated areas in the Island of Maui, Hawaii, renders water resources management a challenge in this complex and ill-defined hydrological system. A previous study in the Galapagos Islands suggests that noble gas temperatures (NGTs) record seasonality in that fractured, rapid infiltration groundwater system rather than the commonly observed mean annual air temperature (MAAT) in sedimentary systems where infiltration is slower thus, providing information on recharge sources and potential flow paths. Here we report noble gas results from the basal aquifer, springs, and rainwater in Maui to explore the potential for noble gases in characterizing this type of complex fractured hydrologic systems. Most samples display a mass-dependent depletion pattern with respect to surface conditions consistent with previous observations both in the Galapagos Islands and Michigan rainwater. Basal aquifer and rainwater noble gas patterns are similar and suggest direct, fast recharge from precipitation to the basal aquifer. In contrast, multiple springs, representative of perched aquifers, display highly variable noble gas concentrations suggesting recharge from a variety of sources. The distinct noble gas patterns for the basal aquifer and springs suggest that basal and perched aquifers are separate entities. Maui rainwater displays high apparent NGTs, incompatible with surface conditions, pointing either to an origin at high altitudes with the presence of ice or an ice-like source of undetermined origin. Overall, noble gas signatures in Maui reflect the source of recharge rather than the expected altitude/temperature relationship commonly observed in sedimentary systems.

Synthesis of streamflow recession curves in dry environments

NASA Astrophysics Data System (ADS)

Arciniega, Saul; Breña-Naranjo, Agustín; Pedrozo-Acuña, Adrían

2015-04-01

The elucidation and predictability of hydrological systems can largely benefit by extracting observed patterns in processes, data and models. Such type of research framework in hydrology, also known as synthesis has gained significant attention over the last decade. For instance, hydrological synthesis implies that the identification of patterns in catchment behavior can enhance the extrapolation of hydrological signatures over large spatial and temporal scales. Hydrological signatures during dry periods such as streamflow recession curves (SRC) are of special interest in regions coping with water scarcity. Indeed, the study of SRCs from observed hydrographs allows to extract information about the storage-discharge relationship of a specific catchment and some of their groundwater hydraulic properties. This work aims at performing a synthesis work of SRCs in semi-arid & arid environments across Northern Mexico. Our dataset consisted in observed daily SRCs in 63 catchments with minima human interferences. Three streamflow recession extraction methods (Vogel, Brutsaert and Aksoy-Wittenberg) along with four recession models (Maillet, Boussinesq, Coutagne y Wittenberg) and three parameter estimation techniques (regressions, lower envelope y data binning) were used to determine the combination among different possible methods, processes and models that better describes SRCs in our study sites. Our results show that the extraction method proposed by Aksoy-Wittenberg along with Coutagne's nonlinear recession model provides a better approximation of SRCs across Northern Mexico, whereas regression was found to be the most adequate parameter estimation method. This study suggests that hydrological synthesis turned out to be an useful framework to identify similar patterns and model parameters during dry periods across Mexico's water-limited environments.

Distributed neural signatures of natural audiovisual speech and music in the human auditory cortex.

PubMed

Salmi, Juha; Koistinen, Olli-Pekka; Glerean, Enrico; Jylänki, Pasi; Vehtari, Aki; Jääskeläinen, Iiro P; Mäkelä, Sasu; Nummenmaa, Lauri; Nummi-Kuisma, Katarina; Nummi, Ilari; Sams, Mikko

2017-08-15

During a conversation or when listening to music, auditory and visual information are combined automatically into audiovisual objects. However, it is still poorly understood how specific type of visual information shapes neural processing of sounds in lifelike stimulus environments. Here we applied multi-voxel pattern analysis to investigate how naturally matching visual input modulates supratemporal cortex activity during processing of naturalistic acoustic speech, singing and instrumental music. Bayesian logistic regression classifiers with sparsity-promoting priors were trained to predict whether the stimulus was audiovisual or auditory, and whether it contained piano playing, speech, or singing. The predictive performances of the classifiers were tested by leaving one participant at a time for testing and training the model using the remaining 15 participants. The signature patterns associated with unimodal auditory stimuli encompassed distributed locations mostly in the middle and superior temporal gyrus (STG/MTG). A pattern regression analysis, based on a continuous acoustic model, revealed that activity in some of these MTG and STG areas were associated with acoustic features present in speech and music stimuli. Concurrent visual stimulus modulated activity in bilateral MTG (speech), lateral aspect of right anterior STG (singing), and bilateral parietal opercular cortex (piano). Our results suggest that specific supratemporal brain areas are involved in processing complex natural speech, singing, and piano playing, and other brain areas located in anterior (facial speech) and posterior (music-related hand actions) supratemporal cortex are influenced by related visual information. Those anterior and posterior supratemporal areas have been linked to stimulus identification and sensory-motor integration, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic structure and signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos).

PubMed

Momigliano, P; Harcourt, R; Robbins, W D; Jaiteh, V; Mahardika, G N; Sembiring, A; Stow, A

2017-09-01

With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos). Using samples from Australia, Indonesia and oceanic reefs in the Indian Ocean, we established that large oceanic distances represent barriers to gene flow, whereas genetic differentiation on continental shelves follows an isolation by distance model. In Australia and Indonesia differentiation at nuclear SNPs was weak, with coral reefs acting as stepping stones maintaining connectivity across large distances. Differentiation of mtDNA was stronger, and more pronounced in females, suggesting sex-biased dispersal. Four independent tests identified a set of loci putatively under selection, indicating that grey reef sharks in eastern Australia are likely under different selective pressures to those in western Australia and Indonesia. Genetic distances averaged across all loci were uncorrelated with genetic distances calculated from outlier loci, supporting the conclusion that different processes underpin genetic divergence in these two data sets. This pattern of heterogeneous genomic differentiation, suggestive of local adaptation, has implications for the conservation of grey reef sharks; furthermore, it highlights that marine species showing little genetic differentiation at neutral loci may exhibit patterns of cryptic genetic structure driven by local selection.

Microbial community assembly patterns under incipient conditions in a basaltic soil system

NASA Astrophysics Data System (ADS)

Sengupta, A.; Stegen, J.; Alves Meira Neto, A.; Wang, Y.; Chorover, J.; Troch, P. A. A.; Maier, R. M.

2017-12-01

In sub-surface environments, the biotic components are critically linked to the abiotic processes. However, there is limited understanding of community establishment, functional associations, and community assembly processes of such microbes in sub-surface environments. This study presents the first analysis of microbial signatures in an incipient terrestrial basalt soil system conducted under controlled conditions. A sub-meter scale sampling of a soil mesocosm revealed the contrasting distribution patterns of simple soil parameters such as bulk density and electrical conductivity. Phylogenetic analysis of 16S rRNA gene indicated the presence of a total 40 bacterial and archaeal phyla, with high relative abundance of Actinobacteria on the surface and highest abundance of Proteobacteria throughout the system. Community diversity patterns were inferred to be dependent on depth profile and average water content in the system. Predicted functional gene analysis suggested mixotrophy lifestyles with both autotrophic and heterotrophic metabolisms, likelihood of a unique salt tolerant methanogenic pathway with links to novel Euryarchea, signatures of an incomplete nitrogen cycle, and predicted enzymes of extracellular iron (II) to iron (III) conversion followed by intracellular uptake, transport and regulation. Null modeling revealed microbial community assembly was predominantly governed by variable selection, but the influence of the variable selection did not show systematic spatial structure. The presence of significant heterogeneity in predicted functions and ecologically deterministic shifts in community composition in a homogeneous incipient basalt highlights the complexity exhibited by microorganisms even in the simplest of environmental systems. This presents an opportunity to further develop our understanding of how microbial communities establish, evolve, impact, and respond in sub-surface environments.

A study to explore the use of orbital remote sensing to determine native arid plant distribution. [Arizona

NASA Technical Reports Server (NTRS)

Mcginnies, W. G. (Principal Investigator); Conn, J. S.; Haase, E. F.; Lepley, L. K.; Musick, H. B.; Foster, K. E.

1975-01-01

The author has identified the following significant results. Research results include a method for determining the reflectivities of natural areas from ERTS data taking into account sun angle and atmospheric effects on the radiance seen by the satellite sensor. Ground truth spectral signature data for various types of scenes, including ground with and without annuals, and various shrubs were collected. Large areas of varnished desert pavement are visible and mappable on ERTS and high altitude aircraft imagery. A large scale and a small scale vegetation pattern were found to be correlated with presence of desert pavement. A comparison of radiometric data with video recordings shows quantitatively that for most areas of desert vegetation, soils are the most influential factor in determining the signature of a scene. Additive and subtractive image processing techniques were applied in the dark room to enhance vegetational aspects of ERTS.

New software to model energy dispersive X-ray diffraction in polycrystalline materials

NASA Astrophysics Data System (ADS)

Ghammraoui, B.; Tabary, J.; Pouget, S.; Paulus, C.; Moulin, V.; Verger, L.; Duvauchelle, Ph.

2012-02-01

Detection of illicit materials, such as explosives or drugs, within mixed samples is a major issue, both for general security and as part of forensic analyses. In this paper, we describe a new code simulating energy dispersive X-ray diffraction patterns in polycrystalline materials. This program, SinFullscat, models diffraction of any object in any diffractometer system taking all physical phenomena, including amorphous background, into account. Many system parameters can be tuned: geometry, collimators (slit and cylindrical), sample properties, X-ray source and detector energy resolution. Good agreement between simulations and experimental data was obtained. Simulations using explosive materials indicated that parameters such as the diffraction angle or the energy resolution of the detector have a significant impact on the diffraction signature of the material inspected. This software will be a convenient tool to test many diffractometer configurations, providing information on the one that best restores the spectral diffraction signature of the materials of interest.

Synchrotron X-ray micro-beam studies of ancient Egyptian make-up

NASA Astrophysics Data System (ADS)

Martinetto, P.; Anne, M.; Dooryhée, E.; Drakopoulos, M.; Dubus, M.; Salomon, J.; Simionovici, A.; Walter, Ph.

2001-07-01

Vases full of make-up are most often present in the burial furniture of Egyptian tombs dated from the pharaonic period. The powdered cosmetics made of isolated grains are analysed to identify their trace element signature. From this signature we identify the provenance of the mineral ingredients in the make-up and we observe different impurities in products, which have been demonstrated as synthetic substances by previous works. Focused X-ray micro-beam ( 2×5 μm2) is successively tuned at 11 keV, below the L III absorption edge of Pb, and 31.8 keV for global characterisation of the metal impurities. The fluorescence signal integrated over each single grain is detected against the X-ray micro-diffraction pattern collected in transmission with a bi-dimensional detector. Furthermore, for galena grains rich in Zn, the XANES signal at the K-absorption edge of Zn shows its immediate nearest-neighbour environment.

Salinity signature of the Pacific Decadal Oscillation

NASA Astrophysics Data System (ADS)

Overland, James E.; Salo, Sigrid; Adams, Jennifer Miletta

Three sites in the North Pacific have temperature and salinity observations in most months for several years before and after 1977. The Gulf of Alaska station (57°N, 148°W) showed a 2°C warming and a 0.6 freshening in salinity at 10 m depth in the 1980s compared to the 1970s. OWS PAPA (50°N, 145°W) and PAPA line station 7 (49.1°N, 132.4°W) show warming of 0.6°C and 0.9°C, with no major salinity change. The decrease in density and increase in stratification in the Gulf of Alaska after 1977 corresponds primarily to a decrease in salinity in the upper 150 m. We propose that while the Pacific Decadal Oscillation has an east/west character in temperature, the salinity signature will have a NNW/SSE character, similar to the pattern of interannual variability in precipitation.

Neuroelectrical Decomposition of Spontaneous Brain Activity Measured with Functional Magnetic Resonance Imaging

PubMed Central

Liu, Zhongming; de Zwart, Jacco A.; Chang, Catie; Duan, Qi; van Gelderen, Peter; Duyn, Jeff H.

2014-01-01

Spontaneous activity in the human brain occurs in complex spatiotemporal patterns that may reflect functionally specialized neural networks. Here, we propose a subspace analysis method to elucidate large-scale networks by the joint analysis of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) data. The new approach is based on the notion that the neuroelectrical activity underlying the fMRI signal may have EEG spectral features that report on regional neuronal dynamics and interregional interactions. Applying this approach to resting healthy adults, we indeed found characteristic spectral signatures in the EEG correlates of spontaneous fMRI signals at individual brain regions as well as the temporal synchronization among widely distributed regions. These spectral signatures not only allowed us to parcel the brain into clusters that resembled the brain's established functional subdivision, but also offered important clues for disentangling the involvement of individual regions in fMRI network activity. PMID:23796947

Discovering causal signaling pathways through gene-expression patterns

PubMed Central

Parikh, Jignesh R.; Klinger, Bertram; Xia, Yu; Marto, Jarrod A.; Blüthgen, Nils

2010-01-01

High-throughput gene-expression studies result in lists of differentially expressed genes. Most current meta-analyses of these gene lists include searching for significant membership of the translated proteins in various signaling pathways. However, such membership enrichment algorithms do not provide insight into which pathways caused the genes to be differentially expressed in the first place. Here, we present an intuitive approach for discovering upstream signaling pathways responsible for regulating these differentially expressed genes. We identify consistently regulated signature genes specific for signal transduction pathways from a panel of single-pathway perturbation experiments. An algorithm that detects overrepresentation of these signature genes in a gene group of interest is used to infer the signaling pathway responsible for regulation. We expose our novel resource and algorithm through a web server called SPEED: Signaling Pathway Enrichment using Experimental Data sets. SPEED can be freely accessed at http://speed.sys-bio.net/. PMID:20494976

Electron Energization and Mixing Observed by MMS in the Vicinity of an Electron Diffusion Region During Magnetopause Reconnection

NASA Technical Reports Server (NTRS)

Chen, Li-Jen; Hesse, Michael; Wang, Shan; Gershman, Daniel; Ergun, Robert; Pollock, Craig; Torbert, Roy; Bessho, Naoki; Daughton, William; Dorelli, John;

Electron energization and mixing observed by MMS in the vicinity of an electron diffusion region during magnetopause reconnection

NASA Astrophysics Data System (ADS)

Chen, Li-Jen; Hesse, Michael; Wang, Shan; Gershman, Daniel; Ergun, Robert; Pollock, Craig; Torbert, Roy; Bessho, Naoki; Daughton, William; Dorelli, John; Giles, Barbara; Strangeway, Robert; Russell, Christopher; Khotyaintsev, Yuri; Burch, Jim; Moore, Thomas; Lavraud, Benoit; Phan, Tai; Avanov, Levon

2016-06-01

Measurements from the Magnetospheric Multiscale (MMS) mission are reported to show distinct features of electron energization and mixing in the diffusion region of the terrestrial magnetopause reconnection. At the ion jet and magnetic field reversals, distribution functions exhibiting signatures of accelerated meandering electrons are observed at an electron out-of-plane flow peak. The meandering signatures manifested as triangular and crescent structures are established features of the electron diffusion region (EDR). Effects of meandering electrons on the electric field normal to the reconnection layer are detected. Parallel acceleration and mixing of the inflowing electrons with exhaust electrons shape the exhaust flow pattern. In the EDR vicinity, the measured distribution functions indicate that locally, the electron energization and mixing physics is captured by two-dimensional reconnection, yet to account for the simultaneous four-point measurements, translational invariant in the third dimension must be violated on the ion-skin-depth scale.

Detection and recognition of targets by using signal polarization properties

NASA Astrophysics Data System (ADS)

Ponomaryov, Volodymyr I.; Peralta-Fabi, Ricardo; Popov, Anatoly V.; Babakov, Mikhail F.

1999-08-01

The quality of radar target recognition can be enhanced by exploiting its polarization signatures. A specialized X-band polarimetric radar was used for target recognition in experimental investigations. The following polarization characteristics connected to the object geometrical properties were investigated: the amplitudes of the polarization matrix elements; an anisotropy coefficient; depolarization coefficient; asymmetry coefficient; the energy of a backscattering signal; object shape factor. A large quantity of polarimetric radar data was measured and processed to form a database of different object and different weather conditions. The histograms of polarization signatures were approximated by a Nakagami distribution, then used for real- time target recognition. The Neyman-Pearson criterion was used for the target detection, and the criterion of the maximum of a posterior probability was used for recognition problem. Some results of experimental verification of pattern recognition and detection of objects with different electrophysical and geometrical characteristics urban in clutter are presented in this paper.

Vacillations induced by interference of stationary and traveling planetary waves

NASA Technical Reports Server (NTRS)

Salby, Murry L.; Garcia, Rolando R.

1987-01-01

The interference pattern produced when a traveling planetary wave propagates over a stationary forced wave is explored, examining the interference signature in a variety of diagnostics. The wave field is first restricted to a diatomic spectrum consisting of two components: a single stationary wave and a single monochromatic traveling wave. A simple barotropic normal mode propagating over a simple stationary plane wave is considered, and closed form solutions are obtained. The wave fields are then restricted spatially, providing more realistic structures without sacrificing the advantages of an analytical solution. Both stationary and traveling wave fields are calculated numerically with the linearized Primitive Equations in a realistic basic state. The mean flow reaction to the fluctuating eddy forcing which results from interference is derived. Synoptic geopotential behavior corresponding to the combined wave and mean flow fields is presented, and the synoptic signature in potential vorticity on isentropic surfaces is examined.

Brain Signature Characterizing the Body-Brain-Mind Axis of Transsexuals

PubMed Central

Chao, Hsiang-Tai; Tu, Pei-Chi; Li, Cheng-Ta; Cheng, Chou-Ming; Su, Tung-Ping; Lee, Ying-Chiao; Hsieh, Jen-Chuen

2013-01-01

Individuals with gender identity disorder (GID), who are commonly referred to as transsexuals (TXs), are afflicted by negative psychosocial stressors. Central to the psychological complex of TXs is the conviction of belonging to the opposite sex. Neuroanatomical and functional brain imaging studies have demonstrated that the GID is associated with brain alterations. In this study, we found that TXs identify, when viewing male-female couples in erotic or non-erotic (“neutral”) interactions, with the couple member of the desired gender in both situations. By means of functional magnetic resonance imaging, we found that the TXs, as opposed to controls (CONs), displayed an increased functional connectivity between the ventral tegmental area, which is associated with dimorphic genital representation, and anterior cingulate cortex subregions, which play a key role in social exclusion, conflict monitoring and punishment adjustment. The neural connectivity pattern suggests a brain signature of the psychosocial distress for the gender-sex incongruity of TXs. PMID:23923023

Golan Heights Groundwater Systems: Separation By REE+Y And Stable Isotopes

NASA Astrophysics Data System (ADS)

Siebert, C.; Geyer, S.; Knoeller, K.; Roediger, T.; Weise, S.; Dulski, P.; Moeller, P.; Guttman, J.

2008-12-01

In a semi-arid to arid country like Israel, all freshwater resources are under (over-) utilization. Particularly, the Golan Heights rank as one of the most important extraction areas of groundwater of good quality and quantity. Additionally the mountain range feed to a high degree the most important freshwater reservoir of Israel, the Sea of Galilee. Hence, knowing the sources and characters of the Golan Heights groundwater systems is an instantaneous demand regarding sustainable management and protection. Within the "German-Israeli-Jordanian-Palestinian Joint Research Program for the Sustainable Utilisation of Aquifer Systems", hundreds of water samples were taken from all over the Jordan-Dead Sea rift-system to understand groundwater flow-systems and salinisation. For that purpose, each sample was analysed for major and minor ions, rare earth elements including yttrium (REY) and stable isotopes of water (d18O, d2H). The REY distribution in groundwater is established during infiltration by the first water-rock interaction and consequently reflects the leachable components of sediments and rocks of the recharge area. In well- developed flow-systems, REY are adsorbed onto pore surfaces are in equilibrium with the percolating groundwater, even if the lithology changes (e.g. inter-aquifer flow). Thus, groundwater sampled from wells and springs still show the REY distribution pattern established in the recharge area. Since high temperatures do not occur in Golan Heights, d2H and d18O are less controlled by water-rock interaction than by climatic and geomorphological factors at the time of replenishment. Applying the REY signature as a grouping criterion of groundwaters, d18O vs. d2H plots yield a new dimension in interpreting isotope data. The combined use of hydrochemical and isotopic methods enabled us to contain the areas of replenishment and the flow-paths of all investigated groundwater in the Golan Heights. Despite location, salinity or temperature of spring or well waters, stable isotopes showed, that the main area of recharge is the elevated Hermon-Massif, with high annually precipitation amounts. The major element composition of fresh water well Alonei HaBashan 3, situated in the basaltic Upper Golan Heights, is defined by a pre-Neogenic limy aquifer and the contact to basalts. However, REY pattern refer to a calcareous infiltration area. Stable isotope signatures are lighter than in the recharge of comparable elevated Upper Galilee. Further to the south, in the Yarmouk gorge hot Mezar springs occur, which show stable isotope signatures even lighter than in water of Alonei Habshan 3. Both, REY pattern and hydrochemistry show infiltration into and contact to the Sr-rich limestone aquifer of the Mt. Scopus group. That adds up to an infiltration area some 50 km to the north, the nearest elevated area where carbonates crop out. Nearby Mezar, hot Hammat Gader springs occur, which show comparable isotopic signatures and hydrochemical composition. However, the REY-patterns indicate infiltration in basalts. By means of those three examples we could show, that the use of a combined hydrochemical and isotopic approach reveals complex and large-scale groundwater infiltration- and flow-systems much better than a focused view on a specific band of elements.

A strategy to discover new organizers identifies a putative heart organizer

PubMed Central

Anderson, Claire; Khan, Mohsin A. F.; Wong, Frances; Solovieva, Tatiana; Oliveira, Nidia M. M.; Baldock, Richard A.; Tickle, Cheryll; Burt, Dave W.; Stern, Claudio D.

2016-01-01

Organizers are regions of the embryo that can both induce new fates and impart pattern on other regions. So far, surprisingly few organizers have been discovered, considering the number of patterned tissue types generated during development. This may be because their discovery has relied on transplantation and ablation experiments. Here we describe a new approach, using chick embryos, to discover organizers based on a common gene expression signature, and use it to uncover the anterior intestinal portal (AIP) endoderm as a putative heart organizer. We show that the AIP can induce cardiac identity from non-cardiac mesoderm and that it can pattern this by specifying ventricular and suppressing atrial regional identity. We also uncover some of the signals responsible. The method holds promise as a tool to discover other novel organizers acting during development. PMID:27557800

Patterns and variability in geochemical signatures and microbial activity within and between diverse cold seep habitats along the lower continental slope, Northern Gulf of Mexico

NASA Astrophysics Data System (ADS)

Bowles, Marshall; Hunter, Kimberley S.; Samarkin, Vladimir; Joye, Samantha

2016-07-01

We collected 69 sediment cores from distinct ecological and geological settings along the deep slope in the Northern Gulf of Mexico to evaluate whether specific geochemical- or habitat-related factors correlated with rates of microbial processes and geochemical signatures. By collecting replicate cores from distinct habitats across multiple sites, we illustrate and quantify the heterogeneity of cold seep geochemistry and microbial activity. These data also document the factors driving unique aspects of the geochemistry of deep slope gas, oil and brine seeps. Surprisingly little variation was observed between replicate (n=2-5) cores within sites for most analytes (except methane), implying that the common practice of collecting one core for geochemical analysis can capture the signature of a habitat in most cases. Depth-integrated concentrations of methane, dissolved inorganic carbon (DIC), and calcium were the predominant geochemical factors that correlated with a site's ecological or geological settings. Pore fluid methane concentration was related to the phosphate and DIC concentration, as well as to rates of sulfate reduction. While distinctions between seep habitats were identified from geochemical signatures, habitat specific geochemistry varied little across sites. The relative concentration of dissolved inorganic nitrogen versus phosphorus suggests that phosphorus availability limits biomass production at cold seeps. Correlations between calcium, chloride, and phosphate concentrations were indicative of brine-associated phosphate transport, suggesting that in addition to the co-migration of methane, dissolved organic carbon, and ammonium with brine, phosphate delivery is also associated with brine advection.

Evidence for geomagnetic imprinting and magnetic navigation in the natal homing of sea turtles.

PubMed

Brothers, J Roger; Lohmann, Kenneth J

2015-02-02

Natal homing is a pattern of behavior in which animals migrate away from their geographic area of origin and then return to reproduce in the same location where they began life [1-3]. Although diverse long-distance migrants accomplish natal homing [1-8], little is known about how they do so. The enigma is epitomized by loggerhead sea turtles (Caretta caretta), which leave their home beaches as hatchlings and migrate across entire ocean basins before returning to nest in the same coastal area where they originated [9, 10]. One hypothesis is that turtles imprint on the unique geomagnetic signature of their natal area and use this information to return [1]. Because Earth's field changes over time, geomagnetic imprinting should cause turtles to change their nesting locations as magnetic signatures drift slightly along coastlines. To investigate, we analyzed a 19-year database of loggerhead nesting sites in the largest sea turtle rookery in North America. Here we report a strong association between the spatial distribution of turtle nests and subtle changes in Earth's magnetic field. Nesting density increased significantly in coastal areas where magnetic signatures of adjacent beach locations converged over time, whereas nesting density decreased in places where magnetic signatures diverged. These findings confirm central predictions of the geomagnetic imprinting hypothesis and provide strong evidence that such imprinting plays an important role in natal homing in sea turtles. The results give credence to initial reports of geomagnetic imprinting in salmon [11, 12] and suggest that similar mechanisms might underlie long-distance natal homing in diverse animals. Copyright © 2015 Elsevier Ltd. All rights reserved.

Seeing shapes in seemingly random spatial patterns: Fractal analysis of Rorschach inkblots

PubMed Central

Taylor, R. P.; Martin, T. P.; Montgomery, R. D.; Smith, J. H.; Micolich, A. P.; Boydston, C.; Scannell, B. C.; Fairbanks, M. S.; Spehar, B.

2017-01-01

Rorschach inkblots have had a striking impact on the worlds of art and science because of the remarkable variety of associations with recognizable and namable objects they induce. Originally adopted as a projective psychological tool to probe mental health, psychologists and artists have more recently interpreted the variety of induced images simply as a signature of the observers’ creativity. Here we analyze the relationship between the spatial scaling parameters of the inkblot patterns and the number of induced associations, and suggest that the perceived images are induced by the fractal characteristics of the blot edges. We discuss how this relationship explains the frequent observation of images in natural scenery. PMID:28196082

Advanced Doppler radar physiological sensing technique for drone detection

NASA Astrophysics Data System (ADS)

Yoon, Ji Hwan; Xu, Hao; Garcia Carrillo, Luis R.

2017-05-01

A 24 GHz medium-range human detecting sensor, using the Doppler Radar Physiological Sensing (DRPS) technique, which can also detect unmanned aerial vehicles (UAVs or drones), is currently under development for potential rescue and anti-drone applications. DRPS systems are specifically designed to remotely monitor small movements of non-metallic human tissues such as cardiopulmonary activity and respiration. Once optimized, the unique capabilities of DRPS could be used to detect UAVs. Initial measurements have shown that DRPS technology is able to detect moving and stationary humans, as well as largely non-metallic multi-rotor drone helicopters. Further data processing will incorporate pattern recognition to detect multiple signatures (motor vibration and hovering patterns) of UAVs.

Probing thyroglobulin in undiluted human serum based on pattern recognition and competitive adsorption of proteins

NASA Astrophysics Data System (ADS)

Wang, Ran; Huang, Shuai; Li, Jing; Chae, Junseok

2014-10-01

Thyroglobulin (Tg) is a sensitive indicator of persistent or recurrent differentiated thyroid cancer of follicular cell origin. Detection of Tg in human serum is challenging as bio-receptors, such as anti-Tg, used in immunoassay have relatively weak binding affinity. We engineer sensing surfaces using the competitive adsorption of proteins, termed the Vroman Effect. Coupled with Surface Plasmon Resonance, the "cross-responsive" interactions of Tg on the engineered surfaces produce uniquely distinguishable multiple signature patterns, which are discriminated using Linear Discriminant Analysis. Tg-spiked samples, down to 2 ng/ml Tg in undiluted human serum, are sensitively and selectively discriminated from the control (undiluted human serum).