A Macroevolutionary Perspective on Multiple Sexual Traits in the Phasianidae (Galliformes)

PubMed Central

Kimball, Rebecca T.; Mary, Colette M. St.; Braun, Edward L.

2011-01-01

Traits involved in sexual signaling are ubiquitous among animals. Although a single trait appears sufficient to convey information, many sexually dimorphic species exhibit multiple sexual signals, which may be costly to signalers and receivers. Given that one signal may be enough, there are many microevolutionary hypotheses to explain the evolution of multiple signals. Here we extend these hypotheses to a macroevolutionary scale and compare those predictions to the patterns of gains and losses of sexual dimorphism in pheasants and partridges. Among nine dimorphic characters, including six intersexual signals and three indicators of competitive ability, all exhibited both gains and losses of dimorphism within the group. Although theories of intersexual selection emphasize gain and elaboration, those six characters exhibited greater rates of loss than gain; in contrast, the competitive traits showed a slight bias towards gains. The available models, when examined in a macroevolutionary framework, did not yield unique predictions, making it difficult to distinguish among them. Even with this limitation, when the predictions of these alternative models were compared with the heterogeneous patterns of evolution of dimorphism in phasianids, it is clear that many different selective processes have been involved in the evolution of sexual signals in this group. PMID:21716735

Automatic Seizure Detection Based on Morphological Features Using One-Dimensional Local Binary Pattern on Long-Term EEG.

PubMed

Shanir, P P Muhammed; Khan, Kashif Ahmad; Khan, Yusuf Uzzaman; Farooq, Omar; Adeli, Hojjat

2017-12-01

Epileptic neurological disorder of the brain is widely diagnosed using the electroencephalography (EEG) technique. EEG signals are nonstationary in nature and show abnormal neural activity during the ictal period. Seizures can be identified by analyzing and obtaining features of EEG signal that can detect these abnormal activities. The present work proposes a novel morphological feature extraction technique based on the local binary pattern (LBP) operator. LBP provides a unique decimal value to a sample point by weighing the binary outcomes after thresholding the neighboring samples with the present sample point. These LBP values assist in capturing the rising and falling edges of the EEG signal, thus providing a morphologically featured discriminating pattern for epilepsy detection. In the present work, the variability in the LBP values is measured by calculating the sum of absolute difference of the consecutive LBP values. Interquartile range is calculated over the preprocessed EEG signal to provide dispersion measure in the signal. For classification purpose, K-nearest neighbor classifier is used, and the performance is evaluated on 896.9 hours of data from CHB-MIT continuous EEG database. Mean accuracy of 99.7% and mean specificity of 99.8% is obtained with average false detection rate of 0.47/h and sensitivity of 99.2% for 136 seizures.

Improving the analytical performance and versatility of paper spray mass spectrometry via paper microfluidics.

PubMed

Murray, Ian; Walker, Glenn; Bereman, Michael S

2016-06-20

Two paper-based microfluidic techniques, photolithography and wax patterning, were investigated for their potential to improve upon the sensitivity, reproducibility, and versatility of paper spray mass spectrometry. The main limitation of photolithography was the significant signal (approximately three orders of magnitude) above background which was attributed to the chemicals used in the photoresist process. Hydrophobic barriers created via wax patterning were discovered to have approximately 2 orders of magnitude less background signal compared to analogous barriers created using photolithography. A minimum printed wax barrier thickness of approximately 0.3 mm was necessary to consistently retain commonly used paper spray solvents (1 : 1 water : acetonitrile/methanol) and avoid leakage. Constricting capillary flow via wax-printed channels yielded both a significant increase in signal and detection time for detection of model analytes. This signal increase, which was attributed to restricting the radial flow of analyte/solvent on paper (i.e., a concentrating effect), afforded a significant increase in sensitivity (p ≪ 0.05) for the detection of pesticides spiked into residential tap water using a five-point calibration curve. Finally, unique mixing designs using wax patterning can be envisioned to perform on-paper analyte derivatization.

A Joint Time-Frequency and Matrix Decomposition Feature Extraction Methodology for Pathological Voice Classification

NASA Astrophysics Data System (ADS)

Ghoraani, Behnaz; Krishnan, Sridhar

2009-12-01

The number of people affected by speech problems is increasing as the modern world places increasing demands on the human voice via mobile telephones, voice recognition software, and interpersonal verbal communications. In this paper, we propose a novel methodology for automatic pattern classification of pathological voices. The main contribution of this paper is extraction of meaningful and unique features using Adaptive time-frequency distribution (TFD) and nonnegative matrix factorization (NMF). We construct Adaptive TFD as an effective signal analysis domain to dynamically track the nonstationarity in the speech and utilize NMF as a matrix decomposition (MD) technique to quantify the constructed TFD. The proposed method extracts meaningful and unique features from the joint TFD of the speech, and automatically identifies and measures the abnormality of the signal. Depending on the abnormality measure of each signal, we classify the signal into normal or pathological. The proposed method is applied on the Massachusetts Eye and Ear Infirmary (MEEI) voice disorders database which consists of 161 pathological and 51 normal speakers, and an overall classification accuracy of 98.6% was achieved.

Physiological controls of large‐scale patterning in planarian regeneration: a molecular and computational perspective on growth and form

PubMed Central

Durant, Fallon; Lobo, Daniel; Hammelman, Jennifer

2016-01-01

Abstract Planaria are complex metazoans that repair damage to their bodies and cease remodeling when a correct anatomy has been achieved. This model system offers a unique opportunity to understand how large‐scale anatomical homeostasis emerges from the activities of individual cells. Much progress has been made on the molecular genetics of stem cell activity in planaria. However, recent data also indicate that the global pattern is regulated by physiological circuits composed of ionic and neurotransmitter signaling. Here, we overview the multi‐scale problem of understanding pattern regulation in planaria, with specific focus on bioelectric signaling via ion channels and gap junctions (electrical synapses), and computational efforts to extract explanatory models from functional and molecular data on regeneration. We present a perspective that interprets results in this fascinating field using concepts from dynamical systems theory and computational neuroscience. Serving as a tractable nexus between genetic, physiological, and computational approaches to pattern regulation, planarian pattern homeostasis harbors many deep insights for regenerative medicine, evolutionary biology, and engineering. PMID:27499881

Genomic expression patterns in medication overuse headaches

PubMed Central

Hershey, Andrew D; Burdine, Danny; Kabbouche, Marielle A; Powers, Scott W

2016-01-01

Background Chronic daily headache (CDH) and chronic migraine (CM) are one of the most frequent problems encountered in neurology, are often difficult to treat, and frequently complicated by medication-overuse headache (MOH). Proper recognition of MOH may alter treatment outcome and prevent long term disability. Objective This study identifies the unique genomic expression pattern MOH that respond to cessation of the overused medication. Methods Baseline occurrence of MOH and typical pattern of response to medication cessation were measured from a large database. Whole blood samples from patients with CM with or without MOH were obtained and their genomic profile was assessed. Affymetrix human U133 plus2 arrays were used to examine the genomic expression patterns prior to treatment and 6–12 weeks later. Headache characterisation and response to treatment based on headache frequency and disability were compared. Results Of 1311 patients reporting daily or continuous headaches, 513 (39.1%) reported overusing analgesic medication. At follow-up, 44.5% had a 50% or greater reduction in headache frequency, while 41.6% had no change. Blood genomic expression patterns were obtained on 33 patients with 19 (57.6%) overusing analgesic medication with a unique genomic expression pattern in MOH that responded to cessation of analgesics. Gene ontology of these samples indicated a significant number were involved with brain and immunological tissues, including multiple signalling pathways and apoptosis. Conclusions Blood genomic patterns can accurately identify MOH patients that respond to medication cessation. These results suggest that MOH involves a unique molecular biology pathway that can be identified with a specific biomarker. PMID:20974594

The MB2 gene family of Plasmodium species has a unique combination of S1 and GTP-binding domains

PubMed Central

Romero, Lisa C; Nguyen, Thanh V; Deville, Benoit; Ogunjumo, Oluwasanmi; James, Anthony A

2004-01-01

Background Identification and characterization of novel Plasmodium gene families is necessary for developing new anti-malarial therapeutics. The products of the Plasmodium falciparum gene, MB2, were shown previously to have a stage-specific pattern of subcellular localization and proteolytic processing. Results Genes homologous to MB2 were identified in five additional parasite species, P. knowlesi, P. gallinaceum, P. berghei, P. yoelii, and P. chabaudi. Sequence comparisons among the MB2 gene products reveal amino acid conservation of structural features, including putative S1 and GTP-binding domains, and putative signal peptides and nuclear localization signals. Conclusions The combination of domains is unique to this gene family and indicates that MB2 genes comprise a novel family and therefore may be a good target for drug development. PMID:15222903

Conservation and divergence of the cyclic adenosine monophosphate-protein kinase A (cAMP-PKA) pathway in two plant-pathogenic fungi: Fusarium graminearum and F. verticillioides.

PubMed

Guo, Li; Breakspear, Andrew; Zhao, Guoyi; Gao, Lixin; Kistler, H Corby; Xu, Jin-Rong; Ma, Li-Jun

2016-02-01

The cyclic adenosine monophosphate-protein kinase A (cAMP-PKA) pathway is a central signalling cascade that transmits extracellular stimuli and governs cell responses through the second messenger cAMP. The importance of cAMP signalling in fungal biology has been well documented and the key conserved components, adenylate cyclase (AC) and the catalytic subunit of PKA (CPKA), have been functionally characterized. However, other genes involved in this signalling pathway and their regulation are not well understood in filamentous fungi. Here, we performed a comparative transcriptomics analysis of AC and CPKA mutants in two closely related fungi: Fusarium graminearum (Fg) and F. verticillioides (Fv). Combining available Fg transcriptomics and phenomics data, we reconstructed the Fg cAMP signalling pathway. We developed a computational program that combines sequence conservation and patterns of orthologous gene expression to facilitate global transcriptomics comparisons between different organisms. We observed highly correlated expression patterns for most orthologues (80%) between Fg and Fv. We also identified a subset of 482 (6%) diverged orthologues, whose expression under all conditions was at least 50% higher in one genome than in the other. This enabled us to dissect the conserved and unique portions of the cAMP-PKA pathway. Although the conserved portions controlled essential functions, such as metabolism, the cell cycle, chromatin remodelling and the oxidative stress response, the diverged portions had species-specific roles, such as the production and detoxification of secondary metabolites unique to each species. The evolution of the cAMP-PKA signalling pathway seems to have contributed directly to fungal divergence and niche adaptation. © 2015 The Authors. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd.

Correction of Microplate Data from High-Throughput Screening.

PubMed

Wang, Yuhong; Huang, Ruili

2016-01-01

High-throughput screening (HTS) makes it possible to collect cellular response data from a large number of cell lines and small molecules in a timely and cost-effective manner. The errors and noises in the microplate-formatted data from HTS have unique characteristics, and they can be generally grouped into three categories: run-wise (temporal, multiple plates), plate-wise (background pattern, single plate), and well-wise (single well). In this chapter, we describe a systematic solution for identifying and correcting such errors and noises, mainly basing on pattern recognition and digital signal processing technologies.

An Exploration of WFC3/IR Dark Current Variation

NASA Astrophysics Data System (ADS)

Sunnquist, B.; Baggett, S.; Long, K. S.

2017-02-01

We use a collection of darks spanning September 2009 to June 2016 to study variations in the dark current in the IR detector on WFC3. Although the darks possess a similar signal pattern across the detector, we find that their median dark rates vary by as much as 0.014 DN/s (0.032 e-/s). The distribution of these median values has a triangular shape with a mean and standard deviation of 0.021 ± 0.0029 DN/s (0.049 ± 0.0069 e-/s). We observe a long term time-dependence in the inboard vertical reference pixel and zeroth read signals; however, these differences do not noticeably affect the calibrated dark signals, and we conclude that the WFC3/IR dark current levels continue to remain stable since launch. The inboard reference pixel signals exhibit a unique, but consistent, pattern around the detector, but this pattern does not evolve noticeably with the median of the science pixels, and a quadrant or row-based reference pixel subtraction strategy does not reduce the spread between the median dark rates. We notice a slight drift in the inboard reference pixel signals up the dark ramps, and the intensity of this drift is related to the median dark current in the science pixels. This holds true using either the horizontal or vertical reference pixels and for darks with a variety of sample sequences.

Triboelectrification-Enabled Self-Powered Data Storage.

PubMed

Kuang, Shuang Yang; Zhu, Guang; Wang, Zhong Lin

2018-02-01

Data storage by any means usually requires an electric driving power for writing or reading. A novel approach for self-powered, triboelectrification-enabled data storage (TEDS) is presented. Data are incorporated into a set of metal-based surface patterns. As a probe slides across the patterned surface, triboelectrification between the scanning probe and the patterns produces alternatively varying voltage signal in quasi-square wave. The trough and crest of the quasi-square wave signal are coded as binary bits of "0" and "1," respectively, while the time span of the trough and the crest is associated with the number of bits. The storage of letters and sentences is demonstrated through either square-shaped or disc-shaped surface patterns. Based on experimental data and numerical calculation, the theoretically predicted maximum data storage density could reach as high as 38.2 Gbit in -2 . Demonstration of real-time data retrieval is realized with the assistance of software interface. For the TEDS reported in this work, the measured voltage signal is self-generated as a result of triboelectrification without the reliance on an external power source. This feature brings about not only low power consumption but also a much more simplified structure. Therefore, this work paves a new path to a unique approach of high-density data storage that may have widespread applications.

The spatial patterning of mouse cone opsin expression is regulated by BMP signaling through downstream effector COUP-TF nuclear receptors

PubMed Central

Satoh, Shinya; Tang, Ke; Iida, Atsumi; Inoue, Mariko; Kodama, Tatsuhiko; Tsai, Sophia Y.; Tsai, Ming-Jer; Furuta, Yasuhide; Watanabe, Sumiko

2009-01-01

Cone photopigments, known as opsins, are pivotal elements and the first detection module employed in color vision. In mice, cone photoreceptors are distributed throughout the retina, and S- and M-opsins have unique expression patterns in the retina with a gradient along the dorsoventral axis; however, the mechanisms regulating the spatial patterning of cone opsin expression have not been well documented. The purpose of this study was to define the mechanisms regulating the spatial patterning of cone opsin expression. By analyzing knockouts for bone morphogenetic protein (BMP) signaling, we found an essential role for BMP in forming cone opsin expression patterns in the retina; however, BMP signaling is activated only transiently in the dorsal half of the retina during early retinal development. Thus, BMP is not likely to play a direct role in opsin gene expression, which starts at a later stage of retinal development. We identified the chicken ovalbumin upstream promoter-transcription factor (COUP-TF) nuclear receptor as a link between BMP and opsin expression. BMP signaling is essential for the correct dorsoventral spatial expression of COUP-TFI and -TFII. Through gain- and loss-of-function analyses, we found that both COUP-TFI and -TFII are required to suppress S-opsin expression in the dorsal retina but that only COUP-TFI plays an essential role in suppressing M-opsin expression in the ventral retina. Based on these findings, we propose a new molecular cascade involving BMP and COUP-TFs that conveys dorsoventral information to direct the expression of cone opsins during retinal development. PMID:19812316

Effects of line-of-sight velocity on spaced-antenna measurements, part 3.5A

NASA Technical Reports Server (NTRS)

Royrvik, O.

1984-01-01

Horizontal wind velocities in the upper atmosphere, particularly the mesosphere, have been measured using a multitude of different techniques. Most techniques are based on stated or unstated assumptions about the wind field that may or may not be true. Some problems with the spaced antenna drifts (SAD) technique that usually appear to be overlooked are investigated. These problems are not unique to the SAD technique; very similar considerations apply to measurement of horizontal wind using multiple-beam Doppler radars as well. Simply stated, the SAD technique relies on scattering from multiple scatterers within an antenna beam of fairly large beam width. The combination of signals with random phase gives rise to an interference pattern on the ground. This pattern will drift across the ground with a velocity twice that of the ionospheric irregularities from which the radar signals are scattered. By using spaced receivers and measuring time delays of the signal fading in different antennas, it is possible to estimate the horizontal drift velocities.

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).

Sall1-dependent signals affect Wnt signaling and ureter tip fate to initiate kidney development.

PubMed

Kiefer, Susan M; Robbins, Lynn; Stumpff, Kelly M; Lin, Congxing; Ma, Liang; Rauchman, Michael

2010-09-01

Development of the metanephric kidney depends on precise control of branching of the ureteric bud. Branching events represent terminal bifurcations that are thought to depend on unique patterns of gene expression in the tip compared with the stalk and are influenced by mesenchymal signals. The metanephric mesenchyme-derived signals that control gene expression at the ureteric bud tip are not well understood. In mouse Sall1 mutants, the ureteric bud grows out and invades the metanephric mesenchyme, but it fails to initiate branching despite tip-specific expression of Ret and Wnt11. The stalk-specific marker Wnt9b and the beta-catenin downstream target Axin2 are ectopically expressed in the mutant ureteric bud tips, suggesting that upregulated canonical Wnt signaling disrupts ureter branching in this mutant. In support of this hypothesis, ureter arrest is rescued by lowering beta-catenin levels in the Sall1 mutant and is phenocopied by ectopic expression of a stabilized beta-catenin in the ureteric bud. Furthermore, transgenic overexpression of Wnt9b in the ureteric bud causes reduced branching in multiple founder lines. These studies indicate that Sall1-dependent signals from the metanephric mesenchyme are required to modulate ureteric bud tip Wnt patterning in order to initiate branching.

Mechanisms of alveolar fibrosis after acute lung injury.

PubMed

Marinelli, W A; Henke, C A; Harmon, K R; Hertz, M I; Bitterman, P B

1990-12-01

In patients who die after severe acute lung injury, a dramatic fibroproliferative response occurs within the alveolar air space, interstitium, and microvessels. Profound shunt physiology, dead space ventilation, and pulmonary hypertension are the physiologic consequences of this fibroproliferative response. The anatomic pattern of the response is unique within each alveolar compartment. For example, the air space is obliterated by granulation tissue, with replicating mesenchymal cells, their connective tissue products, and an expanding network of intra-alveolar capillaries. In contrast, the vascular fibroproliferative response is dominated by mesenchymal cell replication and connective tissue deposition within the walls of microvessels. Despite the unique anatomic features of these fibroproliferative processes, the regulatory signals involved are likely to be similar. Although our current understanding of the signals regulating the fibroproliferative response to acute lung injury is limited, inferences can be made from in vitro studies of mesenchymal cell behavior and several better understood fibroproliferative processes, including wound healing and chronic fibrotic lung diseases. As clinicians, our future ability to enhance effective lung repair will likely utilize therapeutic strategies specifically targeted to the signals that regulate the fibroproliferative process within the alveolar microenvironment.

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.

[Bdellovibrio and like organisms: outstanding predators!

PubMed

Jurkevitch, Édouard; Jacquet, Stéphan

2017-05-01

Obligate predatory bacteria, i.e. bacteria requiring a Gram negative prey cell in order to complete their cell cycle, belong to the polyphyletic group referred to as the Bdellovibrio And Like Organisms (BALO). Predatory interactions between bacteria are complex, yet their dynamics and impact on bacterial communities in the environment are becoming better understood. BALO have unique life cycles: they grow epibiotically with the predator remaining attached to the prey's envelope, dividing in a binary manner or periplasmically, i.e. by penetrating the prey's periplasm to generate a number of progeny cells. The periplasmic life cycle includes unique gene and protein patterns and unique signaling features. These ecological and cellular features, along with applications of the BALO in the medical, agricultural and environmental fields are surveyed. © 2017 médecine/sciences – Inserm.

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish.

PubMed

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-08-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change - an important component of biological conservation and ecosystem management.

Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish

PubMed Central

Giery, Sean T; Layman, Craig A; Langerhans, R Brian

2015-01-01

When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change – an important component of biological conservation and ecosystem management. PMID:26240605

Heterodimerization of TLR2 with TLR1 or TLR6 expands the ligand spectrum but does not lead to differential signaling.

PubMed

Farhat, Katja; Riekenberg, Sabine; Heine, Holger; Debarry, Jennifer; Lang, Roland; Mages, Jörg; Buwitt-Beckmann, Ute; Röschmann, Kristina; Jung, Günther; Wiesmüller, Karl-Heinz; Ulmer, Artur J

2008-03-01

TLR are primary triggers of the innate immune system by recognizing various microorganisms through conserved pathogen-associated molecular patterns. TLR2 is the receptor for a functional recognition of bacterial lipopeptides (LP) and is up-regulated during various disorders such as chronic obstructive pulmonary disease and sepsis. This receptor is unique in its ability to form heteromers with TLR1 or TLR6 to mediate intracellular signaling. According to the fatty acid pattern as well as the assembling of the polypeptide tail, LP can signal through TLR2 in a TLR1- or TLR6-dependent manner. There are also di- and triacylated LP, which stimulate TLR1-deficient cells and TLR6-deficient cells. In this study, we investigated whether heterodimerization evolutionarily developed to broaden the ligand spectrum or to induce different immune responses. We analyzed the signal transduction pathways activated through the different TLR2 dimers using the three LP, palmitic acid (Pam)octanoic acid (Oct)(2)C-(VPGVG)(4)VPGKG, fibroblast-stimulating LP-1, and Pam(2)C-SK(4). Dominant-negative forms of signaling molecules, immunoblotting of MAPK, as well as microarray analysis indicate that all dimers use the same signaling cascade, leading to an identical pattern of gene activation. We conclude that heterodimerization of TLR2 with TLR1 or TLR6 evolutionarily developed to expand the ligand spectrum to enable the innate immune system to recognize the numerous, different structures of LP present in various pathogens. Thus, although mycoplasma and Gram-positive and Gram-negative bacteria may activate different TLR2 dimers, the development of different signal pathways in response to different LP does not seem to be of vital significance for the innate defense system.

Conserved and divergent expression patterns of markers of axial development in the laboratory opossum, Monodelphis domestica.

PubMed

Yoshida, Michio; Kajikawa, Eriko; Yamamoto, Daisuke; Kurokawa, Daisuke; Yonemura, Shigenobu; Kobayashi, Kensaku; Kiyonari, Hiroshi; Aizawa, Shinichi

2016-12-01

Previous comparative studies suggest that the requirement for Nodal in epiblast and hypoblast development is unique to mammalians. Expression of anterior visceral endoderm (AVE) genes in the visceral endoderm and of their orthologs in the hypoblast may be unique to mammalians and avians, and is absent in the reptilian hypoblast. Axis formation in reptiles is signaled by the formation of the posterior marginal epiblast (PME), which expresses a series of primitive streak genes. To assess the phylogenetic origin of Nodal and AVE gene expression and axis formation in amniotes, we examined marker gene expression in gray short-tailed opossum, a metatherian. Nodal was expressed in neither epiblast nor hypoblast of opossum embryos. No AVE genes were expressed in the opossum hypoblast. Attainment of polarity in the embryonic disk was signaled by Nodal, Wnt3a, Fgf8, and Bra expression in the PME at 8.5 days post-coitus. Nodal expression in epiblast or hypoblast may be unique to eutherians. AVE gene expression in visceral endoderm and hypoblast may have been independently acquired in eutherian and avian lineages. PME formation appears to be the event that signals axis formation in reptilian and metatherian embryos, and thus may be an ancestral characteristic of basal amniotes. Developmental Dynamics 245:1176-1188, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A neuronal model of a global workspace in effortful cognitive tasks.

PubMed

Dehaene, S; Kerszberg, M; Changeux, J P

1998-11-24

A minimal hypothesis is proposed concerning the brain processes underlying effortful tasks. It distinguishes two main computational spaces: a unique global workspace composed of distributed and heavily interconnected neurons with long-range axons, and a set of specialized and modular perceptual, motor, memory, evaluative, and attentional processors. Workspace neurons are mobilized in effortful tasks for which the specialized processors do not suffice. They selectively mobilize or suppress, through descending connections, the contribution of specific processor neurons. In the course of task performance, workspace neurons become spontaneously coactivated, forming discrete though variable spatio-temporal patterns subject to modulation by vigilance signals and to selection by reward signals. A computer simulation of the Stroop task shows workspace activation to increase during acquisition of a novel task, effortful execution, and after errors. We outline predictions for spatio-temporal activation patterns during brain imaging, particularly about the contribution of dorsolateral prefrontal cortex and anterior cingulate to the workspace.

Macroenvironmental regulation of hair cycling and collective regenerative behavior.

PubMed

Plikus, Maksim V; Chuong, Cheng-Ming

2014-01-01

The hair follicle (HF) regeneration paradigm provides a unique opportunity for studying the collective behavior of stem cells in living animals. Activation of HF stem cells depends on the core inhibitory BMP and activating WNT signals operating within the HF microenvironment. Additionally, HFs receive multilayered signaling inputs from the extrafollicular macroenvironment, which includes dermis, adipocytes, neighboring HFs, hormones, and external stimuli. These activators/inhibitors are integrated across multiple stem-cell niches to produce dynamic hair growth patterns. Because of their pigmentation, these patterns can be easily studied on live shaved animals. Comparing to autonomous regeneration of one HF, populations of HFs display coupled decision making, allowing for more robust and adaptable regenerative behavior to occur collectively. The generic cellular automata model used to simulate coordinated HF cycling here can be extended to study population-level behavior of other complex biological systems made of cycling elements.

Macroenvironmental Regulation of Hair Cycling and Collective Regenerative Behavior

PubMed Central

Plikus, Maksim V.; Chuong, Cheng-Ming

2014-01-01

The hair follicle (HF) regeneration paradigm provides a unique opportunity for studying the collective behavior of stem cells in living animals. Activation of HF stem cells depends on the core inhibitory BMP and activating WNT signals operating within the HF microenvironment. Additionally, HFs receive multilayered signaling inputs from the extrafollicular macroenvironment, which includes dermis, adipocytes, neighboring HFs, hormones, and external stimuli. These activators/inhibitors are integrated across multiple stem-cell niches to produce dynamic hair growth patterns. Because of their pigmentation, these patterns can be easily studied on live shaved animals. Comparing to autonomous regeneration of one HF, populations of HFs display coupled decision making, allowing for more robust and adaptable regenerative behavior to occur collectively. The generic cellular automata model used to simulate coordinated HF cycling here can be extended to study population-level behavior of other complex biological systems made of cycling elements. PMID:24384813

Vibration Sensor Monitoring of Nickel-Titanium Alloy Turning for Machinability Evaluation.

PubMed

Segreto, Tiziana; Caggiano, Alessandra; Karam, Sara; Teti, Roberto

2017-12-12

Nickel-Titanium (Ni-Ti) alloys are very difficult-to-machine materials causing notable manufacturing problems due to their unique mechanical properties, including superelasticity, high ductility, and severe strain-hardening. In this framework, the aim of this paper is to assess the machinability of Ni-Ti alloys with reference to turning processes in order to realize a reliable and robust in-process identification of machinability conditions. An on-line sensor monitoring procedure based on the acquisition of vibration signals was implemented during the experimental turning tests. The detected vibration sensorial data were processed through an advanced signal processing method in time-frequency domain based on wavelet packet transform (WPT). The extracted sensorial features were used to construct WPT pattern feature vectors to send as input to suitably configured neural networks (NNs) for cognitive pattern recognition in order to evaluate the correlation between input sensorial information and output machinability conditions.

A watermarking algorithm for polysomnography data.

PubMed

Jamasebi, R; Johnson, N L; Kaffashi, F; Redline, S; Loparo, K A

2008-01-01

A blind watermarking algorithm for polysomnography (PSG) data in European Data Format (EDF) has been developed for the identification and attribution of shared data. This is accomplished by hiding a unique identifier in the phase spectrum of each PSG epoch using an undisclosed key so that a third party cannot retrieve the watermark without knowledge of the key. A pattern discovery algorithm is developed to find the watermark pattern even though the data may have been altered. The method is evaluated using 25 PSG studies from the Sleep Heart Health Study database. The integrity of the signal data was determined using time series measures of both the original and watermarked signals, and by determining its effect on scoring sleep stages from the PSG data. The results of the analysis indicate that the proposed watermarking method for PSG data is an effective and efficient way to identify shared data without compromising its intended use.

Vibration Sensor Monitoring of Nickel-Titanium Alloy Turning for Machinability Evaluation

PubMed Central

Segreto, Tiziana; Karam, Sara; Teti, Roberto

2017-01-01

Nickel-Titanium (Ni-Ti) alloys are very difficult-to-machine materials causing notable manufacturing problems due to their unique mechanical properties, including superelasticity, high ductility, and severe strain-hardening. In this framework, the aim of this paper is to assess the machinability of Ni-Ti alloys with reference to turning processes in order to realize a reliable and robust in-process identification of machinability conditions. An on-line sensor monitoring procedure based on the acquisition of vibration signals was implemented during the experimental turning tests. The detected vibration sensorial data were processed through an advanced signal processing method in time-frequency domain based on wavelet packet transform (WPT). The extracted sensorial features were used to construct WPT pattern feature vectors to send as input to suitably configured neural networks (NNs) for cognitive pattern recognition in order to evaluate the correlation between input sensorial information and output machinability conditions. PMID:29231864

Wideband Single-Crystal Transducer for Bone Characterization

NASA Technical Reports Server (NTRS)

Liang, Yu; Snook, Kevin

2012-01-01

The microgravity conditions of space travel result in unique physiological demands on the human body. In particular, the absence of the continual mechanical stresses on the skeletal system that are present on Earth cause the bones to decalcify. Trabecular structure decreases in thickness and increases in spacing, resulting in decreased bone strength and increased risk of injury. Thus, monitoring bone health is a high priority for long-term space travel. A single probe covering all frequency bands of interest would be ideal for such measurements, and this would also minimize storage space and eliminate the complexity of integrating multiple probes. This invention is an ultrasound transducer for the structural characterization of bone. Such characterization measures features of reflected and transmitted ultrasound signals, and correlates these signals with bone structure metrics such as bone mineral density, trabecular spacing, and thickness, etc. The techniques used to determine these various metrics require measurements over a broad range of ultrasound frequencies, and therefore, complete characterization requires the use of several narrowband transducers. This is a single transducer capable of making these measurements in all the required frequency bands. The device achieves this capability through a unique combination of a broadband piezoelectric material; a design incorporating multiple resonator sizes with distinct, overlapping frequency spectra; and a micromachining process for producing the multiple-resonator pattern with common electrode surfaces between the resonators. This device consists of a pattern of resonator bars with common electrodes that is wrapped around a central mandrel such that the radiating faces of the resonators are coplanar and can be simultaneously applied to the sample to be measured. The device operates as both a source and receiver of acoustic energy. It is operated by connection to an electronic system capable of both providing an excitation signal to the transducer and amplifying the signal received from the transducer. The excitation signal may be either a wide-bandwidth signal to excite the transducer across its entire operational spectrum, or a narrow-bandwidth signal optimized for a particular measurement technique. The transducer face is applied to the skin covering the bone to be characterized, and may be operated in through transmission mode using two transducers, or in pulse-echo mode.

Mating regulates neuromodulator ensembles at nerve termini innervating the Drosophila reproductive tract.

PubMed

Heifetz, Yael; Lindner, Moshe; Garini, Yuval; Wolfner, Mariana F

2014-03-31

Upon mating, regions of the female reproductive tract mature and alter their function [1-3], for example to facilitate storage of sperm or control the release of eggs [4-6]. The female's nervous system and neuromodulators play important roles in her responses to mating [7-13]. However, it is difficult to reconcile the reproductive tract's many changing but coordinated events with the small set of neuromodulators present [14-18]. We hypothesized that each part of the reproductive tract contains a characteristic combination of neuromodulators that confer unique identities on each region and that postmating changes in these combinations coordinate subsequent actions. We examined the presence, locations, and levels of neuromodulators and related molecules ("signaling molecules") in the reproductive tract of Drosophila melanogaster females before and after mating: the biogenic amine octopamine, which regulates ovulation rate in Drosophila and locusts [7, 14-20]; serotonin, which regulates muscle contraction in locust oviducts [21]; and the FMRF amide dromyosuppressin, which regulates contraction of Drosophila heart muscle [22] and may regulate muscle contractions in the reproductive tract, if it is expressed there. We find that separate aspects of mating (sperm, seminal proteins, and physical effects) independently modulate the release of signaling molecules. Each reproductive tract subregion displays a characteristic combination of signaling molecule release, resulting in a unique functional identity. These patterns, and thus functions, change reproducibly after mating. Thus, one event (mating) promotes new combinations of signaling molecules that endow different parts of the reproductive tract with unique temporal and spatial identities that facilitate many aspects of fertilization. Copyright © 2014 Elsevier Ltd. All rights reserved.

Rhesus macaques recognize unique multi-modal face-voice relations of familiar individuals and not of unfamiliar ones

PubMed Central

Habbershon, Holly M.; Ahmed, Sarah Z.; Cohen, Yale E.

2013-01-01

Communication signals in non-human primates are inherently multi-modal. However, for laboratory-housed monkeys, there is relatively little evidence in support of the use of multi-modal communication signals in individual recognition. Here, we used a preferential-looking paradigm to test whether laboratory-housed rhesus could “spontaneously” (i.e., in the absence of operant training) use multi-modal communication stimuli to discriminate between known conspecifics. The multi-modal stimulus was a silent movie of two monkeys vocalizing and an audio file of the vocalization from one of the monkeys in the movie. We found that the gaze patterns of those monkeys that knew the individuals in the movie were reliably biased toward the individual that did not produce the vocalization. In contrast, there was not a systematic gaze pattern for those monkeys that did not know the individuals in the movie. These data are consistent with the hypothesis that laboratory-housed rhesus can recognize and distinguish between conspecifics based on auditory and visual communication signals. PMID:23774779

SAR Ambiguity Study for the Cassini Radar

NASA Technical Reports Server (NTRS)

Hensley, Scott; Im, Eastwood; Johnson, William T. K.

1993-01-01

The Cassini Radar's synthetic aperture radar (SAR) ambiguity analysis is unique with respect to other spaceborne SAR ambiguity analyses owing to the non-orbiting spacecraft trajectory, asymmetric antenna pattern, and burst mode of data collection. By properly varying the pointing, burst mode timing, and radar parameters along the trajectory this study shows that the signal-to-ambiguity ratio of better than 15 dB can be achieved for all images obtained by the Cassini Radar.

Constellation of phase singularities in a speckle-like pattern for optical vortex metrology applied to biological kinematic analysis.

PubMed

Wang, Wei; Qiao, Yu; Ishijima, Reika; Yokozeki, Tomoaki; Honda, Daigo; Matsuda, Akihiro; Hanson, Steen G; Takeda, Mitsuo

2008-09-01

A novel technique for biological kinematic analysis is proposed that makes use of the pseudophase singularities in a complex signal generated from a speckle-like pattern. In addition to the information about the locations and the anisotropic core structures of the pseudophase singularities, we also detect the spatial structures of a cluster of phase singularities, which serves as a unique constellation characterizing the mutual position relation between the individual pseudophase singularities. Experimental results of in vivo measurements for a swimming fish along with its kinematic analysis are presented, which demonstrate the validity of the proposed technique.

The "Wow! signal" of the terrestrial genetic code

NASA Astrophysics Data System (ADS)

shCherbak, Vladimir I.; Makukov, Maxim A.

2013-05-01

It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like "signal" in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10-13). The patterns are profound to the extent that the code mapping itself is uniquely deduced from their algebraic representation. The signal displays readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to any natural origin. Plausible ways of embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely efficiently to pass non-biological information.

Pattern recognition applied to seismic signals of Llaima volcano (Chile): An evaluation of station-dependent classifiers

NASA Astrophysics Data System (ADS)

Curilem, Millaray; Huenupan, Fernando; Beltrán, Daniel; San Martin, Cesar; Fuentealba, Gustavo; Franco, Luis; Cardona, Carlos; Acuña, Gonzalo; Chacón, Max; Khan, M. Salman; Becerra Yoma, Nestor

2016-04-01

Automatic pattern recognition applied to seismic signals from volcanoes may assist seismic monitoring by reducing the workload of analysts, allowing them to focus on more challenging activities, such as producing reports, implementing models, and understanding volcanic behaviour. In a previous work, we proposed a structure for automatic classification of seismic events in Llaima volcano, one of the most active volcanoes in the Southern Andes, located in the Araucanía Region of Chile. A database of events taken from three monitoring stations on the volcano was used to create a classification structure, independent of which station provided the signal. The database included three types of volcanic events: tremor, long period, and volcano-tectonic and a contrast group which contains other types of seismic signals. In the present work, we maintain the same classification scheme, but we consider separately the stations information in order to assess whether the complementary information provided by different stations improves the performance of the classifier in recognising seismic patterns. This paper proposes two strategies for combining the information from the stations: i) combining the features extracted from the signals from each station and ii) combining the classifiers of each station. In the first case, the features extracted from the signals from each station are combined forming the input for a single classification structure. In the second, a decision stage combines the results of the classifiers for each station to give a unique output. The results confirm that the station-dependent strategies that combine the features and the classifiers from several stations improves the classification performance, and that the combination of the features provides the best performance. The results show an average improvement of 9% in the classification accuracy when compared with the station-independent method.

Rotary pin-in-maze discriminator

DOEpatents

Benavides, Gilbert L.

1997-01-01

A discriminator apparatus and method that discriminates between a unique signal and any other (incorrect) signal. The unique signal is a sequence of events; each event can assume one of two possible event states. Given the unique signal, a maze wheel is allowed to rotate fully in one direction. Given an incorrect signal, both the maze wheel and a pin wheel lock in position.

PubMed

Gueguen, Marie; Vallin, Benjamin; Glorian, Martine; Blaise, Régis; Limon, Isabelle

2016-01-01

In response to various types of vascular stress, the smooth muscle cells of the vessel wall (VSMCs) change phenotype and acquire the capacity to react to abnormal signals. This phenomenon favors the involvement of these cells in the development of major vascular diseases, such as atherosclerosis, and some complications of angioplasty, such as restenosis. The cyclic adenosine monophosphate (cAMP) pathway plays a key role in the integration of stimuli from the immediate environment and in the development of cellular responses. The temporal and spatial subcellular compartmentalization of cAMP ensures that the signals transmitted are specific. This compartmentalization is dependent on the diversity of (1) proteins directly or indirectly regulating the synthesis, degradation or release of cAMP; (2) intracellular effectors of cAMP; (3) isoforms of all these proteins with unique biochemical properties and unique patterns of regulation and (4) the scaffolding proteins on which the macromolecular complexes are built. This review illustrates the ways in which changes in the profile of adenylyl cyclases (ACs) may play critical roles in signal integration, the response of muscle cells and pathological vascular remodeling. It also illustrates the relevance of the renewed consideration of ACs as potentially interesting treatment targets. © Société de Biologie, 2016.

Peptide vaccine immunotherapy biomarkers and response patterns in pediatric gliomas

PubMed Central

Müller, Sören; Agnihotri, Sameer; Shoger, Karsen E.; Myers, Max I.; Chaparala, Srilakshmi; Villanueva, Clarence R.; Chattopadhyay, Ansuman; Butterfield, Lisa H.; Okada, Hideho; Pollack, Ian F.

2018-01-01

Low-grade gliomas (LGGs) are the most common brain tumor affecting children. We recently reported an early phase clinical trial of a peptide-based vaccine, which elicited consistent antigen-specific T cell responses in pediatric LGG patients. Additionally, we observed radiologic responses of stable disease (SD), partial response (PR), and near-complete/complete response (CR) following therapy. To identify biomarkers of clinical response in peripheral blood, we performed RNA sequencing on PBMC samples collected at multiple time points. Patients who showed CR demonstrated elevated levels of T cell activation markers, accompanied by a cytotoxic T cell response shortly after treatment initiation. At week 34, patients with CR demonstrated both IFN signaling and Poly-IC:LC adjuvant response patterns. Patients with PR demonstrated a unique, late monocyte response signature. Interestingly, HLA-V expression, before or during therapy, and an early monocytic hematopoietic response were strongly associated with SD. Finally, low IDO1 and PD-L1 expression before treatment and early elevated levels of T cell activation markers were associated with prolonged progression-free survival. Overall, our data support the presence of unique peripheral immune patterns in LGG patients associated with different radiographic responses to our peptide vaccine immunotherapy. Future clinical trials, including our ongoing phase II LGG vaccine immunotherapy, should monitor these response patterns. PMID:29618666

Rotary pin-in-maze discriminator

DOEpatents

Benavides, G.L.

1997-05-06

A discriminator apparatus and method that discriminates between a unique signal and any other (incorrect) signal are disclosed. The unique signal is a sequence of events; each event can assume one of two possible event states. Given the unique signal, a maze wheel is allowed to rotate fully in one direction. Given an incorrect signal, both the maze wheel and a pin wheel lock in position. 4 figs.

Notch Signaling in Vascular Smooth Muscle Cells

PubMed Central

Baeten, J.T.; Lilly, B.

2018-01-01

The Notch signaling pathway is a highly conserved pathway involved in cell fate determination in embryonic development and also functions in the regulation of physiological processes in several systems. It plays an especially important role in vascular development and physiology by influencing angiogenesis, vessel patterning, arterial/venous specification, and vascular smooth muscle biology. Aberrant or dysregulated Notch signaling is the cause of or a contributing factor to many vascular disorders, including inherited vascular diseases, such as cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, associated with degeneration of the smooth muscle layer in cerebral arteries. Like most signaling pathways, the Notch signaling axis is influenced by complex interactions with mediators of other signaling pathways. This complexity is also compounded by different members of the Notch family having both overlapping and unique functions. Thus, it is vital to fully understand the roles and interactions of each Notch family member in order to effectively and specifically target their exact contributions to vascular disease. In this chapter, we will review the Notch signaling pathway in vascular smooth muscle cells as it relates to vascular development and human disease. PMID:28212801

Smad2 and Smad3 have differential sensitivity in relaying TGFβ signaling and inversely regulate early lineage specification

PubMed Central

Liu, Ling; Liu, Xu; Ren, Xudong; Tian, Yue; Chen, Zhenyu; Xu, Xiangjie; Du, Yanhua; Jiang, Cizhong; Fang, Yujiang; Liu, Zhongliang; Fan, Beibei; Zhang, Quanbin; Jin, Guohua; Yang, Xiao; Zhang, Xiaoqing

2016-01-01

The transforming growth factor beta (TGFβ) related signaling is one of the most important signaling pathways regulating early developmental events. Smad2 and Smad3 are structurally similar and it is mostly considered that they are equally important in mediating TGFβ signals. Here, we show that Smad3 is an insensitive TGFβ transducer as compared with Smad2. Smad3 preferentially localizes within the nucleus and is thus sequestered from membrane signaling. The ability of Smad3 in oligomerization with Smad4 upon agonist stimulation is also impaired given its unique linker region. Smad2 mediated TGFβ signaling plays a crucial role in epiblast development and patterning of three germ layers. However, signaling unrelated nuclear localized Smad3 is dispensable for TGFβ signaling-mediated epiblast specification, but important for early neural development, an event blocked by TGFβ/Smad2 signaling. Both Smad2 and Smad3 bind to the conserved Smads binding element (SBE), but they show nonoverlapped target gene binding specificity and differential transcriptional activity. We conclude that Smad2 and Smad3 possess differential sensitivities in relaying TGFβ signaling and have distinct roles in regulating early developmental events. PMID:26905010

Smad2 and Smad3 have differential sensitivity in relaying TGFβ signaling and inversely regulate early lineage specification.

PubMed

Liu, Ling; Liu, Xu; Ren, Xudong; Tian, Yue; Chen, Zhenyu; Xu, Xiangjie; Du, Yanhua; Jiang, Cizhong; Fang, Yujiang; Liu, Zhongliang; Fan, Beibei; Zhang, Quanbin; Jin, Guohua; Yang, Xiao; Zhang, Xiaoqing

2016-02-24

The transforming growth factor beta (TGFβ) related signaling is one of the most important signaling pathways regulating early developmental events. Smad2 and Smad3 are structurally similar and it is mostly considered that they are equally important in mediating TGFβ signals. Here, we show that Smad3 is an insensitive TGFβ transducer as compared with Smad2. Smad3 preferentially localizes within the nucleus and is thus sequestered from membrane signaling. The ability of Smad3 in oligomerization with Smad4 upon agonist stimulation is also impaired given its unique linker region. Smad2 mediated TGFβ signaling plays a crucial role in epiblast development and patterning of three germ layers. However, signaling unrelated nuclear localized Smad3 is dispensable for TGFβ signaling-mediated epiblast specification, but important for early neural development, an event blocked by TGFβ/Smad2 signaling. Both Smad2 and Smad3 bind to the conserved Smads binding element (SBE), but they show nonoverlapped target gene binding specificity and differential transcriptional activity. We conclude that Smad2 and Smad3 possess differential sensitivities in relaying TGFβ signaling and have distinct roles in regulating early developmental events.

Architecture of a minimal signaling pathway explains the T-cell response to a 1 million-fold variation in antigen affinity and dose

PubMed Central

Lever, Melissa; Lim, Hong-Sheng; Kruger, Philipp; Nguyen, John; Trendel, Nicola; Abu-Shah, Enas; Maini, Philip Kumar; van der Merwe, Philip Anton

2016-01-01

T cells must respond differently to antigens of varying affinity presented at different doses. Previous attempts to map peptide MHC (pMHC) affinity onto T-cell responses have produced inconsistent patterns of responses, preventing formulations of canonical models of T-cell signaling. Here, a systematic analysis of T-cell responses to 1 million-fold variations in both pMHC affinity and dose produced bell-shaped dose–response curves and different optimal pMHC affinities at different pMHC doses. Using sequential model rejection/identification algorithms, we identified a unique, minimal model of cellular signaling incorporating kinetic proofreading with limited signaling coupled to an incoherent feed-forward loop (KPL-IFF) that reproduces these observations. We show that the KPL-IFF model correctly predicts the T-cell response to antigen copresentation. Our work offers a general approach for studying cellular signaling that does not require full details of biochemical pathways. PMID:27702900

Architecture of a minimal signaling pathway explains the T-cell response to a 1 million-fold variation in antigen affinity and dose.

PubMed

Lever, Melissa; Lim, Hong-Sheng; Kruger, Philipp; Nguyen, John; Trendel, Nicola; Abu-Shah, Enas; Maini, Philip Kumar; van der Merwe, Philip Anton; Dushek, Omer

2016-10-25

T cells must respond differently to antigens of varying affinity presented at different doses. Previous attempts to map peptide MHC (pMHC) affinity onto T-cell responses have produced inconsistent patterns of responses, preventing formulations of canonical models of T-cell signaling. Here, a systematic analysis of T-cell responses to 1 million-fold variations in both pMHC affinity and dose produced bell-shaped dose-response curves and different optimal pMHC affinities at different pMHC doses. Using sequential model rejection/identification algorithms, we identified a unique, minimal model of cellular signaling incorporating kinetic proofreading with limited signaling coupled to an incoherent feed-forward loop (KPL-IFF) that reproduces these observations. We show that the KPL-IFF model correctly predicts the T-cell response to antigen copresentation. Our work offers a general approach for studying cellular signaling that does not require full details of biochemical pathways.

Task-specific Aspects of Goal-directed Word Generation Identified via Simultaneous EEG-fMRI.

PubMed

Shapira-Lichter, Irit; Klovatch, Ilana; Nathan, Dana; Oren, Noga; Hendler, Talma

2016-09-01

Generating words according to a given rule relies on retrieval-related search and postretrieval control processes. Using fMRI, we recently characterized neural patterns of word generation in response to episodic, semantic, and phonemic cues by comparing free recall of wordlists, category fluency, and letter fluency [Shapira-Lichter, I., Oren, N., Jacob, Y., Gruberger, M., & Hendler, T. Portraying the unique contribution of the default mode network to internally driven mnemonic processes. Proceedings of the National Academy of Sciences, U.S.A., 110, 4950-4955, 2013]. Distinct selectivity for each condition was evident, representing discrete aspects of word generation-related memory retrieval. For example, the precuneus, implicated in processing spatiotemporal information, emerged as a key contributor to the episodic condition, which uniquely requires this information. Gamma band is known to play a central role in memory, and increased gamma power has been observed before word generation. Yet, gamma modulation in response to task demands has not been investigated. To capture the task-specific modulation of gamma power, we analyzed the EEG data recorded simultaneously with the aforementioned fMRI, focusing on the activity locked to and immediately preceding word articulation. Transient increases in gamma power were identified in a parietal electrode immediately before episodic and semantic word generation, however, within a different time frame relative to articulation. Gamma increases were followed by an alpha-theta decrease in the episodic condition, a gamma decrease in the semantic condition. This pattern indicates a task-specific modulation of the gamma signal corresponding to the specific demands of each word generation task. The gamma power and fMRI signal from the precuneus were correlated during the episodic condition, implying the existence of a common cognitive construct uniquely required for this task, possibly the reactivation or processing of spatiotemporal information.

Establishment of neurovascular congruency in the mouse whisker system by an independent patterning mechanism.

PubMed

Oh, Won-Jong; Gu, Chenghua

2013-10-16

Nerves and vessels often run parallel to one another, a phenomenon that reflects their functional interdependency. Previous studies have suggested that neurovascular congruency in planar tissues such as skin is established through a "one-patterns-the-other" model, in which either the nervous system or the vascular system precedes developmentally and then instructs the other system to form using its established architecture as a template. Here, we find that, in tissues with complex three-dimensional structures such as the mouse whisker system, neurovascular congruency does not follow the previous model but rather is established via a mechanism in which nerves and vessels are patterned independently. Given the diversity of neurovascular structures in different tissues, guidance signals emanating from a central organizer in the specific target tissue may act as an important mechanism to establish neurovascular congruency patterns that facilitate unique target tissue function. Copyright © 2013 Elsevier Inc. All rights reserved.

Screen-printed nanoparticles as anti-counterfeiting tags

NASA Astrophysics Data System (ADS)

Campos-Cuerva, Carlos; Zieba, Maciej; Sebastian, Victor; Martínez, Gema; Sese, Javier; Irusta, Silvia; Contamina, Vicente; Arruebo, Manuel; Santamaria, Jesus

2016-03-01

Metallic nanoparticles with different physical properties have been screen printed as authentication tags on different types of paper. Gold and silver nanoparticles show unique optical signatures, including sharp emission bandwidths and long lifetimes of the printed label, even under accelerated weathering conditions. Magnetic nanoparticles show distinct physical signals that depend on the size of the nanoparticle itself. They were also screen printed on different substrates and their magnetic signals read out using a magnetic pattern recognition sensor and a vibrating sample magnetometer. The novelty of our work lies in the demonstration that the combination of nanomaterials with optical and magnetic properties on the same printed support is possible, and the resulting combined signals can be used to obtain a user-configurable label, providing a high degree of security in anti-counterfeiting applications using simple commercially-available sensors.

Screen-printed nanoparticles as anti-counterfeiting tags.

PubMed

Campos-Cuerva, Carlos; Zieba, Maciej; Sebastian, Victor; Martínez, Gema; Sese, Javier; Irusta, Silvia; Contamina, Vicente; Arruebo, Manuel; Santamaria, Jesus

2016-03-04

Metallic nanoparticles with different physical properties have been screen printed as authentication tags on different types of paper. Gold and silver nanoparticles show unique optical signatures, including sharp emission bandwidths and long lifetimes of the printed label, even under accelerated weathering conditions. Magnetic nanoparticles show distinct physical signals that depend on the size of the nanoparticle itself. They were also screen printed on different substrates and their magnetic signals read out using a magnetic pattern recognition sensor and a vibrating sample magnetometer. The novelty of our work lies in the demonstration that the combination of nanomaterials with optical and magnetic properties on the same printed support is possible, and the resulting combined signals can be used to obtain a user-configurable label, providing a high degree of security in anti-counterfeiting applications using simple commercially-available sensors.

Analysis of the expression and function of Wnt-5a and Wnt-5b in developing and regenerating axolotl (Ambystoma mexicanum) limbs.

PubMed

Ghosh, Sukla; Roy, Stéphane; Séguin, Carl; Bryant, Susan V; Gardiner, David M

2008-05-01

Urodele amphibians are unique adult vertebrates because they are able to regenerate body parts after amputation. Studies of urodele limb regeneration, the key model system for vertebrate regeneration, have led to an understanding of the origin of blastema cells and the importance of positional interactions between blastema cells in the control of growth and pattern formation. Progress is now being made in the identification of the signaling pathways that regulate dedifferentiation, blastema morphogenesis, growth and pattern formation. Members of the Wnt family of secreted proteins are expressed in developing and regenerating limbs, and have the potential to control growth, pattern formation and differentiation. We have studied the expression of two non-canonical Wnt genes, Wnt-5a and Wnt-5b. We report that they are expressed in equivalent patterns during limb development and limb regeneration in the axolotl (Ambystoma mexicanum), and during limb development in other tetrapods, implying conservation of function. Our analysis of the effects of ectopic Wnt-5a expression is consistent with the hypothesis that canonical Wnt signaling functions during the early stages of regeneration to control the dedifferentiation of stump cells giving rise to the regeneration-competent cells of the blastema.

The heparanome--the enigma of encoding and decoding heparan sulfate sulfation.

PubMed

Lamanna, William C; Kalus, Ina; Padva, Michael; Baldwin, Rebecca J; Merry, Catherine L R; Dierks, Thomas

2007-04-30

Heparan sulfate (HS) is a cell surface carbohydrate polymer modified with sulfate moieties whose highly ordered composition is central to directing specific cell signaling events. The ability of the cell to generate these information rich glycans with such specificity has opened up a new field of "heparanomics" which seeks to understand the systems involved in generating these cell type and developmental stage specific HS sulfation patterns. Unlike other instances where biological information is encrypted as linear sequences in molecules such as DNA, HS sulfation patterns are generated through a non-template driven process. Thus, deciphering the sulfation code and the dynamic nature of its generation has posed a new challenge to system biologists. The recent discovery of two sulfatases, Sulf1 and Sulf2, with the unique ability to edit sulfation patterns at the cell surface, has opened up a new dimension as to how we understand the regulation of HS sulfation patterning and pattern-dependent cell signaling events. This review will focus on the functional relationship between HS sulfation patterning and biological processes. Special attention will be given to Sulf1 and Sulf2 and how these key editing enzymes might act in concert with the HS biosynthetic enzymes to generate and regulate specific HS sulfation patterns in vivo. We will further explore the use of knock out mice as biological models for understanding the dynamic systems involved in generating HS sulfation patterns and their biological relevance. A brief overview of new technologies and innovations summarizes advances in the systems biology field for understanding non-template molecular networks and their influence on the "heparanome".

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

Eventogram: A Visual Representation of Main Events in Biomedical Signals.

PubMed

Elgendi, Mohamed

2016-09-22

Biomedical signals carry valuable physiological information and many researchers have difficulty interpreting and analyzing long-term, one-dimensional, quasi-periodic biomedical signals. Traditionally, biomedical signals are analyzed and visualized using periodogram, spectrogram, and wavelet methods. However, these methods do not offer an informative visualization of main events within the processed signal. This paper attempts to provide an event-related framework to overcome the drawbacks of the traditional visualization methods and describe the main events within the biomedical signal in terms of duration and morphology. Electrocardiogram and photoplethysmogram signals are used in the analysis to demonstrate the differences between the traditional visualization methods, and their performance is compared against the proposed method, referred to as the " eventogram " in this paper. The proposed method is based on two event-related moving averages that visualizes the main time-domain events in the processed biomedical signals. The traditional visualization methods were unable to find dominant events in processed signals while the eventogram was able to visualize dominant events in signals in terms of duration and morphology. Moreover, eventogram -based detection algorithms succeeded with detecting main events in different biomedical signals with a sensitivity and positive predictivity >95%. The output of the eventogram captured unique patterns and signatures of physiological events, which could be used to visualize and identify abnormal waveforms in any quasi-periodic signal.

Functional localization of the human color center by decreased water displacement using diffusion-weighted fMRI.

PubMed

Williams, Rebecca J; Reutens, David C; Hocking, Julia

2015-11-01

Decreased water displacement following increased neural activity has been observed using diffusion-weighted functional MRI (DfMRI) at high b-values. The physiological mechanisms underlying the diffusion signal change may be unique from the standard blood oxygenation level-dependent (BOLD) contrast and closer to the source of neural activity. Whether DfMRI reflects neural activity more directly than BOLD outside the primary cerebral regions remains unclear. Colored and achromatic Mondrian visual stimuli were statistically contrasted to functionally localize the human color center Area V4 in neurologically intact adults. Spatial and temporal properties of DfMRI and BOLD activation were examined across regions of the visual cortex. At the individual level, DfMRI activation patterns showed greater spatial specificity to V4 than BOLD. The BOLD activation patterns were more prominent in the primary visual cortex than DfMRI, where activation was localized to the ventral temporal lobe. Temporally, the diffusion signal change in V4 and V1 both preceded the corresponding hemodynamic response, however the early diffusion signal change was more evident in V1. DfMRI may be of use in imaging applications implementing cognitive subtraction paradigms, and where highly precise individual functional localization is required.

Fourier-Based Diffraction Analysis of Live Caenorhabditis elegans.

PubMed

Magnes, Jenny; Hastings, Harold M; Raley-Susman, Kathleen M; Alivisatos, Clara; Warner, Adam; Hulsey-Vincent, Miranda

2017-09-13

This manuscript describes how to classify nematodes using temporal far-field diffraction signatures. A single C. elegans is suspended in a water column inside an optical cuvette. A 632 nm continuous wave HeNe laser is directed through the cuvette using front surface mirrors. A significant distance of at least 20-30 cm traveled after the light passes through the cuvette ensures a useful far-field (Fraunhofer) diffraction pattern. The diffraction pattern changes in real time as the nematode swims within the laser beam. The photodiode is placed off-center in the diffraction pattern. The voltage signal from the photodiode is observed in real time and recorded using a digital oscilloscope. This process is repeated for 139 wild type and 108 "roller" C. elegans. Wild type worms exhibit a rapid oscillation pattern in solution. The "roller" worms have a mutation in a key component of the cuticle that interferes with smooth locomotion. Time intervals that are not free of saturation and inactivity are discarded. It is practical to divide each average by its maximum to compare relative intensities. The signal for each worm is Fourier transformed so that the frequency pattern for each worm emerges. The signal for each type of worm is averaged. The averaged Fourier spectra for the wild type and the "roller" C. elegans are distinctly different and reveal that the dynamic worm shapes of the two different worm strains can be distinguished using Fourier analysis. The Fourier spectra of each worm strain match an approximate model using two different binary worm shapes that correspond to locomotory moments. The envelope of the averaged frequency distribution for actual and modeled worms confirms the model matches the data. This method can serve as a baseline for Fourier analysis for many microscopic species, as every microorganism will have its unique Fourier spectrum.

Detecting diffusion-diffraction patterns in size distribution phantoms using double-pulsed field gradient NMR: Theory and experiments.

PubMed

Shemesh, Noam; Ozarslan, Evren; Basser, Peter J; Cohen, Yoram

2010-01-21

NMR observable nuclei undergoing restricted diffusion within confining pores are important reporters for microstructural features of porous media including, inter-alia, biological tissues, emulsions and rocks. Diffusion NMR, and especially the single-pulsed field gradient (s-PFG) methodology, is one of the most important noninvasive tools for studying such opaque samples, enabling extraction of important microstructural information from diffusion-diffraction phenomena. However, when the pores are not monodisperse and are characterized by a size distribution, the diffusion-diffraction patterns disappear from the signal decay, and the relevant microstructural information is mostly lost. A recent theoretical study predicted that the diffusion-diffraction patterns in double-PFG (d-PFG) experiments have unique characteristics, such as zero-crossings, that make them more robust with respect to size distributions. In this study, we theoretically compared the signal decay arising from diffusion in isolated cylindrical pores characterized by lognormal size distributions in both s-PFG and d-PFG methodologies using a recently presented general framework for treating diffusion in NMR experiments. We showed the gradual loss of diffusion-diffraction patterns in broadening size distributions in s-PFG and the robustness of the zero-crossings in d-PFG even for very large standard deviations of the size distribution. We then performed s-PFG and d-PFG experiments on well-controlled size distribution phantoms in which the ground-truth is well-known a priori. We showed that the microstructural information, as manifested in the diffusion-diffraction patterns, is lost in the s-PFG experiments, whereas in d-PFG experiments the zero-crossings of the signal persist from which relevant microstructural information can be extracted. This study provides a proof of concept that d-PFG may be useful in obtaining important microstructural features in samples characterized by size distributions.

A novel approach of an absolute coding pattern based on Hamiltonian graph

NASA Astrophysics Data System (ADS)

Wang, Ya'nan; Wang, Huawei; Hao, Fusheng; Liu, Liqiang

2017-02-01

In this paper, a novel approach of an optical type absolute rotary encoder coding pattern is presented. The concept is based on the principle of the absolute encoder to find out a unique sequence that ensures an unambiguous shaft position of any angular. We design a single-ring and a n-by-2 matrix absolute encoder coding pattern by using the variations of Hamiltonian graph principle. 12 encoding bits is used in the single-ring by a linear array CCD to achieve an 1080-position cycle encoding. Besides, a 2-by-2 matrix is used as an unit in the 2-track disk to achieve a 16-bits encoding pattern by using an area array CCD sensor (as a sample). Finally, a higher resolution can be gained by an electronic subdivision of the signals. Compared with the conventional gray or binary code pattern (for a 2n resolution), this new pattern has a higher resolution (2n*n) with less coding tracks, which means the new pattern can lead to a smaller encoder, which is essential in the industrial production.

Unique spatial and cellular expression patterns of Hoxa5, Hoxb4 and Hoxb6 proteins in normal developing murine lung are modified in pulmonary hypoplasia

PubMed Central

Volpe, MaryAnn Vitoria; Wang, Karen Ting Wai; Nielsen, Heber Carl; Chinoy, Mala Romeshchandra

2009-01-01

Background Hox transcription factors modulate signaling pathways controlling organ morphogenesis and maintain cell fate and differentiation in adults. Retinoid signaling, key in regulating Hox expression, is altered in pulmonary hypoplasia. Information on pattern-specific expression of Hox proteins in normal lung development and in pulmonary hypoplasia is minimal. Our objective was to determine how pulmonary hypoplasia alters temporal, spatial and cellular expression of Hoxa5, Hoxb4 and Hoxb6 proteins compared to normal lung development. Methods Temporal, spatial and cellular Hoxa5, Hoxb4 and Hoxb6 expression was studied in normal (untreated) and nitrofen-induced hypoplastic (NT-PH) lungs from gestational day 13.5, 16, 19 fetuses and neonates using western blot and immunohistochemistry. Results Modification of protein levels and spatial and cellular Hox expression patterns in NT-PH lungs was consistent with delayed lung development. Distinct protein isoforms were detected for each Hox protein. Expression levels of the Hoxa5 and Hoxb6 isoforms changed with development and further in NT-PH lungs. Compared to normal lungs, Gd19 and neonatal NT-PH lungs had decreased Hoxb6 and increased Hoxa5 and Hoxb4. Hoxa5 cellular localization changed from mesenchyme to epithelia earlier in normal lungs. Hoxb4 was expressed in mesenchyme and epithelial cells throughout development. Hoxb6 remained mainly in mesenchymal cells around distal airways. Conclusions Unique spatial and cellular expression of Hoxa5, Hoxb4 and Hoxb6 participates in branching morphogenesis and terminal sac formation. Altered Hox protein temporal and cellular balance of expression either contributes to pulmonary hypoplasia or functions as a compensatory mechanism attempting to correct abnormal lung development and maturation in this condition. PMID:18553509

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

Vamathevan, Jessica J., E-mail: jessica.j.vamathevan@gsk.com; Hall, Matthew D.; Hasan, Samiul

Improving drug attrition remains a challenge in pharmaceutical discovery and development. A major cause of early attrition is the demonstration of safety signals which can negate any therapeutic index previously established. Safety attrition needs to be put in context of clinical translation (i.e. human relevance) and is negatively impacted by differences between animal models and human. In order to minimize such an impact, an earlier assessment of pharmacological target homology across animal model species will enhance understanding of the context of animal safety signals and aid species selection during later regulatory toxicology studies. Here we sequenced the genomes of themore » Sus scrofa Göttingen minipig and the Canis familiaris beagle, two widely used animal species in regulatory safety studies. Comparative analyses of these new genomes with other key model organisms, namely mouse, rat, cynomolgus macaque, rhesus macaque, two related breeds (S. scrofa Duroc and C. familiaris boxer) and human reveal considerable variation in gene content. Key genes in toxicology and metabolism studies, such as the UGT2 family, CYP2D6, and SLCO1A2, displayed unique duplication patterns. Comparisons of 317 known human drug targets revealed surprising variation such as species-specific positive selection, duplication and higher occurrences of pseudogenized targets in beagle (41 genes) relative to minipig (19 genes). These data will facilitate the more effective use of animals in biomedical research. - Highlights: • Genomes of the minipig and beagle dog, two species used in pharmaceutical studies. • First systematic comparative genome analysis of human and six experimental animals. • Key drug toxicology genes display unique duplication patterns across species. • Comparison of 317 drug targets show species-specific evolutionary patterns.« less

Comprehending text versus reading words in young readers with varying reading ability: Distinct patterns of functional connectivity from common processing hubs

PubMed Central

Aboud, Katherine S.; Bailey, Stephen K.; Petrill, Stephen A.; Cutting, Laurie E.

2016-01-01

Skilled reading depends on recognizing words efficiently in isolation (word-level processing; WL) and extracting meaning from text (discourse-level processing; DL); deficiencies in either result in poor reading. FMRI has revealed consistent overlapping networks in word and passage reading, as well as unique regions for DL processing, however less is known about how WL and DL processes interact. Here we examined functional connectivity from seed regions derived from where BOLD signal overlapped during word and passage reading in 38 adolescents ranging in reading ability, hypothesizing that even though certain regions support word- and higher-level language, connectivity patterns from overlapping regions would be task modulated. Results indeed revealed that the left-lateralized semantic and working memory (WM) seed regions showed task-dependent functional connectivity patterns: during DL processes, semantic and WM nodes all correlated with the left angular gyrus, a region implicated in semantic memory/coherence building. In contrast, during WL, these nodes coordinated with a traditional WL area (left occipitotemporal region). Additionally, these WL and DL findings were modulated by decoding and comprehension abilities, respectively, with poorer abilities correlating with decreased connectivity. Findings indicate that key regions may uniquely contribute to multiple levels of reading; we speculate that these connectivity patterns may be especially salient for reading outcomes and intervention response. PMID:27147257

T-cell costimulatory pathways in allograft rejection and tolerance.

PubMed

Rothstein, David M; Sayegh, Mohamed H

2003-12-01

The destiny of activated T cells is critical to the ultimate fate of immune response. After encountering antigen, naïve T cells receive signal 1 through the T-cell receptor (TCR)-major histocompatibility complex (MHC) plus antigenic peptide complex and signal 2 through "positive" costimulatory molecules leading to full activation. "Negative" T-cell costimulatory pathways, on the other hand, function to downregulate immune responses. The purpose of this article is to review the current state of knowledge and recent advances in our understanding of the functions of the positive and negative T-cell costimulatory pathways in alloimmune responses. Specifically, we discuss the functions of the CD28:B7 and the tumor necrosis factor receptor (TNFR):tumor necrosis factor (TNF) family of molecules in allograft rejection and tolerance. We address the following important questions: are T-cell costimulatory pathways merely redundant or do they provide distinct and unique functions? What are the important and unique interactions between the various pathways? And, what are the effects and mechanisms of targeting of these pathways in different types and patterns of allograft rejection and tolerance models?

Facial Recognition in a Discus Fish (Cichlidae): Experimental Approach Using Digital Models

PubMed Central

Satoh, Shun; Tanaka, Hirokazu; Kohda, Masanori

2016-01-01

A number of mammals and birds are known to be capable of visually discriminating between familiar and unfamiliar individuals, depending on facial patterns in some species. Many fish also visually recognize other conspecifics individually, and previous studies report that facial color patterns can be an initial signal for individual recognition. For example, a cichlid fish and a damselfish will use individual-specific color patterns that develop only in the facial area. However, it remains to be determined whether the facial area is an especially favorable site for visual signals in fish, and if so why? The monogamous discus fish, Symphysopdon aequifasciatus (Cichlidae), is capable of visually distinguishing its pair-partner from other conspecifics. Discus fish have individual-specific coloration patterns on entire body including the facial area, frontal head, trunk and vertical fins. If the facial area is an inherently important site for the visual cues, this species will use facial patterns for individual recognition, but otherwise they will use patterns on other body parts as well. We used modified digital models to examine whether discus fish use only facial coloration for individual recognition. Digital models of four different combinations of familiar and unfamiliar fish faces and bodies were displayed in frontal and lateral views. Focal fish frequently performed partner-specific displays towards partner-face models, and did aggressive displays towards models of non-partner’s faces. We conclude that to identify individuals this fish does not depend on frontal color patterns but does on lateral facial color patterns, although they have unique color patterns on the other parts of body. We discuss the significance of facial coloration for individual recognition in fish compared with birds and mammals. PMID:27191162

Facial Recognition in a Discus Fish (Cichlidae): Experimental Approach Using Digital Models.

PubMed

Satoh, Shun; Tanaka, Hirokazu; Kohda, Masanori

2016-01-01

A number of mammals and birds are known to be capable of visually discriminating between familiar and unfamiliar individuals, depending on facial patterns in some species. Many fish also visually recognize other conspecifics individually, and previous studies report that facial color patterns can be an initial signal for individual recognition. For example, a cichlid fish and a damselfish will use individual-specific color patterns that develop only in the facial area. However, it remains to be determined whether the facial area is an especially favorable site for visual signals in fish, and if so why? The monogamous discus fish, Symphysopdon aequifasciatus (Cichlidae), is capable of visually distinguishing its pair-partner from other conspecifics. Discus fish have individual-specific coloration patterns on entire body including the facial area, frontal head, trunk and vertical fins. If the facial area is an inherently important site for the visual cues, this species will use facial patterns for individual recognition, but otherwise they will use patterns on other body parts as well. We used modified digital models to examine whether discus fish use only facial coloration for individual recognition. Digital models of four different combinations of familiar and unfamiliar fish faces and bodies were displayed in frontal and lateral views. Focal fish frequently performed partner-specific displays towards partner-face models, and did aggressive displays towards models of non-partner's faces. We conclude that to identify individuals this fish does not depend on frontal color patterns but does on lateral facial color patterns, although they have unique color patterns on the other parts of body. We discuss the significance of facial coloration for individual recognition in fish compared with birds and mammals.

Miles Hand Grenade

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

Harrington, John J.; Buttz, James H.; Maish, Alex B.

2005-11-15

A simulated grenade for MILES-type simulations generates a unique RF signal and a unique audio signal. A detector utilizes the time between receipt of the RF signal and the slower-traveling audio signal to determine the distance between the detector and the simulated grenade.

Rocket investigations of electron precipitation and VLF waves in the Antarctic upper atmosphere

NASA Technical Reports Server (NTRS)

Sheldon, W. R.; Benbrook, J. R.; Bering, E. A.

1988-01-01

The results of two Antarctic rocket campaigns, primarily initiated to investigate electron precipitation stimulated by signals from the Siple-Station ground-based VLF transmitter, are presented. While the primary objective of the campaigns was not achieved, the Siple VLF transmitter facilitated a study of the wave environment in the ionosphere. Standing wave patterns in the ionosphere were observed for the first time by detectors flown aboard the Nike-Tomahawk rockets; the same detectors monitored a continuous signal from the transmitter through the neutral atmosphere and into the ionosphere, providing unique data for comparison with theoretical studies of wave propagation. The measurements of penetrating electron precipitation were interpreted in terms of a model of energetic electron precipitation from the trapped radiational belts.

Chemotaxis in Microfluidic Devices

NASA Astrophysics Data System (ADS)

Wyatt, Danica; Nadkarni, Sharvari; Song, Loling; Voeltz, Camilla; Bodenschatz, Eberhard

2004-03-01

Dictyostelium amoebae use chemical signaling to begin starvation-induced aggregation. Cells generate a complex and dynamic pattern of cyclic AMP that drives their migration toward a central point. While this phenomenon is unique to social amoebae, the signaling pathways of chemotaxis are similar in all eukaryotic cells. Dicty serves as a model organism for imaging these intracellular protein dynamics. To date, chemotaxis has been primarily studied in diffusion-generated gradients in chambers many orders of magnitude larger than a cell. To better quantify which aspects of a gradient trigger a response, we have designed a microfluidic channel that confines cells in an environment where spatiotemporal cAMP concentration can be precisely manipulated. We report results on an early event in the signaling cascade, the translocation of PH domain-containing proteins, which test current models of chemotaxis. This work was supported by the NSF Biocomplexity program and the Nanobiotechnology Center, an STC Program of the NSF under Agreement No. ECS-9876771.

Utilizing the planarian voltage-gated ion channel transcriptome to resolve a role for a Ca2+ channel in neuromuscular function and regeneration.

PubMed

Chan, John D; Zhang, Dan; Liu, Xiaolong; Zarowiecki, Magdalena; Berriman, Matthew; Marchant, Jonathan S

2017-06-01

The robust regenerative capacity of planarian flatworms depends on the orchestration of signaling events from early wounding responses through the stem cell enacted differentiative outcomes that restore appropriate tissue types. Acute signaling events in excitable cells play an important role in determining regenerative polarity, rationalized by the discovery that sub-epidermal muscle cells express critical patterning genes known to control regenerative outcomes. These data imply a dual conductive (neuromuscular signaling) and instructive (anterior-posterior patterning) role for Ca 2+ signaling in planarian regeneration. Here, to facilitate study of acute signaling events in the excitable cell niche, we provide a de novo transcriptome assembly from the planarian Dugesia japonica allowing characterization of the diverse ionotropic portfolio of this model organism. We demonstrate the utility of this resource by proceeding to characterize the individual role of each of the planarian voltage-operated Ca 2+ channels during regeneration, and demonstrate that knockdown of a specific voltage operated Ca 2+ channel (Ca v 1B) that impairs muscle function uniquely creates an environment permissive for anteriorization. Provision of the full transcriptomic dataset should facilitate further investigations of molecules within the planarian voltage-gated channel portfolio to explore the role of excitable cell physiology on regenerative outcomes. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech. Copyright © 2016 Elsevier B.V. All rights reserved.

Targeting IFN-λ: therapeutic implications.

PubMed

Eslam, Mohammed; George, Jacob

2016-12-01

Type-III interferons (IFN-λ), the most recently discovered family of IFNs, shares common features with other family members, but also has many distinctive activities. IFN-λ uniquely has a different receptor complex, and a more focused pattern of tissue expression and signaling effects, from other classes of IFNs. Multiple genome-wide association studies (GWAS) and subsequent validation reports suggest a pivotal role for polymorphisms near the IFNL3 gene in hepatitis C clearance and control, as also for several other epithelial cell tropic viruses. Apart from its antiviral activity, IFN-λ possesses anti-tumor, immune-inflammatory and homeostatic functions. The overlapping effects of IFN-λ with type I IFN, with a restricted tissue expression pattern renders IFN-λ an attractive therapeutic target for viral infection, cancer and autoimmune diseases, with limited side effects. Areas covered: This review will summarize the current and future therapeutic opportunities offered by this most recently discovered family of interferons. Expert opinion: Our knowledge on IFN-λ is rapidly expanding. Though there are many remaining questions and challenges that require elucidation, the unique characteristics of IFN-λ increases enthusiasm that multiple therapeutic options will emerge.

Conserved and divergent functions of Pax6 underlie species-specific neurogenic patterns in the developing amniote brain.

PubMed

Yamashita, Wataru; Takahashi, Masanori; Kikkawa, Takako; Gotoh, Hitoshi; Osumi, Noriko; Ono, Katsuhiko; Nomura, Tadashi

2018-04-16

The evolution of unique organ structures is associated with changes in conserved developmental programs. However, characterizing the functional conservation and variation of homologous transcription factors (TFs) that dictate species-specific cellular dynamics has remained elusive. Here, we dissect shared and divergent functions of Pax6 during amniote brain development. Comparative functional analyses revealed that the neurogenic function of Pax6 is highly conserved in the developing mouse and chick pallium, whereas stage-specific binary functions of Pax6 in neurogenesis are unique to mouse neuronal progenitors, consistent with Pax6-dependent temporal regulation of Notch signaling. Furthermore, we identified that Pax6-dependent enhancer activity of Dbx1 is extensively conserved between mammals and chick, although Dbx1 expression in the developing pallium is highly divergent in these species. Our results suggest that spatiotemporal changes in Pax6-dependent regulatory programs contributed to species-specific neurogenic patterns in mammalian and avian lineages, which underlie the morphological divergence of the amniote pallial architectures. © 2018. Published by The Company of Biologists Ltd.

A Nogo-Like Signaling Perspective from Birth to Adulthood and in Old Age: Brain Expression Patterns of Ligands, Receptors and Modulators

PubMed Central

Smedfors, Gabriella; Olson, Lars; Karlsson, Tobias E.

2018-01-01

An appropriate strength of Nogo-like signaling is important to maintain synaptic homeostasis in the CNS. Disturbances have been associated with schizophrenia, MS and other diseases. Blocking Nogo-like signaling may improve recovery after spinal cord injury, stroke and traumatic brain injury. To understand the interacting roles of an increasing number of ligands, receptors and modulators engaged in Nogo-like signaling, the transcriptional activity of these genes in the same brain areas from birth to old age in the normal brain is needed. Thus, we have quantitatively mapped the innate expression of 11 important genes engaged in Nogo-like signaling. Using in situ hybridization, we located and measured the amount of mRNA encoding Nogo-A, OMgp, NgR1, NgR2, NgR3, Lingo-1, Troy, Olfactomedin, LgI1, ADAM22, and MAG, in 18 different brain areas at six different ages (P0, 1, 2, 4, 14, and 104 weeks). We show gene- and area-specific activities and how the genes undergo dynamic regulation during postnatal development and become stable during adulthood. Hippocampal areas underwent the largest changes over time. We only found differences between individual cortical areas in Troy and MAG. Subcortical areas presented the largest inter-regional differences; lateral and basolateral amygdala had markedly higher expression than other subcortical areas. The widespread differences and unique expression patterns of the different genes involved in Nogo-like signaling suggest that the functional complexes could look vastly different in different areas. PMID:29520216

Patterning mechanisms of the sub-intestinal venous plexus in zebrafish

PubMed Central

Goi, Michela; Childs, Sarah J.

2017-01-01

Despite considerable interest in angiogenesis, organ-specific angiogenesis remains less well characterized. The vessels that absorb nutrients from the yolk and later provide blood supply to the developing digestive system are primarily venous in origin. In zebrafish, these are the vessels of the Sub-intestinal venous plexus (SIVP) and they represent a new candidate model to gain an insight into the mechanisms of venous angiogenesis. Unlike other vessel beds in zebrafish, the SIVP is not stereotypically patterned and lacks obvious sources of patterning information. However, by examining the area of vessel coverage, number of compartments, proliferation and migration speed we have identified common developmental steps in SIVP formation. We applied our analysis of SIVP development to obd mutants that have a mutation in the guidance receptor PlexinD1. obd mutants show dysregulation of nearly all parameters of SIVP formation. We show that the SIVP responds to a unique combination of pathways that control both arterial and venous growth in other systems. Blocking Shh, Notch and Pdgf signaling has no effect on SIVP growth. However Vegf promotes sprouting of the predominantly venous plexus and Bmp promotes outgrowth of the structure. We propose that the SIVP is a unique model to understand novel mechanisms utilized in organ-specific angiogenesis. PMID:26477558

The Brassicaceae Family Displays Divergent, Shoot-Skewed NLR Resistance Gene Expression.

PubMed

Munch, David; Gupta, Vikas; Bachmann, Asger; Busch, Wolfgang; Kelly, Simon; Mun, Terry; Andersen, Stig Uggerhøj

2018-02-01

Nucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial effectors. We hypothesized that NLR expression patterns could reflect organ-specific differences in effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 NLRs from nine plant species. We found stable NLR root/shoot expression ratios within species, suggesting organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most monocot and dicot plant species preferentially expressed NLRs in roots. In contrast, Brassicaceae species, including oilseed rape ( Brassica napus ) and the model plant Arabidopsis ( Arabidopsis thaliana ), were unique in showing NLR expression skewed toward the shoot across multiple phylogenetically distinct groups of NLRs. The Brassicaceae are also outliers in the sense that they have lost the common symbiosis signaling pathway, which enables intracellular infection by root symbionts. While it is unclear if these two events are related, the NLR expression shift identified here suggests that the Brassicaceae may have evolved unique pattern-recognition receptors and antimicrobial root metabolites to substitute for NLR protection. Such innovations in root protection could potentially be exploited in crop rotation schemes or for enhancing root defense systems of non-Brassicaceae crops. © 2018 American Society of Plant Biologists. All Rights Reserved.

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.

Bacterial effectors target the common signaling partner BAK1 to disrupt multiple MAMP receptor-signaling complexes and impede plant immunity.

PubMed

Shan, Libo; He, Ping; Li, Jianming; Heese, Antje; Peck, Scott C; Nürnberger, Thorsten; Martin, Gregory B; Sheen, Jen

2008-07-17

Successful pathogens have evolved strategies to interfere with host immune systems. For example, the ubiquitous plant pathogen Pseudomonas syringae injects two sequence-distinct effectors, AvrPto and AvrPtoB, to intercept convergent innate immune responses stimulated by multiple microbe-associated molecular patterns (MAMPs). However, the direct host targets and precise molecular mechanisms of bacterial effectors remain largely obscure. We show that AvrPto and AvrPtoB bind the Arabidopsis receptor-like kinase BAK1, a shared signaling partner of both the flagellin receptor FLS2 and the brassinosteroid receptor BRI1. This targeting interferes with ligand-dependent association of FLS2 with BAK1 during infection. It also impedes BAK1-dependent host immune responses to diverse other MAMPs and brassinosteroid signaling. Significantly, the structural basis of AvrPto-BAK1 interaction appears to be distinct from AvrPto-Pto association required for effector-triggered immunity. These findings uncover a unique strategy of bacterial pathogenesis where virulence effectors block signal transmission through a key common component of multiple MAMP-receptor complexes.

De-aliasing for signal restoration in Propeller MR imaging.

PubMed

Chiu, Su-Chin; Chang, Hing-Chiu; Chu, Mei-Lan; Wu, Ming-Long; Chung, Hsiao-Wen; Lin, Yi-Ru

2017-02-01

Objects falling outside of the true elliptical field-of-view (FOV) in Propeller imaging show unique aliasing artifacts. This study proposes a de-aliasing approach to restore the signal intensities in Propeller images without extra data acquisition. Computer simulation was performed on the Shepp-Logan head phantom deliberately placed obliquely to examine the signal aliasing. In addition, phantom and human imaging experiments were performed using Propeller imaging with various readouts on a 3.0 Tesla MR scanner. De-aliasing using the proposed method was then performed, with the first low-resolution single-blade image used to find out the aliasing patterns in all the single-blade images, followed by standard Propeller reconstruction. The Propeller images without and with de-aliasing were compared. Computer simulations showed signal loss at the image corners along with aliasing artifacts distributed along directions corresponding to the rotational blades, consistent with clinical observations. The proposed de-aliasing operation successfully restored the correct images in both phantom and human experiments. The de-aliasing operation is an effective adjunct to Propeller MR image reconstruction for retrospective restoration of aliased signals. Copyright © 2016 Elsevier Inc. All rights reserved.

Wideband Single-Crystal Transducer for Bone Characterization

NASA Technical Reports Server (NTRS)

Liang, Yu; Snook, Kevin

2012-01-01

The microgravity conditions of space travel result in unique physiological demands on the human body. In particular, the absence of the continual mechanical stresses on the skeletal system that are present on Earth cause the bones to decalcify. Trabecular structure decreases in thickness and increases in spacing, resulting in decreased bone strength and increased risk of injury. Thus, monitoring bone health is a high priority for long-term space travel. A single probe covering all frequency bands of interest would be ideal for such measurements, and this would also minimize storage space and eliminate the complexity of integrating multiple probes. This invention is an ultrasound transducer for the structural characterization of bone. Such characterization measures features of reflected and transmitted ultrasound signals, and correlates these signals with bone structure metrics such as bone mineral density, trabecular spacing, and thickness, etc. The techniques used to determine these various metrics require measurements over a broad range of ultrasound frequencies, and therefore, complete characterization requires the use of several narrowband transducers. This is a single transducer capable of making these measurements in all the required frequency bands. The device achieves this capability through a unique combination of a broadband piezoelectric material; a design incorporating multiple resonator sizes with distinct, overlapping frequency spectra; and a micromachining process for producing the multiple-resonator pattern with common electrode surfaces between the resonators. This device consists of a pattern of resonator bars with common electrodes that is wrapped around a central mandrel such that the radiating faces of the resonators are coplanar and can be simultaneously applied to the sample to be measured. The device operates as both a source and receiver of acoustic energy. It is operated by connection to an electronic system capable of both providing an excitation signal to the transducer and amplifying the signal received from the transducer. The excitation signal may be either a wide-bandwidth signal to excite the transducer across its entire operational spectrum, or a narrow-bandwidth signal optimized for a particular measurement technique. The transducer face is applied to the skin covering the bone to be characterized, and may be operated in through-transmission mode using two transducers, or in pulse-echo mode. The transducer is a unique combination of material, design, and fabrication technique. It is based on single-crystal lead magnesium niobate lead titanate (PMN-PT) piezoelectric material. As compared to the commonly used piezoceramics, this piezocrystal has superior piezoelectric and elastic properties, which results in devices with superior bandwidth, source level, and power requirements. This design necessitates a single resonant frequency. However, by operating in a transverse length-extensional mode, with the electric field applied orthogonally to the extensional direction, resonators of different sizes can share common electrodes, resulting in a multiply-resonant structure. With carefully sized resonators, and the superior bandwidth of piezocrystal, the resonances can be made to overlap to form a smooth, wide-bandwidth characteristic.

Organic bioelectronics for electronic-to-chemical translation in modulation of neuronal signaling and machine-to-brain interfacing.

PubMed

Larsson, Karin C; Kjäll, Peter; Richter-Dahlfors, Agneta

2013-09-01

A major challenge when creating interfaces for the nervous system is to translate between the signal carriers of the nervous system (ions and neurotransmitters) and those of conventional electronics (electrons). Organic conjugated polymers represent a unique class of materials that utilizes both electrons and ions as charge carriers. Based on these materials, we have established a series of novel communication interfaces between electronic components and biological systems. The organic electronic ion pump (OEIP) presented in this review is made of the polymer-polyelectrolyte system poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS). The OEIP translates electronic signals into electrophoretic migration of ions and neurotransmitters. We demonstrate how spatio-temporally controlled delivery of ions and neurotransmitters can be used to modulate intracellular Ca(2+) signaling in neuronal cells in the absence of convective disturbances. The electronic control of delivery enables strict control of dynamic parameters, such as amplitude and frequency of Ca(2+) responses, and can be used to generate temporal patterns mimicking naturally occurring Ca(2+) oscillations. To enable further control of the ionic signals we developed the electrophoretic chemical transistor, an analog of the traditional transistor used to amplify and/or switch electronic signals. Finally, we demonstrate the use of the OEIP in a new "machine-to-brain" interface by modulating brainstem responses in vivo. This review highlights the potential of communication interfaces based on conjugated polymers in generating complex, high-resolution, signal patterns to control cell physiology. We foresee widespread applications for these devices in biomedical research and in future medical devices within multiple therapeutic areas. This article is part of a Special Issue entitled Organic Bioelectronics-Novel Applications in Biomedicine. Copyright © 2012 Elsevier B.V. All rights reserved.

Second-harmonic patterned polarization-analyzed reflection confocal microscope

NASA Astrophysics Data System (ADS)

Okoro, Chukwuemeka; Toussaint, Kimani C.

2017-08-01

We introduce the second-harmonic patterned polarization-analyzed reflection confocal (SPPARC) microscope-a multimodal imaging platform that integrates Mueller matrix polarimetry with reflection confocal and second-harmonic generation (SHG) microscopy. SPPARC microscopy provides label-free three-dimensional (3-D), SHG-patterned confocal images that lend themselves to spatially dependent, linear polarimetric analysis for extraction of rich polarization information based on the Mueller calculus. To demonstrate its capabilities, we use SPPARC microscopy to analyze both porcine tendon and ligament samples and find differences in both circular degree-of-polarization and depolarization parameters. Moreover, using the collagen-generated SHG signal as an endogenous counterstain, we show that the technique can be used to provide 3-D polarimetric information of the surrounding extrafibrillar matrix plus cells or EFMC region. The unique characteristics of SPPARC microscopy holds strong potential for it to more accurately and quantitatively describe microstructural changes in collagen-rich samples in three spatial dimensions.

Worldwide patterns of bird colouration on islands.

PubMed

Doutrelant, Claire; Paquet, Matthieu; Renoult, Julien P; Grégoire, Arnaud; Crochet, Pierre-André; Covas, Rita

2016-05-01

Island environments share distinctive characteristics that offer unique opportunities to investigate parallel evolution. Previous research has produced evidence of an island syndrome for morphological traits, life-history strategies and ecological niches, but little is known about the response to insularity of other important traits such as animal signals. Here, we tested whether birds' plumage colouration is part of the island syndrome. We analysed with spectrophotometry the colouration of 116 species endemic to islands and their 116 closest mainland relatives. We found a pattern of reduced brightness and colour intensity for both sexes on islands. In addition, we found a decrease in the number of colour patches on islands that, in males, was associated with a decrease in the number of same-family sympatric species. These results demonstrate a worldwide pattern of parallel colour changes on islands and suggest that a relaxation of selection on species recognition may be one of the mechanisms involved. © 2016 John Wiley & Sons Ltd/CNRS.

Real-time particulate mass measurement based on laser scattering

NASA Astrophysics Data System (ADS)

Rentz, Julia H.; Mansur, David; Vaillancourt, Robert; Schundler, Elizabeth; Evans, Thomas

2005-11-01

OPTRA has developed a new approach to the determination of particulate size distribution from a measured, composite, laser angular scatter pattern. Drawing from the field of infrared spectroscopy, OPTRA has employed a multicomponent analysis technique which uniquely recognizes patterns associated with each particle size "bin" over a broad range of sizes. The technique is particularly appropriate for overlapping patterns where large signals are potentially obscuring weak ones. OPTRA has also investigated a method for accurately training the algorithms without the use of representative particles for any given application. This streamlined calibration applies a one-time measured "instrument function" to theoretical Mie patterns to create the training data for the algorithms. OPTRA has demonstrated this algorithmic technique on a compact, rugged, laser scatter sensor head we developed for gas turbine engine emissions measurements. The sensor contains a miniature violet solid state laser and an array of silicon photodiodes, both of which are commercial off the shelf. The algorithmic technique can also be used with any commercially available laser scatter system.

Intracellular GPCRs Play Key Roles in Synaptic Plasticity.

PubMed

Jong, Yuh-Jiin I; Harmon, Steven K; O'Malley, Karen L

2018-02-16

The trillions of synaptic connections within the human brain are shaped by experience and neuronal activity, both of which underlie synaptic plasticity and ultimately learning and memory. G protein-coupled receptors (GPCRs) play key roles in synaptic plasticity by strengthening or weakening synapses and/or shaping dendritic spines. While most studies of synaptic plasticity have focused on cell surface receptors and their downstream signaling partners, emerging data point to a critical new role for the very same receptors to signal from inside the cell. Intracellular receptors have been localized to the nucleus, endoplasmic reticulum, lysosome, and mitochondria. From these intracellular positions, such receptors may couple to different signaling systems, display unique desensitization patterns, and/or show distinct patterns of subcellular distribution. Intracellular GPCRs can be activated at the cell surface, endocytosed, and transported to an intracellular site or simply activated in situ by de novo ligand synthesis, diffusion of permeable ligands, or active transport of non-permeable ligands. Current findings reinforce the notion that intracellular GPCRs play a dynamic role in synaptic plasticity and learning and memory. As new intracellular GPCR roles are defined, the need to selectively tailor agonists and/or antagonists to both intracellular and cell surface receptors may lead to the development of more effective therapeutic tools.

Passive tire pressure sensor and method

DOEpatents

Pfeifer, Kent Bryant; Williams, Robert Leslie; Waldschmidt, Robert Lee; Morgan, Catherine Hook

2006-08-29

A surface acoustic wave device includes a micro-machined pressure transducer for monitoring tire pressure. The device is configured having a micro-machined cavity that is sealed with a flexible conductive membrane. When an external tire pressure equivalent to the cavity pressure is detected, the membrane makes contact with ridges on the backside of the surface acoustic wave device. The ridges are electrically connected to conductive fingers of the device. When the detected pressure is correct, selected fingers on the device will be grounded producing patterned acoustic reflections to an impulse RF signal. When the external tire pressure is less than the cavity reference pressure, a reduced reflected signal to the receiver results. The sensor may further be constructed so as to identify itself by a unique reflected identification pulse series.

Passive tire pressure sensor and method

DOEpatents

Pfeifer, Kent Bryant; Williams, Robert Leslie; Waldschmidt, Robert Lee; Morgan, Catherine Hook

2007-09-04

A surface acoustic wave device includes a micro-machined pressure transducer for monitoring tire pressure. The device is configured having a micro-machined cavity that is sealed with a flexible conductive membrane. When an external tire pressure equivalent to the cavity pressure is detected, the membrane makes contact with ridges on the backside of the surface acoustic wave device. The ridges are electrically connected to conductive fingers of the device. When the detected pressure is correct, selected fingers on the device will be grounded producing patterned acoustic reflections to an impulse RF signal. When the external tire pressure is less than the cavity reference pressure, a reduced reflected signal to the receiver results. The sensor may further be constructed so as to identify itself by a unique reflected identification pulse series.

Lensless high-resolution photoacoustic imaging scanner for in vivo skin imaging

NASA Astrophysics Data System (ADS)

Ida, Taiichiro; Iwazaki, Hideaki; Omuro, Toshiyuki; Kawaguchi, Yasushi; Tsunoi, Yasuyuki; Kawauchi, Satoko; Sato, Shunichi

2018-02-01

We previously launched a high-resolution photoacoustic (PA) imaging scanner based on a unique lensless design for in vivo skin imaging. The design, imaging algorithm and characteristics of the system are described in this paper. Neither an optical lens nor an acoustic lens is used in the system. In the imaging head, four sensor elements are arranged quadrilaterally, and by checking the phase differences for PA waves detected with these four sensors, a set of PA signals only originating from a chromophore located on the sensor center axis is extracted for constructing an image. A phantom study using a carbon fiber showed a depth-independent horizontal resolution of 84.0 ± 3.5 µm, and the scan direction-dependent variation of PA signals was about ± 20%. We then performed imaging of vasculature phantoms: patterns of red ink lines with widths of 100 or 200 μm formed in an acrylic block co-polymer. The patterns were visualized with high contrast, showing the capability for imaging arterioles and venues in the skin. Vasculatures in rat burn models and healthy human skin were also clearly visualized in vivo.

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.

Common and unique representations in pFC for face and place attractiveness.

PubMed

Pegors, Teresa K; Kable, Joseph W; Chatterjee, Anjan; Epstein, Russell A

2015-05-01

Although previous neuroimaging research has identified overlapping correlates of subjective value across different reward types in the ventromedial pFC (vmPFC), it is not clear whether this "common currency" evaluative signal extends to the aesthetic domain. To examine this issue, we scanned human participants with fMRI while they made attractiveness judgments of faces and places-two stimulus categories that are associated with different underlying rewards, have very different visual properties, and are rarely compared with each other. We found overlapping signals for face and place attractiveness in the vmPFC, consistent with the idea that this region codes a signal for value that applies across disparate reward types and across both economic and aesthetic judgments. However, we also identified a subregion of vmPFC within which activity patterns for face and place attractiveness were distinguishable, suggesting that some category-specific attractiveness information is retained in this region. Finally, we observed two separate functional regions in lateral OFC: one region that exhibited a category-unique response to face attractiveness and another region that responded strongly to faces but was insensitive to their value. Our results suggest that vmPFC supports a common mechanism for reward evaluation while also retaining a degree of category-specific information, whereas lateral OFC may be involved in basic reward processing that is specific to only some stimulus categories.

Dynamic changes in global microRNAome and transcriptome reveal complex miRNA-mRNA regulated host response to Japanese Encephalitis Virus in microglial cells

PubMed Central

Kumari, Bharti; Jain, Pratistha; Das, Shaoli; Ghosal, Suman; Hazra, Bibhabasu; Trivedi, Ashish Chandra; Basu, Anirban; Chakrabarti, Jayprokas; Vrati, Sudhanshu; Banerjee, Arup

2016-01-01

Microglia cells in the brain play essential role during Japanese Encephalitis Virus (JEV) infection and may lead to change in microRNA (miRNA) and mRNA profile. These changes may together control disease outcome. Using Affymetrix microarray platform, we profiled cellular miRNA and mRNA expression at multiple time points during viral infection in human microglial (CHME3) cells. In silico analysis of microarray data revealed a phased pattern of miRNAs expression, associated with JEV replication and provided unique signatures of infection. Target prediction and pathway enrichment analysis identified anti correlation between differentially expressed miRNA and the gene expression at multiple time point which ultimately affected diverse signaling pathways including Notch signaling pathways in microglia. Activation of Notch pathway during JEV infection was demonstrated in vitro and in vivo. The expression of a subset of miRNAs that target multiple genes in Notch signaling pathways were suppressed and their overexpression could affect JEV induced immune response. Further analysis provided evidence for the possible presence of cellular competing endogenous RNA (ceRNA) associated with innate immune response. Collectively, our data provide a uniquely comprehensive view of the changes in the host miRNAs induced by JEV during cellular infection and identify Notch pathway in modulating microglia mediated inflammation. PMID:26838068

Dynamic changes in global microRNAome and transcriptome reveal complex miRNA-mRNA regulated host response to Japanese Encephalitis Virus in microglial cells.

PubMed

Kumari, Bharti; Jain, Pratistha; Das, Shaoli; Ghosal, Suman; Hazra, Bibhabasu; Trivedi, Ashish Chandra; Basu, Anirban; Chakrabarti, Jayprokas; Vrati, Sudhanshu; Banerjee, Arup

2016-02-03

Microglia cells in the brain play essential role during Japanese Encephalitis Virus (JEV) infection and may lead to change in microRNA (miRNA) and mRNA profile. These changes may together control disease outcome. Using Affymetrix microarray platform, we profiled cellular miRNA and mRNA expression at multiple time points during viral infection in human microglial (CHME3) cells. In silico analysis of microarray data revealed a phased pattern of miRNAs expression, associated with JEV replication and provided unique signatures of infection. Target prediction and pathway enrichment analysis identified anti correlation between differentially expressed miRNA and the gene expression at multiple time point which ultimately affected diverse signaling pathways including Notch signaling pathways in microglia. Activation of Notch pathway during JEV infection was demonstrated in vitro and in vivo. The expression of a subset of miRNAs that target multiple genes in Notch signaling pathways were suppressed and their overexpression could affect JEV induced immune response. Further analysis provided evidence for the possible presence of cellular competing endogenous RNA (ceRNA) associated with innate immune response. Collectively, our data provide a uniquely comprehensive view of the changes in the host miRNAs induced by JEV during cellular infection and identify Notch pathway in modulating microglia mediated inflammation.

Faunal assemblages and multi-scale habitat patterns in headwater tributaries of the South Fork Trinity River - an unregulated river embedded within a multiple-use landscape

USGS Publications Warehouse

Welsh, H.H.; Hodgson, G.R.; Duda, J.J.; Emlen, J.M.

2010-01-01

Headwaters can represent 80% of stream kilometers in a watershed, and they also have unique physical and biological properties that have only recently been recognized for their importance in sustaining healthy functioning stream networks and their ecological services. We sampled 60 headwater tributaries in the South Fork Trinity River, a 2,430 km2, mostly forested, multiple-use watershed in northwestern California. Our objectives were: (1) to differentiate unique headwater types using 69 abiotic and vegetation variables measured at three spatial scales, and then to reduce these to informative subsets; (2) determine if distinct biota occupied the different tributary types; (3) determine the environmental attributes associated with the presence and abundance of these biotic assemblages; and (4) using niche modeling, determine key attribute thresholds to illustrate how these biota could be employed as metrics of system integrity and ecological services. Several taxa were sufficiently abundant and widespread to use as bio-indicators: the presence and abundance of steelhead trout (Oncorhynchus mykiss), herpetofauna (reptile and amphibian) species richness, and signal crayfish (Pacifastacus leniusculus) represented different trophic positions, value as commercial resources (steelhead), sensitivity to environmental stress (amphibians), and indicators of biodiversity (herpetofauna species richness). Herpetofauna species richness did not differ, but abundances of steelhead trout, signal crayfish, and amphibian richness all differed significantly among tributary types. Niche models indicated that distribution and abundance patterns in both riparian and aquatic environments were associated with physical and structural attributes at multiple spatial scales, both within and around reaches. The bio-indicators responded to unique sets of attributes, reflecting the high environmental heterogeneity in headwater tributaries across this large watershed. These niche attributes represented a wide range of headwater environments, indicating responses to a number of natural and anthropogenic conditions, and demonstrated the value of using a suite of bio-indicators to elucidate watershed conditions, and to examine numerous disturbances that may influence ecological integrity.

Identification of unique expression signatures and therapeutic targets in esophageal squamous cell carcinoma

PubMed Central

2012-01-01

Background Esophageal squamous cell carcinoma (ESCC), the predominant histological subtype of esophageal cancer, is characterized by high mortality. Previous work identified important mRNA expression differences between normal and tumor cells; however, to date there are limited ex vivo studies examining expression changes occurring during normal esophageal squamous cell differentiation versus those associated with tumorigenesis. In this study, we used a unique tissue microdissection strategy and microarrays to measure gene expression profiles associated with cell differentiation versus tumorigenesis in twelve cases of patient-matched normal basal squamous epithelial cells (NB), normal differentiated squamous epithelium (ND), and squamous cell cancer. Class comparison and pathway analysis were used to compare NB versus tumor in a search for unique therapeutic targets. Results As a first step towards this goal, gene expression profiles and pathways were evaluated. Overall, ND expression patterns were markedly different from NB and tumor; whereas, tumor and NB were more closely related. Tumor showed a general decrease in differentially expressed genes relative to NB as opposed to ND that exhibited the opposite trend. FSH and IgG networks were most highly dysregulated in normal differentiation and tumorigenesis, respectively. DNA repair pathways were generally elevated in NB and tumor relative to ND indicating involvement in both normal and pathological growth. PDGF signaling pathway and 12 individual genes unique to the tumor/NB comparison were identified as therapeutic targets, and 10 associated ESCC gene-drug pairs were identified. We further examined the protein expression level and the distribution patterns of four genes: ODC1, POSTN, ASPA and IGF2BP3. Ultimately, three genes (ODC1, POSTN, ASPA) were verified to be dysregulated in the same pattern at both the mRNA and protein levels. Conclusions These data reveal insight into genes and molecular pathways mediating ESCC development and provide information potentially useful in designing novel therapeutic interventions for this tumor type. PMID:22280838

New screening strategy and analysis for identification of allosteric modulators for glucagon-like peptide-1 receptor using GLP-1 (9-36) amide.

PubMed

Nakane, Atsushi; Gotoh, Yusuke; Ichihara, Junji; Nagata, Hidetaka

2015-12-15

The glucagon-like peptide-1 receptor (GLP-1R) is an important physiologic regulator of insulin secretion and a major therapeutic target for diabetes mellitus. GLP-1 (7-36) amide (active form of GLP-1) is truncated to GLP-1 (9-36) amide, which has been described as a weak agonist of GLP-1R and the major form of GLP-1 in the circulation. New classes of positive allosteric modulators (PAMs) for GLP-1R may offer improved therapeutic profiles. To identify these new classes, we developed novel and robust primary and secondary high-throughput screening (HTS) systems in which PAMs were identified to enhance the GLP-1R signaling induced by GLP-1 (9-36) amide. Screening enabled identification of two compounds, HIT-465 and HIT-736, which possessed new patterns of modulation of GLP-1R. We investigated the ability of these compounds to modify GLP-1R signaling enhanced GLP-1 (9-36) amide- and/or GLP-1 (7-36) amide-mediated cyclic adenosine monophosphate (cAMP) accumulation. These compounds also had unique profiles with regard to allosteric modulation of multiple downstream signaling (PathHunter β-arrestin signaling, PathHunter internalization signaling, microscopy-based internalization assay). We found allosteric modulation patterns to be obviously different among HIT-465, HIT-736, and Novo Nordisk compound 2. This work may enable the design of new classes of drug candidates by targeting modulation of GLP-1 (7-36) amide and GLP-1 (9-36) amide. Copyright © 2015 Elsevier Inc. All rights reserved.

Detection of MET amplification in gastroesophageal tumor specimens using IQFISH.

PubMed

Jørgensen, Jan Trøst; Nielsen, Karsten Bork; Mollerup, Jens; Jepsen, Anna; Go, Ning

2017-12-01

The gene mesenchymal epithelial transition factor ( MET ) is a proto-oncogene that encodes a transmembrane receptor with intrinsic tyrosine kinase activity known as Met or cMet. MET is found to be amplified in several human cancers including gastroesophageal cancer. Here we report the MET amplification prevalence data from 159 consecutive tumor specimens from patients with gastric (G), gastroesophageal junction (GEJ) and esophageal (E) adenocarcinoma, using a novel fluorescence in situ hybridization (FISH) assay, MET /CEN-7 IQFISH Probe Mix [an investigational use only (IUO) assay]. MET amplification was defined as a MET /CEN-7 ratio ≥2.0. Furthermore, the link between the MET signal distribution and amplification status was investigated. The prevalence of MET amplification was found to be 6.9%. The FISH assay demonstrated a high inter-observer reproducibility. The inter-observer results showed a 100% overall agreement with respect to the MET status (amplified/non-amplified). The inter-observer CV was estimated to 11.8% (95% CI: 10.2-13.4). For the signal distribution, the inter-observer agreement was reported to be 98.7%. We also report an association of MET amplification and a unique signal distribution pattern in the G/GEJ/E tumor specimens. We found that the prevalence of MET amplification was markedly higher in tumors specimens with a heterogeneous (66.7%) versus homogeneous (2.0%) signal distribution. Furthermore, specimens with a heterogeneous signal distribution had a statically significantly higher median MET /CEN-7 ratio (2.35 versus 1.04; P<0.0001). The novel FISH assay showed a high inter-observer reproducibility both with respect to amplification status and signal distribution. Based on the finding in the study it is suggested that MET amplification mainly is associated with tumor cells that is represented by a heterogonous growth pattern.

Category representations in the brain are both discretely localized and widely distributed.

PubMed

Shehzad, Zarrar; McCarthy, Gregory

2018-06-01

Whether category information is discretely localized or represented widely in the brain remains a contentious issue. Initial functional MRI studies supported the localizationist perspective that category information is represented in discrete brain regions. More recent fMRI studies using machine learning pattern classification techniques provide evidence for widespread distributed representations. However, these latter studies have not typically accounted for shared information. Here, we find strong support for distributed representations when brain regions are considered separately. However, localized representations are revealed by using analytical methods that separate unique from shared information among brain regions. The distributed nature of shared information and the localized nature of unique information suggest that brain connectivity may encourage spreading of information but category-specific computations are carried out in distinct domain-specific regions. NEW & NOTEWORTHY Whether visual category information is localized in unique domain-specific brain regions or distributed in many domain-general brain regions is hotly contested. We resolve this debate by using multivariate analyses to parse functional MRI signals from different brain regions into unique and shared variance. Our findings support elements of both models and show information is initially localized and then shared among other regions leading to distributed representations being observed.

A Repeat Look at Repeating Patterns

ERIC Educational Resources Information Center

Markworth, Kimberly A.

2016-01-01

A "repeating pattern" is a cyclical repetition of an identifiable core. Children in the primary grades usually begin pattern work with fairly simple patterns, such as AB, ABC, or ABB patterns. The unique letters represent unique elements, whereas the sequence of letters represents the core that is repeated. Based on color, shape,…

Transcriptome analysis of the painted lady butterfly, Vanessa cardui during wing color pattern development.

PubMed

Connahs, Heidi; Rhen, Turk; Simmons, Rebecca B

2016-03-31

Butterfly wing color patterns are an important model system for understanding the evolution and development of morphological diversity and animal pigmentation. Wing color patterns develop from a complex network composed of highly conserved patterning genes and pigmentation pathways. Patterning genes are involved in regulating pigment synthesis however the temporal expression dynamics of these interacting networks is poorly understood. Here, we employ next generation sequencing to examine expression patterns of the gene network underlying wing development in the nymphalid butterfly, Vanessa cardui. We identified 9, 376 differentially expressed transcripts during wing color pattern development, including genes involved in patterning, pigmentation and gene regulation. Differential expression of these genes was highest at the pre-ommochrome stage compared to early pupal and late melanin stages. Overall, an increasing number of genes were down-regulated during the progression of wing development. We observed dynamic expression patterns of a large number of pigment genes from the ommochrome, melanin and also pteridine pathways, including contrasting patterns of expression for paralogs of the yellow gene family. Surprisingly, many patterning genes previously associated with butterfly pattern elements were not significantly up-regulated at any time during pupation, although many other transcription factors were differentially expressed. Several genes involved in Notch signaling were significantly up-regulated during the pre-ommochrome stage including slow border cells, bunched and pebbles; the function of these genes in the development of butterfly wings is currently unknown. Many genes involved in ecdysone signaling were also significantly up-regulated during early pupal and late melanin stages and exhibited opposing patterns of expression relative to the ecdysone receptor. Finally, a comparison across four butterfly transcriptomes revealed 28 transcripts common to all four species that have no known homologs in other metazoans. This study provides a comprehensive list of differentially expressed transcripts during wing development, revealing potential candidate genes that may be involved in regulating butterfly wing patterns. Some differentially expressed genes have no known homologs possibly representing genes unique to butterflies. Results from this study also indicate that development of nymphalid wing patterns may arise not only from melanin and ommochrome pigments but also the pteridine pigment pathway.

Short-term forecasting of urban rail transit ridership based on ARIMA and wavelet decomposition

NASA Astrophysics Data System (ADS)

Wang, Xuemei; Zhang, Ning; Chen, Ying; Zhang, Yunlong

2018-05-01

Due to different functions and land use types, there are significant differences in ridership patterns among different urban rail transit stations. Considering the characteristics of different ridership and coping with the uncertainty, periodical and stochastic natures of short-term passenger flow, and this paper proposes a novel hybrid methodology that combines the autoregressive integrated moving average (ARIMA) model and wavelet decomposition, which has strong strengths in signal processing, to short-term ridership forecasting. The seasonal ARIMA is used to represent the relatively stable and regular ridership patterns while the wavelet decomposition is used to capture the stochastic or sometimes drastic changing characteristics of ridership patterns. The inclusion of wavelet decomposition and reconstruction provides the hybrid model with a unique strength in capturing sudden change in ridership patterns associated with certain rail stations. The case study is carried out by analyzing real ridership data of Metro Line 1 in Nanjing, China. The experimental results indicate that the hybrid method is superior to the individual ARIMA model for all ridership patterns, but particularly advantageous in predicting ridership at stations often associated with sudden pattern changes due to special events.

Practical relevance of pattern uniqueness in forensic science.

PubMed

Jayaprakash, Paul T

2013-09-10

Uniqueness being unprovable, it has recently been argued that individualization in forensic science is irrelevant and, probability, as applied for DNA profiles, should be applied for all identifications. Critiques against uniqueness have omitted physical matching, a realistic and tangible individualization that supports uniqueness. Describing case examples illustrating pattern matches including physical matching, it is indicated that individualizations are practically relevant for forensic science as they establish facts on a definitive basis providing firm leads benefitting criminal investigation. As a tenet of forensic identification, uniqueness forms a fundamental paradigm relevant for individualization. Evidence on the indeterministic and stochastic causal pathways of characteristics in patterns available in the related fields of science sufficiently supports the proposition of uniqueness. Characteristics involved in physical matching and matching achieved in patterned evidence existing in the state of nature are not events amenable for counting; instead these are ensemble of visible units occupying the entire pattern area stretching the probability of re-occurrence of a verisimilitude pattern into infinity offering epistemic support to uniqueness. Observational methods are as respectable as instrumental or statistical methods since they are capable of generating results that are tangible and obviously valid as in physical matching. Applying the probabilistic interpretation used for DNA profiles to the other patterns would be unbefitting since these two are disparate, the causal pathways of the events, the loci, in the manipulated DNA profiles being determinable. While uniqueness enables individualizations, it does not vouch for eliminating errors. Instead of dismissing uniqueness and individualization, accepting errors as human or system failures and seeking remedial measures would benefit forensic science practice and criminal investigation. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

The Network Spinal Wave as a Central Pattern Generator.

PubMed

Senzon, Simon A; Epstein, Donald M; Lemberger, Daniel

2016-07-01

This article explains the research on a unique spinal wave visibly observed in association with network spinal analysis care. Since 1997, the network wave has been studied using surface electromyography (sEMG), characterized mathematically, and determined to be a unique and repeatable phenomenon. The authors provide a narrative review of the research and a context for the network wave's development. The sEMG research demonstrates that the movement of the musculature of the spine during the wave phenomenon is electromagnetic and mechanical. The changes running along the spine were characterized mathematically at three distinct levels of care. Additionally, the wave has the mathematical properties of a central pattern generator (CPG). The network wave may be the first CPG discovered in the spine unrelated to locomotion. The mathematical characterization of the signal also demonstrates coherence at a distance between the sacral to cervical spine. According to mathematical engineers, based on studies conducted a decade apart, the wave itself is a robust phenomenon and the detection methods for this coherence may represent a new measure for central nervous system health. This phenomenon has implications for recovery from spinal cord injury and for reorganizational healing development.

The Network Spinal Wave as a Central Pattern Generator

PubMed Central

Epstein, Donald M.; Lemberger, Daniel

2016-01-01

Abstract Objectives: This article explains the research on a unique spinal wave visibly observed in association with network spinal analysis care. Since 1997, the network wave has been studied using surface electromyography (sEMG), characterized mathematically, and determined to be a unique and repeatable phenomenon. Methods: The authors provide a narrative review of the research and a context for the network wave's development. Results: The sEMG research demonstrates that the movement of the musculature of the spine during the wave phenomenon is electromagnetic and mechanical. The changes running along the spine were characterized mathematically at three distinct levels of care. Additionally, the wave has the mathematical properties of a central pattern generator (CPG). Conclusions: The network wave may be the first CPG discovered in the spine unrelated to locomotion. The mathematical characterization of the signal also demonstrates coherence at a distance between the sacral to cervical spine. According to mathematical engineers, based on studies conducted a decade apart, the wave itself is a robust phenomenon and the detection methods for this coherence may represent a new measure for central nervous system health. This phenomenon has implications for recovery from spinal cord injury and for reorganizational healing development. PMID:27243963

Seasonal Abscisic Acid Signal and a Basic Leucine Zipper Transcription Factor, DkbZIP5, Regulate Proanthocyanidin Biosynthesis in Persimmon Fruit1[C][W][OA

PubMed Central

Akagi, Takashi; Katayama-Ikegami, Ayako; Kobayashi, Shozo; Sato, Akihiko; Kono, Atsushi; Yonemori, Keizo

2012-01-01

Proanthocyanidins (PAs) are secondary metabolites that contribute to plant protection and crop quality. Persimmon (Diospyros kaki) has a unique characteristic of accumulating large amounts of PAs, particularly in its fruit. Normal astringent-type and mutant nonastringent-type fruits show different PA accumulation patterns depending on the seasonal expression patterns of DkMyb4, which is a Myb transcription factor (TF) regulating many PA pathway genes in persimmon. In this study, attempts were made to identify the factors involved in DkMyb4 expression and the resultant PA accumulation in persimmon fruit. Treatment with abscisic acid (ABA) and an ABA biosynthesis inhibitor resulted in differential changes in the expression patterns of DkMyb4 and PA biosynthesis in astringent-type and nonastringent-type fruits depending on the development stage. To obtain an ABA-signaling TF, we isolated a full-length basic leucine zipper (bZIP) TF, DkbZIP5, which is highly expressed in persimmon fruit. We also showed that ectopic DkbZIP5 overexpression in persimmon calluses induced the up-regulation of DkMyb4 and the resultant PA biosynthesis. In addition, a detailed molecular characterization using the electrophoretic mobility shift assay and transient reporter assay indicated that DkbZIP5 recognized ABA-responsive elements in the promoter region of DkMyb4 and acted as a direct regulator of DkMyb4 in an ABA-dependent manner. These results suggest that ABA signals may be involved in PA biosynthesis in persimmon fruit via DkMyb4 activation by DkbZIP5. PMID:22190340

Analysis of the acoustic spectral signature of prosthetic heart valves in patients experiencing atrial fibrillation

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

Scott, D.D.; Jones, H.E.

1994-05-06

Prosthetic heart valves have increased the life span of many patients with life threatening heart conditions. These valves have proven extremely reliable adding years to what would have been weeks to a patient`s life. Prosthetic valves, like the heart however, can suffer from this constant work load. A small number of valves have experienced structural fractures of the outlet strut due to fatigue. To study this problem a non-intrusive method to classify valves has been developed. By extracting from an acoustic signal the opening sounds which directly contain information from the outlet strut and then developing features which are suppliedmore » to an adaptive classification scheme (neural network) the condition of the valve can be determined. The opening sound extraction process has proved to be a classification problem itself. Due to the uniqueness of each heart and the occasional irregularity of the acoustic pattern it is often questionable as to the integrity of a given signal (beat), especially one occurring during an irregular beat pattern. A common cause of these irregular patterns is a condition known as atrial fibrillation, a prevalent arrhythmia among patients with prosthetic hear valves. Atrial fibrillation is suspected when the ECG shows no obvious P-waves. The atria do not contract and relax correctly to help contribute to ventricular filling during a normal cardiac cycle. Sometimes this leads to irregular patterns in the acoustic data. This study compares normal beat patterns to irregular patterns of the same heart. By analyzing the spectral content of the beats it can be determined whether or not these irregular patterns can contribute to the classification of a heart valve or if they should be avoided. The results have shown that the opening sounds which occur during irregular beat patterns contain the same spectral information as the opening which occur during a normal beat pattern of the same heart and these beats can be used for classification.« less

G-protein coupled receptor expression patterns delineate medulloblastoma subgroups

PubMed Central

2013-01-01

Background Medulloblastoma is the most common malignant brain tumor in children. Genetic profiling has identified four principle tumor subgroups; each subgroup is characterized by different initiating mutations, genetic and clinical profiles, and prognoses. The two most well-defined subgroups are caused by overactive signaling in the WNT and SHH mitogenic pathways; less is understood about Groups 3 and 4 medulloblastoma. Identification of tumor subgroup using molecular classification is set to become an important component of medulloblastoma diagnosis and staging, and will likely guide therapeutic options. However, thus far, few druggable targets have emerged. G-protein coupled receptors (GPCRs) possess characteristics that make them ideal targets for molecular imaging and therapeutics; drugs targeting GPCRs account for 30-40% of all current pharmaceuticals. While expression patterns of many proteins in human medulloblastoma subgroups have been discerned, the expression pattern of GPCRs in medulloblastoma has not been investigated. We hypothesized that analysis of GPCR expression would identify clear subsets of medulloblastoma and suggest distinct GPCRs that might serve as molecular targets for both imaging and therapy. Results Our study found that medulloblastoma tumors fall into distinct clusters based solely on GPCR expression patterns. Normal cerebellum clustered separately from the tumor samples. Further, two of the tumor clusters correspond with high fidelity to the WNT and SHH subgroups of medulloblastoma. Distinct over-expressed GPCRs emerge; for example, LGR5 and GPR64 are significantly and uniquely over-expressed in the WNT subgroup of tumors, while PTGER4 is over-expressed in the SHH subgroup. Uniquely under-expressed GPCRs were also observed. Our key findings were independently validated using a large international dataset. Conclusions Our results identify GPCRs with potential to act as imaging and therapeutic targets. Elucidating tumorigenic pathways is a secondary benefit to identifying differential GPCR expression patterns in medulloblastoma tumors. PMID:24252460

Autophagic control of RLR signaling

PubMed Central

Tal, Michal Caspi; Iwasaki, Akiko

2013-01-01

Innate immunity to viral infection is initiated within the infected cells through the recognition of unique viral signatures by pattern recognition receptors (PRRs) that mediate the induction of potent antiviral factor, type I interferons (IFNs). Infection with RNA viruses is recognized by the members of the retinoic acid inducible gene I (RIG-I)-like receptor (RLR) family in the cytosol. Our recent study demonstrates that IFN production in response to RNA viral ligands is increased in the absence of autophagy. The process of autophagy functions as an internal clean-up crew within the cell, shuttling damaged cellular organelles and long-lived proteins to the lysosomes for degradation. Our data show that the absence of autophagy leads to the amplification of RLR signaling in two ways. First, in the absence of autophagy, mitochondria accumulate within the cell leading to the build up of mitochondrial associated protein, IPS-1, a key signaling protein for RLRs. Second, damaged mitochondria that are not degraded in the absence of autophagy provide a source of reactive oxygen species (ROS), which amplify RLR signaling in Atg5 knockout cells. Our study provides the first link between ROS and cytosolic signaling mediated by the RLRs, and suggests the importance of autophagy in the regulation of signaling emanating from mitochondria. PMID:19571662

Mating behaviour of Pseudodiaptomus annandalei (Copepoda, Calanoida) in calm and turbulent waters

NASA Astrophysics Data System (ADS)

Lee, C. H.; Dahms, H. U.; Cheng, S. H.; Souissi, S.; Schmitt, F. G.; Kumar, R.; Hwang, J. S.

2009-04-01

Behavioral observations of male copepods reveal that they commonly follow female copepods' footprints to find their mates. Female generated environmental signals are primarily of hydromechanical or chemical quality. The intensity of hydromechanical or chemical signals is affected by the hydrodynamic conditions which in turn may modulate a copepod's ability to sense signals in their search for mates in the aquatic environment. We studied the patterns and efficiency of the copepod Pseudodiaptomus annandalei to mate at still and turbulent water conditions during day and night and in different shape and volume experimental containers. The ability of courtship in P. annandalei was recorded to be a negative function of hydromechanical disturbances as the successful mating was observed in still water only. Under turbulent condition males were not able to track a female properly. We records in the present study that both, sequential and simultaneous taxi mechanisms are used by the male P. annandalei to follow either hydromechanic or chemical signals. Our results further reveal that males follow a signal more accurately characterized as a trail. The ability of P. annandalei males to track a three-dimensional trail appears unique, and possibly depends on the persistence of fluid-borne hydromechanical or chemical signals created in low Reynolds number hydrodynamic regimes. Keywords: Mating behavior, Turbulence, Flow, Hydrodynamic conditions

Stem Cells, Patterning and Regeneration in Planarians: Self-Organization at the Organismal Scale.

PubMed

Rink, Jochen C

2018-01-01

The establishment of size and shape remains a fundamental challenge in biological research that planarian flatworms uniquely epitomize. Planarians can regenerate complete and perfectly proportioned animals from tiny and arbitrarily shaped tissue pieces; they continuously renew all organismal cell types from abundant pluripotent stem cells, yet maintain shape and anatomy in the face of constant turnover; they grow when feeding and literally degrow when starving, while scaling form and function over as much as a 40-fold range in body length or an 800-fold change in total cell numbers. This review provides a broad overview of the current understanding of the planarian stem cell system, the mechanisms that pattern the planarian body plan and how the interplay between patterning signals and cell fate choices orchestrates regeneration. What emerges is a conceptual framework for the maintenance and regeneration of the planarian body plan on basis of the interplay between pluripotent stem cells and self-organizing patterns and further, the general utility of planarians as model system for the mechanistic basis of size and shape.

Regulation of cell-fate determination in Dictyostelium.

PubMed

Brown, J M; Firtel, R A

1999-12-15

A key step in the development of all multicellular organisms is the differentiation of specialized cell types. The eukaryotic microorganism Dictyostelium discoideum provides a unique experimental system for studying cell-type determination and spatial patterning in a developing multicellular organism. Unlike metazoans, which become multicellular by undergoing many rounds of cell division after fertilization of an egg, the social amoeba Dictyostelium achieves multicellularity by the aggregation of approximately 10(5) cells in response to nutrient depletion. Following aggregation, cell-type differentiation and morphogenesis result in a multicellular organism with only a few cell types that exhibit a defined patterning along the anterior-posterior axis of the organism. Analysis of the mechanisms that control these processes is facilitated by the relative simplicity of Dictyostelium development and the availability of molecular, genetic, and cell biological tools. Interestingly, analysis has shown that many molecules that play integral roles in the development of higher eukaryotes, such as PKA, STATs, and GSK-3, are also essential for cell-type differentiation and patterning in Dictyostelium. The role of these and other signaling pathways in the induction, maintenance, and patterning of cell types during Dictyostelium development is discussed.

Assessing D-Region Ionospheric Electron Densities with Transionospheric VLF Signals

NASA Astrophysics Data System (ADS)

Worthington, E. R.; Cohen, M.

2016-12-01

Very Low Frequency (VLF, 3-30 kHz) electromagnetic radiation emitted from ground-based sources, such as VLF transmitters or lightning strokes, is generally confined between the Earth's surface and the base of the ionosphere. These boundaries result in waveguide-like propagation modes that travel away from the source, often over great distances. In the vicinity of the source, a unique interference pattern exists that is largely determined by the D-region of the ionosphere which forms the upper boundary. A small portion of this VLF radiation escapes the ionosphere allowing the waveguide interference pattern to be observable to satellites in low-earth orbit (LEO). Techniques for estimating D-region electron densities using VLF satellite measurements are presented. These techniques are then validated using measurements taken by the satellite DEMETER. During its six-year mission, DEMETER completed hundreds of passes above well-characterized VLF transmitters while taking measurements of electric and magnetic field strengths. The waveguide interference pattern described above is clearly visible in these measurements, and features from the interference pattern are used to derive D-region electron density profiles.

Stripes and belly-spots – a review of pigment cell morphogenesis in vertebrates

PubMed Central

Kelsh, Robert N.; Harris, Melissa L.; Colanesi, Sarah; Erickson, Carol A.

2009-01-01

Pigment patterns in the integument have long-attracted attention from both scientists and non-scientists alike since their natural attractiveness combines with their excellence as models for the general problem of pattern formation. Pigment cells are formed from the neural crest and must migrate to reach their final locations. In this review, we focus on our current understanding of mechanisms underlying the control of pigment cell migration and patterning in diverse vertebrates. The model systems discussed here –chick, mouse, and zebrafish – each provide unique insights into the major morphogenetic events driving pigment pattern formation. In birds and mammals, melanoblasts must be specified before they can migrate on the dorsolateral pathway. Transmembrane receptors involved in guiding them onto this route include EphB2 and Ednrb2 in chick, and Kit in mouse. Terminal migration depends, in part, upon extracellular matrix reorganization by ADAMTS20. Invasion of the ectoderm, especially into the feather germ and hair follicles, requires specific signals that are beginning to be characterized. We summarize our current understanding of the mechanisms regulating melanoblast number and organization in the epidermis. We note the apparent differences in pigment pattern formation in poikilothermic vertebrates when compared with birds and mammals. With more pigment cell types, migration pathways are more complex and largely unexplored; nevertheless, a role for Kit signaling in melanophore migration is clear and indicates that at least some patterning mechanisms may be highly conserved. We summarize the multiple factors thought to contribute to zebrafish embryonic pigment pattern formation, highlighting a recent study identifying Sdf1a as one factor crucial for regulation of melanophore positioning. Finally, we discuss the mechanisms generating a second, metamorphic pigment pattern in adult fish, emphasizing recent studies strengthening the evidence that undifferentiated progenitor cells play a major role in generating adult pigment cells. PMID:18977309

Astronomical component estimation (ACE v.1) by time-variant sinusoidal modeling

NASA Astrophysics Data System (ADS)

Sinnesael, Matthias; Zivanovic, Miroslav; De Vleeschouwer, David; Claeys, Philippe; Schoukens, Johan

2016-09-01

Accurately deciphering periodic variations in paleoclimate proxy signals is essential for cyclostratigraphy. Classical spectral analysis often relies on methods based on (fast) Fourier transformation. This technique has no unique solution separating variations in amplitude and frequency. This characteristic can make it difficult to correctly interpret a proxy's power spectrum or to accurately evaluate simultaneous changes in amplitude and frequency in evolutionary analyses. This drawback is circumvented by using a polynomial approach to estimate instantaneous amplitude and frequency in orbital components. This approach was proven useful to characterize audio signals (music and speech), which are non-stationary in nature. Paleoclimate proxy signals and audio signals share similar dynamics; the only difference is the frequency relationship between the different components. A harmonic-frequency relationship exists in audio signals, whereas this relation is non-harmonic in paleoclimate signals. However, this difference is irrelevant for the problem of separating simultaneous changes in amplitude and frequency. Using an approach with overlapping analysis frames, the model (Astronomical Component Estimation, version 1: ACE v.1) captures time variations of an orbital component by modulating a stationary sinusoid centered at its mean frequency, with a single polynomial. Hence, the parameters that determine the model are the mean frequency of the orbital component and the polynomial coefficients. The first parameter depends on geologic interpretations, whereas the latter are estimated by means of linear least-squares. As output, the model provides the orbital component waveform, either in the depth or time domain. Uncertainty analyses of the model estimates are performed using Monte Carlo simulations. Furthermore, it allows for a unique decomposition of the signal into its instantaneous amplitude and frequency. Frequency modulation patterns reconstruct changes in accumulation rate, whereas amplitude modulation identifies eccentricity-modulated precession. The functioning of the time-variant sinusoidal model is illustrated and validated using a synthetic insolation signal. The new modeling approach is tested on two case studies: (1) a Pliocene-Pleistocene benthic δ18O record from Ocean Drilling Program (ODP) Site 846 and (2) a Danian magnetic susceptibility record from the Contessa Highway section, Gubbio, Italy.

Vibration Signaling in Mobile Devices for Emergency Alerting: A Study with Deaf Evaluators

ERIC Educational Resources Information Center

Harkins, Judith; Tucker, Paula E.; Williams, Norman; Sauro, Jeff

2010-01-01

In the United States, a nationwide Commercial Mobile Alert Service (CMAS) is being planned to alert cellular mobile device subscribers to emergencies occurring near the location of the mobile device. The plan specifies a unique audio attention signal as well as a unique vibration attention signal (for mobile devices set to vibrate) to identify…

Robot Comedy Lab: experimenting with the social dynamics of live performance

PubMed Central

Katevas, Kleomenis; Healey, Patrick G. T.; Harris, Matthew Tobias

2015-01-01

The success of live comedy depends on a performer's ability to “work” an audience. Ethnographic studies suggest that this involves the co-ordinated use of subtle social signals such as body orientation, gesture, gaze by both performers and audience members. Robots provide a unique opportunity to test the effects of these signals experimentally. Using a life-size humanoid robot, programmed to perform a stand-up comedy routine, we manipulated the robot's patterns of gesture and gaze and examined their effects on the real-time responses of a live audience. The strength and type of responses were captured using SHORE™computer vision analytics. The results highlight the complex, reciprocal social dynamics of performer and audience behavior. People respond more positively when the robot looks at them, negatively when it looks away and performative gestures also contribute to different patterns of audience response. This demonstrates how the responses of individual audience members depend on the specific interaction they're having with the performer. This work provides insights into how to design more effective, more socially engaging forms of robot interaction that can be used in a variety of service contexts. PMID:26379585

Uric Acid Spherulites in the Reflector Layer of Firefly Light Organ

PubMed Central

Goh, King-Siang; Sheu, Hwo-Shuenn; Hua, Tzu-En; Kang, Mei-Hua; Li, Chia-Wei

2013-01-01

Background In firefly light organs, reflector layer is a specialized tissue which is believed to play a key role for increasing the bioluminescence intensity through reflection. However, the nature of this unique tissue remains elusive. In this report, we investigated the role, fine structure and nature of the reflector layer in the light organ of adult Luciola cerata. Principal Findings Our results indicated that the reflector layer is capable of reflecting bioluminescence, and contains abundant uric acid. Electron microscopy (EM) demonstrated that the cytosol of the reflector layer's cells is filled with densely packed spherical granules, which should be the uric acid granules. These granules are highly regular in size (∼700 nm in diameter), and exhibit a radial internal structure. X-ray diffraction (XRD) analyses revealed that an intense single peak pattern with a d-spacing value of 0.320 nm is specifically detected in the light organ, and is highly similar to the diffraction peak pattern and d-spacing value of needle-formed crystals of monosodium urate monohydrate. However, the molar ratio evaluation of uric acid to various cations (K+, Na+, Ca2+ and Mg2+) in the light organ deduced that only a few uric acid molecules were in the form of urate salts. Thus, non-salt uric acid should be the source of the diffraction signal detected in the light organ. Conclusions In the light organ, the intense single peak diffraction signal might come from a unique needle-like uric acid form, which is different from other known structures of non-salt uric acid form. The finding of a radial structure in the granules of reflector layer implies that the spherical uric acid granules might be formed by the radial arrangement of needle-formed packing matter. PMID:23441187

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

PubMed Central

Shen, Yingjia; Ji, Guoli; Haas, Brian J.; Wu, Xiaohui; Zheng, Jianti; Reese, Greg J.; Li, Qingshun Quinn

2008-01-01

The position of a poly(A) site of eukaryotic mRNA is determined by sequence signals in pre-mRNA and a group of polyadenylation factors. To reveal rice poly(A) signals at a genome level, we constructed a dataset of 55 742 authenticated poly(A) sites and characterized the poly(A) signals. This resulted in identifying the typical tripartite cis-elements, including FUE, NUE and CE, as previously observed in Arabidopsis. The average size of the 3′-UTR was 289 nucleotides. When mapped to the genome, however, 15% of these poly(A) sites were found to be located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site (excluding microheterogeneity sites), and 13% had four or more poly(A) sites. About 4% of the analyzed genes possessed alternative poly(A) sites at their introns, 5′-UTRs, or protein coding regions. The authenticity of these alternative poly(A) sites was partially confirmed using MPSS data. Analysis of nucleotide profile and signal patterns indicated that there may be a different set of poly(A) signals for those poly(A) sites found in the coding regions. Based on the features of rice poly(A) signals, an updated algorithm termed PASS-Rice was designed to predict poly(A) sites. PMID:18411206

A Space-Based Observational Strategy for Hydrogen Cosmology Using Dynamic Polarimetry and Pattern Recognition

NASA Astrophysics Data System (ADS)

Burns, Jack O.; Nhan, Bang; Bradley, Richard F.; Tauscher, Keith A.; Rapetti, David; Switzer, Eric

2018-06-01

The redshifted 21-cm monopole is expected to be a powerful probe of the epoch of the first stars and galaxies (10 < z < 80). The global 21-cm signal is sensitive to the thermal and ionization state of hydrogen gas and thus provides a tracer of sources of energetic photons—primarily hot stars and accreting black holes—which ionize and heat the high redshift intergalactic medium. In this talk, we present a strategy for observations of the global spectrum with a satellite placed in low lunar orbit, performing night-time 10-50 MHz observations, while on the farside to avoid terrestrial radio frequency interference, ionospheric corruption, and solar radio emissions. The primary challenge is observing a relatively weak signal in the presence of a strong galactic/extragalactic foreground. We employ a new technique using dynamic or projection-induced polarimetry that separates the polarized foreground from the unpolarized 21-cm signal. Initial results from a ground-based prototype called the Cosmic Twilight Polarimeter will be described which tentatively reveal the presence of the expected polarization signature from the foreground. Dynamic polarimetry, when combined with sophisticated pattern recognition techniques based on training sets, machine learning, and statistical information criteria offer promise for precise extraction of the 21-cm spectrum. We describe a new SmallSat mission concept, the Dark Ages Polarimetry Pathfinder (DAPPer), that will utilize these novel approaches for extending the recent detection of a 78 MHz signal down to lower frequencies where we can uniquely probe evidence for the first stars and dark matter.

Multi-frequency communication system and method

DOEpatents

Carrender, Curtis Lee; Gilbert, Ronald W.

2004-06-01

A multi-frequency RFID remote communication system is provided that includes a plurality of RFID tags configured to receive a first signal and to return a second signal, the second signal having a first frequency component and a second frequency component, the second frequency component including data unique to each remote RFID tag. The system further includes a reader configured to transmit an interrogation signal and to receive remote signals from the tags. A first signal processor, preferably a mixer, removes an intermediate frequency component from the received signal, and a second processor, preferably a second mixer, analyzes the IF frequency component to output data that is unique to each remote tag.

Hot-blooded singers: endothermy facilitates crepuscular signaling in African platypleurine cicadas (Hemiptera: Cicadidae: Platypleura spp.).

PubMed

Sanborn, Allen F; Villet, Martin H; Phillips, Polly K

2003-07-01

The cicada genus Platypleura has a wide distribution across Africa and southern Asia. We describe endothermic thermoregulation in four South African species that show crepuscular signaling behavior. This is the first evidence of thermoregulation in platypleurine cicadas. Field measurements of body temperature ( T(b)) show that these animals regulate T(b) through endogenous heat production. Maximum T(b) measured was 22.1 degrees C above ambient temperature during calling activity at dusk. The mean T(b) during dusk activity did not differ from the mean T(b) during diurnal activity. A unique behavior for cicadas, a temperature-dependent telescoping pulsation of the abdomen, was observed in the laboratory during endogenous warm-up. This behavior is part of a unique method of heat generation in endothermic cicadas. Males generally call from trunks and branches within the canopy and appear to use endothermy even when the sun is available to elevate T(b). Endothermy may provide the cicadas with the advantage of decreasing predation and acoustic competition by permitting calling from perches that most complement their cryptic coloration patterns and that ectotherms cannot use due to thermal constraints. In addition, endothermy may permit calling activity during crepuscular hours when atmospheric conditions are optimal for acoustic communication and predation risks are minimal.

Conditional clustering of temporal expression profiles

PubMed Central

Wang, Ling; Montano, Monty; Rarick, Matt; Sebastiani, Paola

2008-01-01

Background Many microarray experiments produce temporal profiles in different biological conditions but common cluster techniques are not able to analyze the data conditional on the biological conditions. Results This article presents a novel technique to cluster data from time course microarray experiments performed across several experimental conditions. Our algorithm uses polynomial models to describe the gene expression patterns over time, a full Bayesian approach with proper conjugate priors to make the algorithm invariant to linear transformations, and an iterative procedure to identify genes that have a common temporal expression profile across two or more experimental conditions, and genes that have a unique temporal profile in a specific condition. Conclusion We use simulated data to evaluate the effectiveness of this new algorithm in finding the correct number of clusters and in identifying genes with common and unique profiles. We also use the algorithm to characterize the response of human T cells to stimulations of antigen-receptor signaling gene expression temporal profiles measured in six different biological conditions and we identify common and unique genes. These studies suggest that the methodology proposed here is useful in identifying and distinguishing uniquely stimulated genes from commonly stimulated genes in response to variable stimuli. Software for using this clustering method is available from the project home page. PMID:18334028

Somatosensory responses in a human motor cortex

PubMed Central

Donoghue, John P.; Hochberg, Leigh R.

2013-01-01

Somatic sensory signals provide a major source of feedback to motor cortex. Changes in somatosensory systems after stroke or injury could profoundly influence brain computer interfaces (BCI) being developed to create new output signals from motor cortex activity patterns. We had the unique opportunity to study the responses of hand/arm area neurons in primary motor cortex to passive joint manipulation in a person with a long-standing brain stem stroke but intact sensory pathways. Neurons responded to passive manipulation of the contralateral shoulder, elbow, or wrist as predicted from prior studies of intact primates. Thus fundamental properties and organization were preserved despite arm/hand paralysis and damage to cortical outputs. The same neurons were engaged by attempted arm actions. These results indicate that intact sensory pathways retain the potential to influence primary motor cortex firing rates years after cortical outputs are interrupted and may contribute to online decoding of motor intentions for BCI applications. PMID:23343902

A signal processing framework for simultaneous detection of multiple environmental contaminants

NASA Astrophysics Data System (ADS)

Chakraborty, Subhadeep; Manahan, Michael P.; Mench, Matthew M.

2013-11-01

The possibility of large-scale attacks using chemical warfare agents (CWAs) has exposed the critical need for fundamental research enabling the reliable, unambiguous and early detection of trace CWAs and toxic industrial chemicals. This paper presents a unique approach for the identification and classification of simultaneously present multiple environmental contaminants by perturbing an electrochemical (EC) sensor with an oscillating potential for the extraction of statistically rich information from the current response. The dynamic response, being a function of the degree and mechanism of contamination, is then processed with a symbolic dynamic filter for the extraction of representative patterns, which are then classified using a trained neural network. The approach presented in this paper promises to extend the sensing power and sensitivity of these EC sensors by augmenting and complementing sensor technology with state-of-the-art embedded real-time signal processing capabilities.

The signaling helix: a common functional theme in diverse signaling proteins

PubMed Central

Anantharaman, Vivek; Balaji, S; Aravind, L

2006-01-01

Background The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood. Results Using sensitive sequence analysis methods we identify a conserved helical segment of around 40 residues in a wide range of signaling proteins, including numerous sensor histidine kinases such as Sln1p, and receptor guanylyl cyclases such as the atrial natriuretic peptide receptor and nitric oxide receptors. We term this helical segment the signaling (S)-helix and present evidence that it forms a novel parallel coiled-coil element, distinct from previously known helical segments in signaling proteins, such as the Dimerization-Histidine phosphotransfer module of histidine kinases, the intra-cellular domains of the chemotaxis receptors, inter-GAF domain helical linkers and the α-helical HAMP module. Analysis of domain architectures allowed us to reconstruct the domain-neighborhood graph for the S-helix, which showed that the S-helix almost always occurs between two signaling domains. Several striking patterns in the domain neighborhood of the S-helix also became evident from the graph. It most often separates diverse N-terminal sensory domains from various C-terminal catalytic signaling domains such as histidine kinases, cNMP cyclase, PP2C phosphatases, NtrC-like AAA+ ATPases and diguanylate cyclases. It might also occur between two sensory domains such as PAS domains and occasionally between a DNA-binding HTH domain and a sensory domain. The sequence conservation pattern of the S-helix revealed the presence of a unique constellation of polar residues in the dimer-interface positions within the central heptad of the coiled-coil formed by the S-helix. Conclusion Combining these observations with previously reported mutagenesis studies on different S-helix-containing proteins we suggest that it functions as a switch that prevents constitutive activation of linked downstream signaling domains. However, upon occurrence of specific conformational changes due to binding of ligand or other sensory inputs in a linked upstream domain it transmits the signal to the downstream domain. Thus, the S-helix represents one of the most prevalent functional themes involved in the flow of signals between modules in diverse prokaryote-type multi-domain signaling proteins. Reviewers This article was reviewed by Frank Eisenhaber, Arcady Mushegian and Sandor Pongor. PMID:16953892

Mechanical design in embryos: mechanical signalling, robustness and developmental defects.

PubMed

Davidson, Lance A

2017-05-19

Embryos are shaped by the precise application of force against the resistant structures of multicellular tissues. Forces may be generated, guided and resisted by cells, extracellular matrix, interstitial fluids, and how they are organized and bound within the tissue's architecture. In this review, we summarize our current thoughts on the multiple roles of mechanics in direct shaping, mechanical signalling and robustness of development. Genetic programmes of development interact with environmental cues to direct the composition of the early embryo and endow cells with active force production. Biophysical advances now provide experimental tools to measure mechanical resistance and collective forces during morphogenesis and are allowing integration of this field with studies of signalling and patterning during development. We focus this review on concepts that highlight this integration, and how the unique contributions of mechanical cues and gradients might be tested side by side with conventional signalling systems. We conclude with speculation on the integration of large-scale programmes of development, and how mechanical responses may ensure robust development and serve as constraints on programmes of tissue self-assembly.This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'. © 2017 The Author(s).

Determining Locations by Use of Networks of Passive Beacons

NASA Technical Reports Server (NTRS)

Okino, Clayton; Gray, Andrew; Jennings, Esther

2009-01-01

Networks of passive radio beacons spanning moderate-sized terrain areas have been proposed to aid navigation of small robotic aircraft that would be used to explore Saturn s moon Titan. Such networks could also be used on Earth to aid navigation of robotic aircraft, land vehicles, or vessels engaged in exploration or reconnaissance in situations or locations (e.g., underwater locations) in which Global Positioning System (GPS) signals are unreliable or unavailable. Prior to use, it would be necessary to pre-position the beacons at known locations that would be determined by use of one or more precise independent global navigation system(s). Thereafter, while navigating over the area spanned by a given network of passive beacons, an exploratory robot would use the beacons to determine its position precisely relative to the known beacon positions (see figure). If it were necessary for the robot to explore multiple, separated terrain areas spanned by different networks of beacons, the robot could use a long-haul, relatively coarse global navigation system for the lower-precision position determination needed during transit between such areas. The proposed method of precise determination of position of an exploratory robot relative to the positions of passive radio beacons is based partly on the principles of radar and partly on the principles of radio-frequency identification (RFID) tags. The robot would transmit radar-like signals that would be modified and reflected by the passive beacons. The distance to each beacon would be determined from the roundtrip propagation time and/or round-trip phase shift of the signal returning from that beacon. Signals returned from different beacons could be distinguished by means of their RFID characteristics. Alternatively or in addition, the antenna of each beacon could be designed to radiate in a unique pattern that could be identified by the navigation system. Also, alternatively or in addition, sets of identical beacons could be deployed in unique configurations such that the navigation system could identify their unique combinations of radio-frequency reflections as an alternative to leveraging the uniqueness of the RFID tags. The degree of dimensional accuracy would depend not only on the locations of the beacons but also on the number of beacon signals received, the number of samples of each signal, the motion of the robot, and the time intervals between samples. At one extreme, a single sample of the return signal from a single beacon could be used to determine the distance from that beacon and hence to determine that the robot is located somewhere on a sphere, the radius of which equals that distance and the center of which lies at the beacon. In a less extreme example, the three-dimensional position of the robot could be determined with fair precision from a single sample of the signal from each of three beacons. In intermediate cases, position estimates could be refined and/or position ambiguities could be resolved by use of supplementary readings of an altimeter and other instruments aboard the robot.

Half-precessional climate forcing of Indian Ocean monsoon dynamics on the East African equator

NASA Astrophysics Data System (ADS)

Verschuren, D.; Sinninghe Damste, J. S.; Moernaut, J.; Kristen, I.; Fagot, M.; Blaauw, M.; Haug, G. H.; Project Members, C.

2008-12-01

The EuroCLIMATE project CHALLACEA produced a detailed multi-proxy reconstruction of the climate history of equatorial East Africa, based on the sediment record of Lake Challa, a 4.2 km2, 92-m deep crater lake on the lower East slope of Mt. Kilimanjaro (Kenya/Tanzania). Relatively stable sedimentation dynamics over the past 25,000 years resulted in a unique combination of high temporal resolution, excellent radiometric (210Pb, 14C) age control, and confidence that recording parameters of the climatic proxy signals extracted from the sediment have remained constant through time. The equatorial (3 deg. S) location of our study site in East Africa, where seasonal migration of convective activity spans the widest latitude range worldwide, produced unique information on how varying rainfall contributions from the northeasterly and southeasterly Indian Ocean monsoons shaped regional climate history. The Challa proxy records for temperature (TEX86) and moisture balance (reflection-seismic stratigraphy and the BIT index of soil bacterial input) uniquely weave together tropical climate variability at orbital and shorter time scales. The temporal pattern of reconstructed moisture balance bears the clear signature of half- precessional insolation forcing of Indian Ocean monsoon dynamics, modified by northern-latitude influence on moisture-balance variation at millennial and century time scales. During peak glacial time (but not immediately before) and the Younger Dryas, NH ice sheet influences overrode local insolation influence on monsoon intensity. After the NH ice sheets had melted and a relatively stable interglacial temperature regime developed, precession-driven summer insolation became the dominant determinant of regional moisture balance, with anti-phased patterns of Holocene hydrological change in the northern and southern (sub)tropics, and a uniquely hybrid pattern on the East African equator. In the last 2-3000 years a series of multi-century droughts with links to high latitude climate variability exerted widespread influence across the African continent. In northern and western tropical Africa these drought episodes accentuated the late- Holocene drying trend; in southern tropical Africa they mitigated or aborted the trend to increasing monsoon rainfall prescribed by SH insolation forcing.

Cell signaling and transcription factor genes expressed during whole body regeneration in a colonial chordate.

PubMed

Rinkevich, Yuval; Rinkevich, Baruch; Reshef, Ram

2008-10-12

The restoration of adults from fragments of blood vessels in botryllid ascidians (termed whole body regeneration [WBR]) represents an inimitable event in the chordates, which is poorly understood on the mechanistic level. To elucidate mechanisms underlying this phenomenon, a subtracted EST library for early WBR stages was previously assembled, revealing 76 putative genes belonging to major signaling pathways, including Notch/Delta, JAK/STAT, protein kinases, nuclear receptors, Ras oncogene family members, G-Protein coupled receptor (GPCR) and transforming growth factor beta (TGF-beta) signaling. RT-PCR on selected transcripts documented specific up-regulation in only regenerating fragments, pointing to a broad activation of these signaling pathways at onset of WBR. The followed-up expression pattern of seven representative transcripts from JAK/STAT signaling (Bl-STAT), the Ras oncogene family (Bl-Rap1A, Bl-Rab-33), the protein kinase family (Bl-Mnk), Bl-Cnot, Bl-Slit and Bl-Bax inhibitor, revealed systemic and site specific activations during WBR in a sub-population of circulatory cells. WBR in the non-vertebrate chordate Botrylloides leachi is a multifaceted phenomenon, presided by a complex array of cell signaling and transcription factors. Above results, provide a first insight into the whole genome molecular machinery of this unique regeneration process, and reveal the broad participation of cell signaling and transcription factors in the process. While regeneration involves the participation of specific cell populations, WBR signals are systemically expressed at the organism level.

Candida glabrata's Genome Plasticity Confers a Unique Pattern of Expressed Cell Wall Proteins.

PubMed

López-Fuentes, Eunice; Gutiérrez-Escobedo, Guadalupe; Timmermans, Bea; Van Dijck, Patrick; De Las Peñas, Alejandro; Castaño, Irene

2018-06-05

Candida glabrata is the second most common cause of candidemia, and its ability to adhere to different host cell types, to microorganisms, and to medical devices are important virulence factors. Here, we consider three characteristics that confer extraordinary advantages to C. glabrata within the host. (1) C. glabrata has a large number of genes encoding for adhesins most of which are localized at subtelomeric regions. The number and sequence of these genes varies substantially depending on the strain, indicating that C. glabrata can tolerate high genomic plasticity; (2) The largest family of CWPs (cell wall proteins) is the EPA (epithelial adhesin) family of adhesins. Epa1 is the major adhesin and mediates adherence to epithelial, endothelial and immune cells. Several layers of regulation like subtelomeric silencing, cis- acting regulatory regions, activators, nutritional signaling, and stress conditions tightly regulate the expression of many adhesin-encoding genes in C. glabrata , while many others are not expressed. Importantly, there is a connection between acquired resistance to xenobiotics and increased adherence; (3) Other subfamilies of adhesins mediate adherence to Candida albicans , allowing C. glabrata to efficiently invade the oral epithelium and form robust biofilms. It is noteworthy that every C. glabrata strain analyzed presents a unique pattern of CWPs at the cell surface.

The Mid-Infrared Instrument for the James Webb Space Telescope, VIII: The MIRI Focal Plane System

NASA Astrophysics Data System (ADS)

Ressler, M. E.; Sukhatme, K. G.; Franklin, B. R.; Mahoney, J. C.; Thelen, M. P.; Bouchet, P.; Colbert, J. W.; Cracraft, Misty; Dicken, D.; Gastaud, R.; Goodson, G. B.; Eccleston, Paul; Moreau, V.; Rieke, G. H.; Schneider, Analyn

2015-07-01

We describe the layout and unique features of the focal plane system for MIRI. We begin with the detector array and its readout integrated circuit (combining the amplifier unit cells and the multiplexer), the electronics, and the steps by which the data collection is controlled and the output signals are digitized and delivered to the JWST spacecraft electronics system. We then discuss the operation of this MIRI data system, including detector readout patterns, operation of subarrays, and data formats. Finally, we summarize the performance of the system, including remaining anomalies that need to be corrected in the data pipeline.

Monitoring of cerebral hemodynamics and oxygenation by continuous-wave optical spectroscopy during asphyxia in newborn piglets

NASA Astrophysics Data System (ADS)

Stankovic, Miljan R.; Fujii, Alan M.; Kirby, Debra; Boas, David A.; Ntziachristos, Vasilis; Stubblefield, Phillip G.

1997-12-01

The present study demonstrated that optical variables HbT and SmcO2 can be used to monitor changes in cerebral hemodynamics and oxygenation during asphyxia. Unfortunately none of the individual optical variables alone could be used to monitor changes in cerebral hemodynamics and oxygenation under a variety of possible clinical circumstances. However, all variables together, forming patterns unique to the commonly occurring physiological conditions, might potentially serve as a `silver standard' to aid interpretations of optical signals in clinical settings where `gold standard' techniques are not available, i.g. in the human fetus and neonate.

Monitoring of cerebral hemodynamics and oxygenation by continuous-wave optical spectroscopy during asphyxia in newborn piglets

NASA Astrophysics Data System (ADS)

Stankovic, Miljan R.; Fujii, Alan M.; Kirby, Debra; Boas, David A.; Ntziachristos, Vasilis; Stubblefield, Phillip G.

1998-01-01

The present study demonstrated that optical variables HbT and SmcO2 can be used to monitor changes in cerebral hemodynamics and oxygenation during asphyxia. Unfortunately none of the individual optical variables alone could be used to monitor changes in cerebral hemodynamics and oxygenation under a variety of possible clinical circumstances. However, all variables together, forming patterns unique to the commonly occurring physiological conditions, might potentially serve as a `silver standard' to aid interpretations of optical signals in clinical settings where `gold standard' techniques are not available, i.g. in the human fetus and neonate.

Cross correlation anomaly detection system

NASA Technical Reports Server (NTRS)

Micka, E. Z. (Inventor)

1975-01-01

This invention provides a method for automatically inspecting the surface of an object, such as an integrated circuit chip, whereby the data obtained by the light reflected from the surface, caused by a scanning light beam, is automatically compared with data representing acceptable values for each unique surface. A signal output provided indicated of acceptance or rejection of the chip. Acceptance is based on predetermined statistical confidence intervals calculated from known good regions of the object being tested, or their representative values. The method can utilize a known good chip, a photographic mask from which the I.C. was fabricated, or a computer stored replica of each pattern being tested.

A preliminary investigation of bird classification by Doppler radar

NASA Technical Reports Server (NTRS)

Martinson, L. W.

1973-01-01

A preliminary study of the application of Doppler radar to the classification of birds is reported. The desirability for improvements in bird classification stems primarily from the hazards they present to jet aircraft in flight and in the vicinity of airports. A secondary need exists in the study of bird migration. The wing body and tail motion of a bird in flight reflect signals which, when analyzed properly present a signature of wing beat pattern which is unique for each bird species. Although the results of this investigation did not validate the feasibility of classifying bird species, they do indicate that a more thorough investigation is warranted. Certain gross characteristics such as wing beat rates, multiple bird patterns, and bird maneuverability, were indicated clearly in the results. Large birds with slow wing beat rates appear to be the most optimum subject for further study with the X-band Doppler radar used in this investigation.

Prediction Errors but Not Sharpened Signals Simulate Multivoxel fMRI Patterns during Speech Perception

PubMed Central

Davis, Matthew H.

2016-01-01

Successful perception depends on combining sensory input with prior knowledge. However, the underlying mechanism by which these two sources of information are combined is unknown. In speech perception, as in other domains, two functionally distinct coding schemes have been proposed for how expectations influence representation of sensory evidence. Traditional models suggest that expected features of the speech input are enhanced or sharpened via interactive activation (Sharpened Signals). Conversely, Predictive Coding suggests that expected features are suppressed so that unexpected features of the speech input (Prediction Errors) are processed further. The present work is aimed at distinguishing between these two accounts of how prior knowledge influences speech perception. By combining behavioural, univariate, and multivariate fMRI measures of how sensory detail and prior expectations influence speech perception with computational modelling, we provide evidence in favour of Prediction Error computations. Increased sensory detail and informative expectations have additive behavioural and univariate neural effects because they both improve the accuracy of word report and reduce the BOLD signal in lateral temporal lobe regions. However, sensory detail and informative expectations have interacting effects on speech representations shown by multivariate fMRI in the posterior superior temporal sulcus. When prior knowledge was absent, increased sensory detail enhanced the amount of speech information measured in superior temporal multivoxel patterns, but with informative expectations, increased sensory detail reduced the amount of measured information. Computational simulations of Sharpened Signals and Prediction Errors during speech perception could both explain these behavioural and univariate fMRI observations. However, the multivariate fMRI observations were uniquely simulated by a Prediction Error and not a Sharpened Signal model. The interaction between prior expectation and sensory detail provides evidence for a Predictive Coding account of speech perception. Our work establishes methods that can be used to distinguish representations of Prediction Error and Sharpened Signals in other perceptual domains. PMID:27846209

Detection of MET amplification in gastroesophageal tumor specimens using IQFISH

PubMed Central

Nielsen, Karsten Bork; Mollerup, Jens; Jepsen, Anna; Go, Ning

2017-01-01

Background The gene mesenchymal epithelial transition factor (MET) is a proto-oncogene that encodes a transmembrane receptor with intrinsic tyrosine kinase activity known as Met or cMet. MET is found to be amplified in several human cancers including gastroesophageal cancer. Methods Here we report the MET amplification prevalence data from 159 consecutive tumor specimens from patients with gastric (G), gastroesophageal junction (GEJ) and esophageal (E) adenocarcinoma, using a novel fluorescence in situ hybridization (FISH) assay, MET/CEN-7 IQFISH Probe Mix [an investigational use only (IUO) assay]. MET amplification was defined as a MET/CEN-7 ratio ≥2.0. Furthermore, the link between the MET signal distribution and amplification status was investigated. Results The prevalence of MET amplification was found to be 6.9%. The FISH assay demonstrated a high inter-observer reproducibility. The inter-observer results showed a 100% overall agreement with respect to the MET status (amplified/non-amplified). The inter-observer CV was estimated to 11.8% (95% CI: 10.2–13.4). For the signal distribution, the inter-observer agreement was reported to be 98.7%. We also report an association of MET amplification and a unique signal distribution pattern in the G/GEJ/E tumor specimens. We found that the prevalence of MET amplification was markedly higher in tumors specimens with a heterogeneous (66.7%) versus homogeneous (2.0%) signal distribution. Furthermore, specimens with a heterogeneous signal distribution had a statically significantly higher median MET/CEN-7 ratio (2.35 versus 1.04; P<0.0001). Conclusions The novel FISH assay showed a high inter-observer reproducibility both with respect to amplification status and signal distribution. Based on the finding in the study it is suggested that MET amplification mainly is associated with tumor cells that is represented by a heterogonous growth pattern. PMID:29285491

Genetic and Cellular Mechanisms Regulating Anterior Foregut and Esophageal Development

PubMed Central

Jacobs, Ian J.; Ku, Wei-Yao; Que, Jianwen

2012-01-01

Separation of the single anterior foregut tube into the esophagus and trachea involves cell proliferation and differentiation, as well as dynamic changes in cell-cell adhesion and migration. These biological processes are regulated and coordinated at multiple levels through the interplay of the epithelium and mesenchyme. Genetic studies and in vitro modeling have shed light on relevant regulatory networks that include a number of transcription factors and signaling pathways. These signaling molecules exhibit unique expression patterns and play specific functions in their respective territories before the separation process occurs. Disruption of regulatory networks inevitably leads to defective separation and malformation of the trachea and esophagus and results in the formation of a relatively common birth defect, esophageal atresia with or without tracheoesophageal fistula (EA/TEF). Significantly, some of the signaling pathways and transcription factors involved in anterior foregut separation continue to play important roles in the morphogenesis of the individual organs. In this review, we will focus on new findings related to these different developmental processes and discuss them in the context of developmental disorders (or birth defects) commonly seen in clinics. PMID:22750256

Mapping PTGERs to the Ovulatory Follicle: Regional Responses to the Ovulatory PGE2 Signal1

PubMed Central

Kim, Soon Ok; Duffy, Diane M.

2016-01-01

Prostaglandin E2 (PGE2) is a key intrafollicular mediator of ovulation in many, if not all, mammalian species. PGE2 acts at follicular cells via four distinct PGE2 receptors (PTGERs). Within the ovulatory follicle, each cell type (e.g., oocyte, cumulus granulosa cell, mural granulosa cell, theca cell, endothelial cell) expresses a different subset of the four PTGERs. Expression of a subset of PTGERs has consequences for the generation of intracellular signals and ultimately the unique functions of follicular cells that respond to PGE2. Just as the ovulatory LH surge regulates PGE2 synthesis, the LH surge also regulates expression of the four PTGERs. The pattern of expression of the four PTGERs among follicular cells before and after the LH surge forms a spatial and temporal map of PGE2 responses. Differential PTGER expression, coupled with activation of cell-specific intracellular signals, may explain how a single paracrine mediator can have pleotropic actions within the ovulatory follicle. Understanding the role of each PTGER in ovulation may point to previously unappreciated opportunities to both promote and prevent fertility. PMID:27307073

Multimode and multistate ladder oscillator and frequency recognition device

NASA Technical Reports Server (NTRS)

Aumann, Herbert M. (Inventor)

1976-01-01

A ladder oscillator composed of capacitive and inductive impedances connected together to form a ladder network which has a chosen number N oscillation modes at N different frequencies. Each oscillation mode is characterized by a unique standing wave voltage pattern along the nodes of the ladder oscillator, with the mode in which the ladder oscillator is oscillating being determinable from the amplitudes or phase of the oscillations at the nodes. A logic circuit may be connected to the nodes of the oscillator to compare the phases of selected nodes and thereby determine which mode the oscillator is oscillating in. A ladder oscillator composed of passive capacitive and inductive impedances can be utilized as a frequency recognition device, since the passive ladder oscillator will display the characteristic standing wave patterns if an input signal impressed upon the ladder oscillator is close to one of the mode frequencies of the oscillator. A CL ladder oscillator having series capacitive impedances and shunt inductive impedances can exhibit sustained and autonomous oscillations if active nonlinear devices are connected in parallel with the shunt inductive impedances. The active CL ladder oscillator can be synchronized to input frequencies impressed upon the oscillator, and will continue to oscillate after the input signal has been removed at a mode frequency which is, in general, nearest to the input signal frequency. Autonomous oscillations may also be obtained as desired from the active CL ladder oscillator at the mode frequencies.

Ciliary behavior of a negatively phototactic Chlamydomonas reinhardtii.

PubMed

Josef, Keith; Saranak, Jureepan; Foster, Kenneth W

2005-06-01

With an instrument that can record the motion of both cilia of the unicellular alga Chlamydomonas reinhardtii for many hours, the behavioral differences of its two cilia have been studied to determine their specific role in phototaxis. The organism was held on a fixed micropipette with the plane of ciliary beating rotated into the imaging plane of a quadrant photodetector. The responses to square-wave light patterns of a wide range of temporal frequencies were used to characterize the responses of each cilium. Eighty-one cells were examined showing an unexpectedly diverse range of responses. Plausible common signals for the linear and nonlinear signals from the cell body are suggested. Three independent ciliary measures--the beat frequency, stroke velocity, and phasing of the two cilia--have been identified. The cell body communicates to the cilia the direction of phototaxis the cell desires to go, the absolute light intensity, and the appropriate graded transient response for tracking the light source. The complexity revealed by each measure of the ciliary response indicates many independent variables are involved in the net phototactic response. In spite of their morphological similarity, the two cilia of Chlamydomonas respond uniquely. Probably the signals from the cell body fan out to independent pathways in the cilia. Each cilium modifies the input in its own way. The change in the pattern of the effective and recovery strokes of each cilium associated with negative phototaxis has been demonstrated and its involvement in phototactic turning is described. Copyright (c) 2005 Wiley-Liss, Inc.

Shared and unique patterns of phenotypic diversification along a stream gradient in two congeneric species

NASA Astrophysics Data System (ADS)

Jourdan, Jonas; Krause, Sarah T.; Lazar, V. Max; Zimmer, Claudia; Sommer-Trembo, Carolin; Arias-Rodriguez, Lenin; Klaus, Sebastian; Riesch, Rüdiger; Plath, Martin

2016-12-01

Stream ecosystems show gradual variation of various selection factors, which can result in a zonation of species distributions and gradient evolution of morphological and life-history traits within species. Identifying the selective agents underlying such phenotypic evolution is challenging as different species could show shared and/or unique (species-specific) responses to components of the river gradient. We studied a stream gradient inhabited by two mosquitofishes (genus Gambusia) in the Río Grijalva basin in southern Mexico and found a patchy distribution pattern of both congeners along a stretch of 100 km, whereby one species was usually dominant at a given site. We uncovered both shared and unique patterns of diversification: some components of the stream gradient, including differences in piscine predation pressure, drove shared patterns of phenotypic divergence, especially in females. Other components of the gradient, particularly abiotic factors (max. annual temperature and temperature range) resulted in unique patterns of divergence, especially in males. Our study highlights the complexity of selective regimes in stream ecosystems. It exemplifies that even closely related, congeneric species can respond in unique ways to the same components of the river gradient and shows how both sexes can exhibit quite different patterns of divergence in multivariate phenotypic character suites.

Shared and unique patterns of phenotypic diversification along a stream gradient in two congeneric species

PubMed Central

Jourdan, Jonas; Krause, Sarah T.; Lazar, V. Max; Zimmer, Claudia; Sommer-Trembo, Carolin; Arias-Rodriguez, Lenin; Klaus, Sebastian; Riesch, Rüdiger; Plath, Martin

2016-01-01

Stream ecosystems show gradual variation of various selection factors, which can result in a zonation of species distributions and gradient evolution of morphological and life-history traits within species. Identifying the selective agents underlying such phenotypic evolution is challenging as different species could show shared and/or unique (species-specific) responses to components of the river gradient. We studied a stream gradient inhabited by two mosquitofishes (genus Gambusia) in the Río Grijalva basin in southern Mexico and found a patchy distribution pattern of both congeners along a stretch of 100 km, whereby one species was usually dominant at a given site. We uncovered both shared and unique patterns of diversification: some components of the stream gradient, including differences in piscine predation pressure, drove shared patterns of phenotypic divergence, especially in females. Other components of the gradient, particularly abiotic factors (max. annual temperature and temperature range) resulted in unique patterns of divergence, especially in males. Our study highlights the complexity of selective regimes in stream ecosystems. It exemplifies that even closely related, congeneric species can respond in unique ways to the same components of the river gradient and shows how both sexes can exhibit quite different patterns of divergence in multivariate phenotypic character suites. PMID:27982114

Shared and unique patterns of phenotypic diversification along a stream gradient in two congeneric species.

PubMed

Jourdan, Jonas; Krause, Sarah T; Lazar, V Max; Zimmer, Claudia; Sommer-Trembo, Carolin; Arias-Rodriguez, Lenin; Klaus, Sebastian; Riesch, Rüdiger; Plath, Martin

2016-12-16

Stream ecosystems show gradual variation of various selection factors, which can result in a zonation of species distributions and gradient evolution of morphological and life-history traits within species. Identifying the selective agents underlying such phenotypic evolution is challenging as different species could show shared and/or unique (species-specific) responses to components of the river gradient. We studied a stream gradient inhabited by two mosquitofishes (genus Gambusia) in the Río Grijalva basin in southern Mexico and found a patchy distribution pattern of both congeners along a stretch of 100 km, whereby one species was usually dominant at a given site. We uncovered both shared and unique patterns of diversification: some components of the stream gradient, including differences in piscine predation pressure, drove shared patterns of phenotypic divergence, especially in females. Other components of the gradient, particularly abiotic factors (max. annual temperature and temperature range) resulted in unique patterns of divergence, especially in males. Our study highlights the complexity of selective regimes in stream ecosystems. It exemplifies that even closely related, congeneric species can respond in unique ways to the same components of the river gradient and shows how both sexes can exhibit quite different patterns of divergence in multivariate phenotypic character suites.

The Drosophila T-box transcription factor Midline functions within the Notch-Delta signaling pathway to specify sensory organ precursor cell fates and regulates cell survival within the eye imaginal disc.

PubMed

Das, Sudeshna; Chen, Q Brent; Saucier, Joseph D; Drescher, Brandon; Zong, Yan; Morgan, Sarah; Forstall, John; Meriwether, Andrew; Toranzo, Randy; Leal, Sandra M

2013-01-01

We report that the T-box transcription factor Midline (Mid), an evolutionary conserved homolog of the vertebrate Tbx20 protein, functions within the Notch-Delta signaling pathway essential for specifying the fates of sensory organ precursor (SOP) cells. These findings complement an established history of research showing that Mid regulates the cell-fate specification of diverse cell types within the developing heart, epidermis and central nervous system. Tbx20 has been detected in unique neuronal and epithelial cells of embryonic eye tissues in both mice and humans. However, the mechanisms by which either Mid or Tbx20 function to regulate cell-fate specification or other critical aspects of eye development including cell survival have not yet been elucidated. We have also gathered preliminary evidence suggesting that Mid may play an indirect, but vital role in selecting SOP cells within the third-instar larval eye disc by regulating the expression of the proneural gene atonal. During subsequent pupal stages, Mid specifies SOP cell fates as a member of the Notch-Delta signaling hierarchy and is essential for maintaining cell viability by inhibiting apoptotic pathways. We present several new hypotheses that seek to understand the role of Mid in regulating developmental processes downstream of the Notch receptor that are critical for specifying unique cell fates, patterning the adult eye and maintaining cellular homeostasis during eye disc morphogenesis. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Establishment of embryonic neuroepithelial cell lines exhibiting an epiplastic expression pattern of region specific markers.

PubMed

Nardelli, Jeannette; Catala, Martin; Charnay, Patrick

2003-09-15

Neuroepithelial b2T cells were derived from the hindbrain and the spinal cord of mouse transgenic embryos, which expressed SV40 T antigen under the control of a Hoxb2 enhancer. Strikingly, b2T cell lines of either origin exhibit a very similar gene expression pattern, including markers of the hindbrain and the spinal cord, such as Hox genes, but not of more anterior cephalic regions. In addition, the broad expression pattern of b2T cells, probably linked to culture conditions, appeared to be appropriately modulated when the cells were reimplanted at different longitudinal levels into chick host embryos, suggesting that these cells are responsive to exogenous signalling mechanisms. Further support for these allegations was obtained by culturing b2T cells in defined medium and by assessing the expression of Krox20, an odd-numbered rhombomere marker, which appeared to be modulated by a complex interplay between FGF, retinoic acid (RA), and noggin. With respect to these as yet unique properties, b2T cells constitute an original alternative tool to in vivo models for the analysis of molecular pathways involved in the patterning of the neural tube. Copyright 2003 Wiley-Liss, Inc.

Distributed affective space represents multiple emotion categories across the human brain

PubMed Central

Saarimäki, Heini; Ejtehadian, Lara Farzaneh; Jääskeläinen, Iiro P; Vuilleumier, Patrik; Sams, Mikko; Nummenmaa, Lauri

2018-01-01

Abstract The functional organization of human emotion systems as well as their neuroanatomical basis and segregation in the brain remains unresolved. Here, we used pattern classification and hierarchical clustering to characterize the organization of a wide array of emotion categories in the human brain. We induced 14 emotions (6 ‘basic’, e.g. fear and anger; and 8 ‘non-basic’, e.g. shame and gratitude) and a neutral state using guided mental imagery while participants' brain activity was measured with functional magnetic resonance imaging (fMRI). Twelve out of 14 emotions could be reliably classified from the haemodynamic signals. All emotions engaged a multitude of brain areas, primarily in midline cortices including anterior and posterior cingulate gyri and precuneus, in subcortical regions, and in motor regions including cerebellum and premotor cortex. Similarity of subjective emotional experiences was associated with similarity of the corresponding neural activation patterns. We conclude that different basic and non-basic emotions have distinguishable neural bases characterized by specific, distributed activation patterns in widespread cortical and subcortical circuits. Regionally differentiated engagement of these circuits defines the unique neural activity pattern and the corresponding subjective feeling associated with each emotion. PMID:29618125

EEG Oscillatory States: Universality, Uniqueness and Specificity across Healthy-Normal, Altered and Pathological Brain Conditions

PubMed Central

Fingelkurts, Alexander A.; Fingelkurts, Andrew A.

2014-01-01

For the first time the dynamic repertoires and oscillatory types of local EEG states in 13 diverse conditions (examined over 9 studies) that covered healthy-normal, altered and pathological brain states were quantified within the same methodological and conceptual framework. EEG oscillatory states were assessed by the probability-classification analysis of short-term EEG spectral patterns. The results demonstrated that brain activity consists of a limited repertoire of local EEG states in any of the examined conditions. The size of the state repertoires was associated with changes in cognition and vigilance or neuropsychopathologic conditions. Additionally universal, optional and unique EEG states across 13 diverse conditions were observed. It was demonstrated also that EEG oscillations which constituted EEG states were characteristic for different groups of conditions in accordance to oscillations’ functional significance. The results suggested that (a) there is a limit in the number of local states available to the cortex and many ways in which these local states can rearrange themselves and still produce the same global state and (b) EEG individuality is determined by varying proportions of universal, optional and unique oscillatory states. The results enriched our understanding about dynamic microstructure of EEG-signal. PMID:24505292

Long-range dismount activity classification: LODAC

NASA Astrophysics Data System (ADS)

Garagic, Denis; Peskoe, Jacob; Liu, Fang; Cuevas, Manuel; Freeman, Andrew M.; Rhodes, Bradley J.

2014-06-01

Continuous classification of dismount types (including gender, age, ethnicity) and their activities (such as walking, running) evolving over space and time is challenging. Limited sensor resolution (often exacerbated as a function of platform standoff distance) and clutter from shadows in dense target environments, unfavorable environmental conditions, and the normal properties of real data all contribute to the challenge. The unique and innovative aspect of our approach is a synthesis of multimodal signal processing with incremental non-parametric, hierarchical Bayesian machine learning methods to create a new kind of target classification architecture. This architecture is designed from the ground up to optimally exploit correlations among the multiple sensing modalities (multimodal data fusion) and rapidly and continuously learns (online self-tuning) patterns of distinct classes of dismounts given little a priori information. This increases classification performance in the presence of challenges posed by anti-access/area denial (A2/AD) sensing. To fuse multimodal features, Long-range Dismount Activity Classification (LODAC) develops a novel statistical information theoretic approach for multimodal data fusion that jointly models multimodal data (i.e., a probabilistic model for cross-modal signal generation) and discovers the critical cross-modal correlations by identifying components (features) with maximal mutual information (MI) which is efficiently estimated using non-parametric entropy models. LODAC develops a generic probabilistic pattern learning and classification framework based on a new class of hierarchical Bayesian learning algorithms for efficiently discovering recurring patterns (classes of dismounts) in multiple simultaneous time series (sensor modalities) at multiple levels of feature granularity.

Concerted vs. Sequential. Two Activation Patterns of Vast Arrays of Intracellular Ca2+ Channels in Muscle

PubMed Central

Zhou, Jinsong; Brum, Gustavo; González, Adom; Launikonis, Bradley S.; Stern, Michael D.; Ríos, Eduardo

2005-01-01

To signal cell responses, Ca2+ is released from storage through intracellular Ca2+ channels. Unlike most plasmalemmal channels, these are clustered in quasi-crystalline arrays, which should endow them with unique properties. Two distinct patterns of local activation of Ca2+ release were revealed in images of Ca2+ sparks in permeabilized cells of amphibian muscle. In the presence of sulfate, an anion that enters the SR and precipitates Ca2+, sparks became wider than in the conventional, glutamate-based solution. Some of these were “protoplatykurtic” (had a flat top from early on), suggesting an extensive array of channels that activate simultaneously. Under these conditions the rate of production of signal mass was roughly constant during the rise time of the spark and could be as high as 5 μm3 ms−1, consistent with a release current >50 pA since the beginning of the event. This pattern, called “concerted activation,” was observed also in rat muscle fibers. When sulfate was combined with a reduced cytosolic [Ca2+] (50 nM) these sparks coexisted (and interfered) with a sequential progression of channel opening, probably mediated by Ca2+-induced Ca2+ release (CICR). Sequential propagation, observed only in frogs, may require parajunctional channels, of RyR isoform β, which are absent in the rat. Concerted opening instead appears to be a property of RyR α in the amphibian and the homologous isoform 1 in the mammal. PMID:16186560

Scoring Tools for the Analysis of Infant Respiratory Inductive Plethysmography Signals.

PubMed

Robles-Rubio, Carlos Alejandro; Bertolizio, Gianluca; Brown, Karen A; Kearney, Robert E

2015-01-01

Infants recovering from anesthesia are at risk of life threatening Postoperative Apnea (POA). POA events are rare, and so the study of POA requires the analysis of long cardiorespiratory records. Manual scoring is the preferred method of analysis for these data, but it is limited by low intra- and inter-scorer repeatability. Furthermore, recommended scoring rules do not provide a comprehensive description of the respiratory patterns. This work describes a set of manual scoring tools that address these limitations. These tools include: (i) a set of definitions and scoring rules for 6 mutually exclusive, unique patterns that fully characterize infant respiratory inductive plethysmography (RIP) signals; (ii) RIPScore, a graphical, manual scoring software to apply these rules to infant data; (iii) a library of data segments representing each of the 6 patterns; (iv) a fully automated, interactive formal training protocol to standardize the analysis and establish intra- and inter-scorer repeatability; and (v) a quality control method to monitor scorer ongoing performance over time. To evaluate these tools, three scorers from varied backgrounds were recruited and trained to reach a performance level similar to that of an expert. These scorers used RIPScore to analyze data from infants at risk of POA in two separate, independent instances. Scorers performed with high accuracy and consistency, analyzed data efficiently, had very good intra- and inter-scorer repeatability, and exhibited only minor confusion between patterns. These results indicate that our tools represent an excellent method for the analysis of respiratory patterns in long data records. Although the tools were developed for the study of POA, their use extends to any study of respiratory patterns using RIP (e.g., sleep apnea, extubation readiness). Moreover, by establishing and monitoring scorer repeatability, our tools enable the analysis of large data sets by multiple scorers, which is essential for longitudinal and multicenter studies.

Intramembranous valine linked to schizophrenia is required for neuregulin 1 regulation of the morphological development of cortical neurons

PubMed Central

Chen, Yachi; Hancock, Melissa L.; Role, Lorna W.; Talmage, David A.

2010-01-01

Neuregulin 1 (NRG1) signaling is critical to various aspects of neuronal development and function. Among different NRG1 isoforms, the Type III isoforms of NRG1 are unique in their ability to signal via the intracellular domain following γ-secretase-dependent intramembranous processing. However, the functional consequences of Type III NRG1 signaling via its intracellular domain are largely unknown. In this study, we have identified mutations within Type III NRG1 that disrupt intramembranous proteolytic processing and abolish intracellular domain signaling. In particular, substitutions at valine 321, previously linked to schizophrenia risks, result in NRG1 proteins that fail to undergo γ-secretase-mediated nuclear localization and transcriptional activation. Using processing-defective mutants of Type III NRG1, we demonstrate that the intracellular domain signaling is specifically required for NRG1 regulation of the growth and branching of cortical dendrites but not axons. Consistent with the role of Type III NRG1 signaling via the intracellular domain in the initial patterning of cortical dendrites, our findings from pharmacological and genetic studies indicate that Type III NRG1 functions in dendritic development independent of ERBB kinase activity. Taken together, these results support the proposal that aberrant intracellular processing and defective signaling via the intracellular domain of Type III NRG1 impair a subset of NRG1 functions in cortical development and contribute to abnormal neuroconnectivity implicated in schizophrenia. PMID:20610754

Suomi satellite brings to light a unique frontier of nighttime environmental sensing capabilities

PubMed Central

Miller, Steven D.; Mills, Stephen P.; Elvidge, Christopher D.; Lindsey, Daniel T.; Lee, Thomas F.; Hawkins, Jeffrey D.

2012-01-01

Most environmental satellite radiometers use solar reflectance information when it is available during the day but must resort at night to emission signals from infrared bands, which offer poor sensitivity to low-level clouds and surface features. A few sensors can take advantage of moonlight, but the inconsistent availability of the lunar source limits measurement utility. Here we show that the Day/Night Band (DNB) low-light visible sensor on the recently launched Suomi National Polar-orbiting Partnership (NPP) satellite has the unique ability to image cloud and surface features by way of reflected airglow, starlight, and zodiacal light illumination. Examples collected during new moon reveal not only meteorological and surface features, but also the direct emission of airglow structures in the mesosphere, including expansive regions of diffuse glow and wave patterns forced by tropospheric convection. The ability to leverage diffuse illumination sources for nocturnal environmental sensing applications extends the advantages of visible-light information to moonless nights. PMID:22984179

An organizing activity is required for head patterning and cell fate specification in the polychaete annelid Capitella teleta: new insights into cell-cell signaling in Lophotrochozoa.

PubMed

Amiel, Aldine R; Henry, Jonathan Q; Seaver, Elaine C

2013-07-01

Many lophotrochozoans (i.e., molluscs, annelids, nemerteans, and polyclad flatworms) display a well-conserved early developmental program called spiral cleavage that contrasts with the high diversity of adult body forms present in this group. Due to this stereotypical development, each cell can be uniquely identified and its lineage history known following intracellular injection of lineage tracers. Cell deletion experiments performed mainly in molluscs have demonstrated that one or two cells associated with the endomesodermal lineage represent an embryonic organizer of subsequent development and are causally involved in cell fate and body patterning. Utilizing the published fate map of the spiral-cleaving annelid Capitella teleta, we used infrared laser cell deletions to dissect the role of individual cells on the patterning of the larval body. Thirteen uniquely identifiable individual blastomeres and two double cell combination deletions were studied to assess larval phenotypes by scoring multiple morphological structures and cell type-specific molecular markers differentially expressed along the antero-posterior and dorso-ventral axes. Surprisingly, our results show that in C. teleta, the cellular identity of the "organizing cell" and the timing of the organizing activity are different from that of other spiralians. retain-->In C. teleta, the ectodermal primary somatoblast, 2d, is the key cell responsible for organizing activity during early embryonic development, and is necessary for bilateral symmetry and dorso-ventral axis organization of the head as well as neural, foregut and mesoderm tissue formation. Furthermore, we show that the ERK/MAPK signaling pathway does not appear to be involved in organizing activity in retain-->C. teleta. This contrasts with data from molluscs and the molecular mechanism suggested for another polychaete, Hydroides elegans, highlighting likely molecular level variation among spiralian embryos. These results reinforce the idea that an embryonic organizing activity is present across spiralians. Our data also emphasize the developmental variation within lophotrochozoans, and may ultimately provide insight into the role of developmental processes in the evolution of diverse body forms in metazoans. Copyright © 2013 Elsevier Inc. All rights reserved.

Associative memory of phase-coded spatiotemporal patterns in leaky Integrate and Fire networks.

PubMed

Scarpetta, Silvia; Giacco, Ferdinando

2013-04-01

We study the collective dynamics of a Leaky Integrate and Fire network in which precise relative phase relationship of spikes among neurons are stored, as attractors of the dynamics, and selectively replayed at different time scales. Using an STDP-based learning process, we store in the connectivity several phase-coded spike patterns, and we find that, depending on the excitability of the network, different working regimes are possible, with transient or persistent replay activity induced by a brief signal. We introduce an order parameter to evaluate the similarity between stored and recalled phase-coded pattern, and measure the storage capacity. Modulation of spiking thresholds during replay changes the frequency of the collective oscillation or the number of spikes per cycle, keeping preserved the phases relationship. This allows a coding scheme in which phase, rate and frequency are dissociable. Robustness with respect to noise and heterogeneity of neurons parameters is studied, showing that, since dynamics is a retrieval process, neurons preserve stable precise phase relationship among units, keeping a unique frequency of oscillation, even in noisy conditions and with heterogeneity of internal parameters of the units.

Flow-pattern Guided Fabrication of High-density Barcode Antibody Microarray

PubMed Central

Ramirez, Lisa S.; Wang, Jun

2016-01-01

Antibody microarray as a well-developed technology is currently challenged by a few other established or emerging high-throughput technologies. In this report, we renovate the antibody microarray technology by using a novel approach for manufacturing and by introducing new features. The fabrication of our high-density antibody microarray is accomplished through perpendicularly oriented flow-patterning of single stranded DNAs and subsequent conversion mediated by DNA-antibody conjugates. This protocol outlines the critical steps in flow-patterning DNA, producing and purifying DNA-antibody conjugates, and assessing the quality of the fabricated microarray. The uniformity and sensitivity are comparable with conventional microarrays, while our microarray fabrication does not require the assistance of an array printer and can be performed in most research laboratories. The other major advantage is that the size of our microarray units is 10 times smaller than that of printed arrays, offering the unique capability of analyzing functional proteins from single cells when interfacing with generic microchip designs. This barcode technology can be widely employed in biomarker detection, cell signaling studies, tissue engineering, and a variety of clinical applications. PMID:26780370

Expression analysis of genes encoding double B-box zinc finger proteins in maize.

PubMed

Li, Wenlan; Wang, Jingchao; Sun, Qi; Li, Wencai; Yu, Yanli; Zhao, Meng; Meng, Zhaodong

2017-11-01

The B-box proteins play key roles in plant development. The double B-box (DBB) family is one of the subfamily of the B-box family, with two B-box domains and without a CCT domain. In this study, 12 maize double B-box genes (ZmDBBs) were identified through a genome-wide survey. Phylogenetic analysis of DBB proteins from maize, rice, Sorghum bicolor, Arabidopsis, and poplar classified them into five major clades. Gene duplication analysis indicated that segmental duplications made a large contribution to the expansion of ZmDBBs. Furthermore, a large number of cis-acting regulatory elements related to plant development, response to light and phytohormone were identified in the promoter regions of the ZmDBB genes. The expression patterns of the ZmDBB genes in various tissues and different developmental stages demonstrated that ZmDBBs might play essential roles in plant development, and some ZmDBB genes might have unique function in specific developmental stages. In addition, several ZmDBB genes showed diurnal expression pattern. The expression levels of some ZmDBB genes changed significantly under light/dark treatment conditions and phytohormone treatments, implying that they might participate in light signaling pathway and hormone signaling. Our results will provide new information to better understand the complexity of the DBB gene family in maize.

Afro-American Patterns of Cognition: A Review of Research.

ERIC Educational Resources Information Center

Shade, Barbara J.

Specific and unique information processing patterns have been developed by Black Americans as a result of coping with and adapting to a color-conscious society. A review of the literature shows that the major variation in the processing of information which seems to be uniquely Black American occurs in their patterns of perception. Specifically,…

Orbital component extraction by time-variant sinusoidal modeling.

NASA Astrophysics Data System (ADS)

Sinnesael, Matthias; Zivanovic, Miroslav; De Vleeschouwer, David; Claeys, Philippe; Schoukens, Johan

2016-04-01

Accurately deciphering periodic variations in paleoclimate proxy signals is essential for cyclostratigraphy. Classical spectral analysis often relies on methods based on the (Fast) Fourier Transformation. This technique has no unique solution separating variations in amplitude and frequency. This characteristic makes it difficult to correctly interpret a proxy's power spectrum or to accurately evaluate simultaneous changes in amplitude and frequency in evolutionary analyses. Here, we circumvent this drawback by using a polynomial approach to estimate instantaneous amplitude and frequency in orbital components. This approach has been proven useful to characterize audio signals (music and speech), which are non-stationary in nature (Zivanovic and Schoukens, 2010, 2012). Paleoclimate proxy signals and audio signals have in nature similar dynamics; the only difference is the frequency relationship between the different components. A harmonic frequency relationship exists in audio signals, whereas this relation is non-harmonic in paleoclimate signals. However, the latter difference is irrelevant for the problem at hand. Using a sliding window approach, the model captures time variations of an orbital component by modulating a stationary sinusoid centered at its mean frequency, with a single polynomial. Hence, the parameters that determine the model are the mean frequency of the orbital component and the polynomial coefficients. The first parameter depends on geologic interpretation, whereas the latter are estimated by means of linear least-squares. As an output, the model provides the orbital component waveform, either in the depth or time domain. Furthermore, it allows for a unique decomposition of the signal into its instantaneous amplitude and frequency. Frequency modulation patterns can be used to reconstruct changes in accumulation rate, whereas amplitude modulation can be used to reconstruct e.g. eccentricity-modulated precession. The time-variant sinusoidal model is applied to well-established Pleistocene benthic isotope records to evaluate its performance. Zivanovic M. and Schoukens J. (2010) On The Polynomial Approximation for Time-Variant Harmonic Signal Modeling. IEEE Transactions On Audio, Speech, and Language Processing vol. 19, no. 3, pp. 458-467. Doi: 10.1109/TASL.2010.2049673. Zivanovic M. and Schoukens J. (2012) Single and Piecewise Polynomials for Modeling of Pitched Sounds. IEEE Transactions On Audio, Speech, and Language Processing vol. 20, no. 4, pp. 1270-1281. Doi: 10.1109/TASL.2011.2174228.

Unique identification code for medical fundus images using blood vessel pattern for tele-ophthalmology applications.

PubMed

Singh, Anushikha; Dutta, Malay Kishore; Sharma, Dilip Kumar

2016-10-01

Identification of fundus images during transmission and storage in database for tele-ophthalmology applications is an important issue in modern era. The proposed work presents a novel accurate method for generation of unique identification code for identification of fundus images for tele-ophthalmology applications and storage in databases. Unlike existing methods of steganography and watermarking, this method does not tamper the medical image as nothing is embedded in this approach and there is no loss of medical information. Strategic combination of unique blood vessel pattern and patient ID is considered for generation of unique identification code for the digital fundus images. Segmented blood vessel pattern near the optic disc is strategically combined with patient ID for generation of a unique identification code for the image. The proposed method of medical image identification is tested on the publically available DRIVE and MESSIDOR database of fundus image and results are encouraging. Experimental results indicate the uniqueness of identification code and lossless recovery of patient identity from unique identification code for integrity verification of fundus images. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Analysis of Traffic Signals on a Software-Defined Network for Detection and Classification of a Man-in-the-Middle Attack

DTIC Science & Technology

2017-09-01

unique characteristics of reported anomalies in the collected traffic signals to build a classification framework. Other cyber events, such as a...Furthermore, we identify unique characteristics of reported anomalies in the collected traffic signals to build a classification framework. Other cyber...2]. The applications build flow rules using network topology information provided by the control plane [1]. Since the control plane is able to

Feature in Antenna Pattern for Pointing and Orientation Determination

NASA Technical Reports Server (NTRS)

Rochblatt, David (Inventor)

2016-01-01

Systems and methods for antenna pointing are disclosed. A transmit antenna system having an adjustable boresight transmits a signal exhibiting a far-field pattern including a feature (e.g. a V-Notch) in a polarization of the signal disposed at a fixed position off a beam peak of the far-field pattern of the signal. A receive antenna system scans across the far-field pattern of the signal in the polarization to locate the feature and determine a pointing error of the adjustable boresight therefrom. The system may be applied to a cross-polarization of the signal where a co-polarization of the signal is simultaneously used for telecommunication.

Ionic signaling in plant responses to gravity and touch

NASA Technical Reports Server (NTRS)

Fasano, Jeremiah M.; Massa, Gioia D.; Gilroy, Simon

2002-01-01

Touch and gravity are two of the many stimuli that plants must integrate to generate an appropriate growth response. Due to the mechanical nature of both of these signals, shared signal transduction elements could well form the basis of the cross-talk between these two sensory systems. However, touch stimulation must elicit signaling events across the plasma membrane whereas gravity sensing is thought to represent transformation of an internal force, amyloplast sedimentation, to signal transduction events. In addition, factors such as turgor pressure and presence of the cell wall may also place unique constraints on these plant mechanosensory systems. Even so, the candidate signal transduction elements in both plant touch and gravity sensing, changes in Ca2+, pH and membrane potential, do mirror the known ionic basis of signaling in animal mechanosensory cells. Distinct spatial and temporal signatures of Ca2+ ions may encode information about the different mechanosignaling stimuli. Signals such as Ca2+ waves or action potentials may also rapidly transfer information perceived in one cell throughout a tissue or organ leading to the systemic reactions characteristic of plant touch and gravity responses. Longer-term growth responses are likely sustained via changes in gene expression and asymmetries in compounds such as inositol-1,4,5-triphosphate (IP3) and calmodulin. Thus, it seems likely that plant mechanoperception involves both spatial and temporal encoding of information at all levels, from the cell to the whole plant. Defining this patterning will be a critical step towards understanding how plants integrate information from multiple mechanical stimuli to an appropriate growth response.

Cobalt Alloy Implant Debris Induces Inflammation and Bone Loss Primarily through Danger Signaling, Not TLR4 Activation: Implications for DAMP-ening Implant Related Inflammation

PubMed Central

Samelko, Lauryn; Landgraeber, Stefan; McAllister, Kyron; Jacobs, Joshua; Hallab, Nadim James

2016-01-01

Cobalt alloy debris has been implicated as causative in the early failure of some designs of current total joint implants. The ability of implant debris to cause excessive inflammation via danger signaling (NLRP3 inflammasome) vs. pathogen associated pattern recognition receptors (e.g. Toll-like receptors; TLRs) remains controversial. Recently, specific non-conserved histidines on human TLR4 have been shown activated by cobalt and nickel ions in solution. However, whether this TLR activation is directly or indirectly an effect of metals or secondary endogenous alarmins (danger-associated molecular patterns, DAMPs) elicited by danger signaling, remains unknown and contentious. Our study indicates that in both a human macrophage cell line (THP-1) and primary human macrophages, as well as an in vivo murine model of inflammatory osteolysis, that Cobalt-alloy particle induced NLRP3 inflammasome danger signaling inflammatory responses were highly dominant relative to TLR4 activation, as measured respectively by IL-1β or TNF-α, IL-6, IL-10, tissue histology and quantitative bone loss measurement. Despite the lack of metal binding histidines H456 and H458 in murine TLR4, murine calvaria challenge with Cobalt alloy particles induced significant macrophage driven in vivo inflammation and bone loss inflammatory osteolysis, whereas LPS calvaria challenge alone did not. Additionally, no significant increase (p<0.05) in inflammation and inflammatory bone loss by LPS co-challenge with Cobalt vs. Cobalt alone was evident, even at high levels of LPS (i.e. levels commiserate with hematogenous levels in fatal sepsis, >500pg/mL). Therefore, not only do the results of this investigation support Cobalt alloy danger signaling induced inflammation, but under normal homeostasis low levels of hematogenous PAMPs (<2pg/mL) from Gram-negative bacteria, seem to have negligible contribution to the danger signaling responses elicited by Cobalt alloy metal implant debris. This suggests the unique nature of Cobalt alloy particle bioreactivity is strong enough to illicit danger signaling that secondarily activate concomitant TLR activation, and may in part explain Cobalt particulate associated inflammatory and toxicity-like reactions of specific orthopedic implants. PMID:27467577

Intracellular signalling and plasma hormone profiles associated with the expression of unconditioned and conditioned fear and anxiety in female rats.

PubMed

Simone, Jonathan J; McCormick, Cheryl M

2017-02-01

There is considerable overlap in the neural regions and intracellular signalling pathways implicated in anxiety and fear, although less is known in females. Here, we investigated whether unconditioned and conditioned fear are associated with distinct patterns of expression of extracellular signal-regulated kinase-1 and -2 (ERK1/2), protein kinase B (Akt), and calcineurin (CaN) (proteins that are key regulators of the expression of and/or memory processes of fear and anxiety) in the dorsal and ventral hippocampus, medial prefrontal cortex, and amygdala (important regions in neural fear circuitry) of adult female rats, and used a multivariate approach to find patterns of signalling that might discriminate between the different states of fear. To isolate fear to the conditioned cue from generalized fear to the test context, rats were conditioned to an auditory tone (i.e. tone paired with footshock) and twenty-four hours later exposed to a novel context in the presence or absence of the conditioned cue. A third group that was exposed to the conditioning context without undergoing fear conditioning was included to control for unconditioned responses to the testing procedures, which are anxiogenic. A discriminate function analysis and MANOVA determined that hippocampal signalling best discriminated the three groups from each other. The addition of values for plasma concentrations of corticosterone and progesterone (as indices of activation of the hypothalamic-pituitary-adrenal stress axis) to statistical analyses increased the separation of the three groups. There was high degree of association among the three signalling molecules in the four brain regions within each group. There was an absence of the associations between the medial prefrontal cortex and the amygdala in the cued fear recall group that were strong for the non-conditioned group. These results demonstrated unique neuronal and hormonal signalling profiles associated with unconditioned, generalized, and conditioned fear expression in females and highlight the importance of including appropriate comparisons to best discriminate between these different emotional states. Copyright © 2016 Elsevier Inc. All rights reserved.

Notch Decoys that Selectively Block Dll/Notch or Jagged/Notch Disrupt Angiogenesis by Unique Mechanisms to Inhibit Tumor Growth

PubMed Central

Kangsamaksin, Thaned; Murtomaki, Aino; Kofler, Natalie M.; Cuervo, Henar; Chaudhri, Reyhaan A.; Tattersall, Ian W.; Rosenstiel, Paul E.; Shawber, Carrie J.; Kitajewski, Jan

2015-01-01

A pro-angiogenic role for Jagged-dependent activation of Notch signaling in the endothelium has yet to be described. Using proteins that encoded different NOTCH1 EGF-like repeats, we identified unique regions of DLL-class and JAG-class ligand/receptor interactions, and developed Notch decoys that function as ligand-specific Notch inhibitors. N110-24 decoy blocked JAG1/JAG2-mediated NOTCH1 signaling, angiogenic sprouting in vitro and retinal angiogenesis, demonstrating JAG-dependent Notch signal activation promotes angiogenesis. In tumors, N110-24 decoy reduced angiogenic sprouting, vessel perfusion, pericyte coverage, and tumor growth. JAG/NOTCH signaling uniquely inhibited expression of anti-angiogenic sVEFGFR-1/sFlt-1. N11-13 decoy interfered with DLL1/DLL4-mediated NOTCH1 signaling and caused endothelial hypersprouting in vitro, in retinal angiogenesis and in tumors. Thus, blockade of JAG- or DLL-mediated Notch signaling inhibits angiogenesis by distinct mechanisms. JAG/Notch signaling positively regulates angiogenesis by suppressing sVEGFR-1/sFlt-1 and promoting mural/endothelial cell interactions. Blockade of JAG-class ligands represents a novel, viable therapeutic approach to block tumor angiogenesis and growth. PMID:25387766

Self-organizing neural network models for visual pattern recognition.

PubMed

Fukushima, K

1987-01-01

Two neural network models for visual pattern recognition are discussed. The first model, called a "neocognitron", is a hierarchical multilayered network which has only afferent synaptic connections. It can acquire the ability to recognize patterns by "learning-without-a-teacher": the repeated presentation of a set of training patterns is sufficient, and no information about the categories of the patterns is necessary. The cells of the highest stage eventually become "gnostic cells", whose response shows the final result of the pattern-recognition of the network. Pattern recognition is performed on the basis of similarity in shape between patterns, and is not affected by deformation, nor by changes in size, nor by shifts in the position of the stimulus pattern. The second model has not only afferent but also efferent synaptic connections, and is endowed with the function of selective attention. The afferent and the efferent signals interact with each other in the hierarchical network: the efferent signals, that is, the signals for selective attention, have a facilitating effect on the afferent signals, and at the same time, the afferent signals gate efferent signal flow. When a complex figure, consisting of two patterns or more, is presented to the model, it is segmented into individual patterns, and each pattern is recognized separately. Even if one of the patterns to which the models is paying selective attention is affected by noise or defects, the model can "recall" the complete pattern from which the noise has been eliminated and the defects corrected.

Exploring the molecular aspects associated with testicular germ cell tumors: a review

PubMed Central

Facchini, Gaetano; Rossetti, Sabrina; Cavaliere, Carla; D’Aniello, Carmine; Di Franco, Rossella; Iovane, Gelsomina; Grimaldi, Giovanni; Piscitelli, Raffaele; Muto, Paolo; Botti, Gerardo; Perdonà, Sisto; Veneziani, Bianca Maria; Berretta, Massimiliano; Montanari, Micaela

2018-01-01

Testicular germ cell tumors (TGCTs) represent the most common solid tumors affecting young men. They constitute a distinct entity because of their embryonic origin and their unique biological behavior. Recent preclinical data regarding biological signaling machinery as well as genetic and epigenetic mechanisms associated with molecular patterns of tumors have contribute to explain the pathogenesis and the differentiation of TGCTs and to understand the mechanisms responsible for the development of resistance to treatment. In this review, we discuss the main genetic and epigenetic events associated with TGCTs development in order to better define their role in the pathogenesis of these tumors and in cisplatin-acquired resistance. PMID:29416701

Nanofabrication with a helium ion microscope

NASA Astrophysics Data System (ADS)

Maas, Diederik; van Veldhoven, Emile; Chen, Ping; Sidorkin, Vadim; Salemink, Huub; van der Drift, Emile..; Alkemade, Paul

2010-03-01

The recently introduced helium ion microscope (HIM) is capable of imaging and fabrication of nanostructures thanks to its sub-nanometer sized ion probe. The unique interaction of the helium ions with the sample material provides very localized secondary electron emission, thus providing a valuable signal for high-resolution imaging as well as a mechanism for very precise nanofabrication. The low proximity effects, due to the low yield of backscattered ions and the confinement of the forward scattered ions into a narrow cone, enable patterning of ultra-dense sub-10 nm structures. This paper presents various nanofabrication results obtained with direct-write, with scanning helium ion beam lithography, and with helium ion beam induced deposition.

Specificity in Toll-like receptor signalling through distinct effector functions of TRAF3 and TRAF6.

PubMed

Häcker, Hans; Redecke, Vanessa; Blagoev, Blagoy; Kratchmarova, Irina; Hsu, Li-Chung; Wang, Gang G; Kamps, Mark P; Raz, Eyal; Wagner, Hermann; Häcker, Georg; Mann, Matthias; Karin, Michael

2006-01-12

Toll-like receptors (TLRs) are activated by pathogen-associated molecular patterns to induce innate immune responses and production of pro-inflammatory cytokines, interferons and anti-inflammatory cytokines. TLRs activate downstream effectors through adaptors that contain Toll/interleukin-1 receptor (TIR) domains, but the mechanisms accounting for diversification of TLR effector functions are unclear. To dissect biochemically TLR signalling, we established a system for isolating signalling complexes assembled by dimerized adaptors. Using MyD88 as a prototypical adaptor, we identified TNF receptor-associated factor 3 (TRAF3) as a new component of TIR signalling complexes that is recruited along with TRAF6. Using myeloid cells from TRAF3- and TRAF6-deficient mice, we show that TRAF3 is essential for the induction of type I interferons (IFN) and the anti-inflammatory cytokine interleukin-10 (IL-10), but is dispensable for expression of pro-inflammatory cytokines. In fact, TRAF3-deficient cells overproduce pro-inflammatory cytokines owing to defective IL-10 production. Despite their structural similarity, the functions of TRAF3 and TRAF6 are largely distinct. TRAF3 is also recruited to the adaptor TRIF (Toll/IL-1 receptor domain-containing adaptor-inducing IFN-beta) and is required for marshalling the protein kinase TBK1 (also called NAK) into TIR signalling complexes, thereby explaining its unique role in activation of the IFN response.

Isoforms of receptors of fibroblast growth factors.

PubMed

Gong, Siew-Ging

2014-12-01

The breadth and scope of Fibroblast Growth Factor signaling is immense, with documentation of its role in almost every organism and system studied so far. FGF ligands signal through a family of four distinct tyrosine kinase receptors, the FGF receptors (FGFRs). One contribution to the diversity of function and signaling of FGFs and their receptors arises from the numerous alternative splicing variants that have been documented in the FGFR literature. The present review discusses the types and roles of alternatively spliced variants of the FGFR family members and the significant impact of alternative splicing on the physiological functions of five broad classes of FGFR isoforms. Some characterized known regulatory mechanisms of alternative splicing and future directions in studies of FGFR alternative splicing are also discussed. Presence, absence, and/or the combination of specific exons within each FGFR protein impart upon each individual isoform its unique function and expression pattern during normal function and in diseased states (e.g., in cancers and birth defects). A better understanding of the diversity of FGF signaling in different developmental contexts and diseased states can be achieved through increased knowledge of the presence of specific FGFR isoforms and their impact on downstream signaling and functions. Modern high-throughput techniques afford an opportunity to explore the distribution and function of isoforms of FGFR during development and in diseases. © 2014 Wiley Periodicals, Inc.

Neurotrophic regulation of epidermal dedifferentiation during wound healing and limb regeneration in the axolotl (Ambystoma mexicanum).

PubMed

Satoh, A; Graham, G M C; Bryant, S V; Gardiner, D M

2008-07-15

Adult urodeles (salamanders) are unique in their ability to regenerate complex organs perfectly. The recently developed Accessory Limb Model (ALM) in the axolotl provides an opportunity to identify and characterize the essential signaling events that control the early steps in limb regeneration. The ALM demonstrates that limb regeneration progresses in a stepwise fashion that is dependent on signals from the wound epidermis, nerves and dermal fibroblasts from opposite sides of the limb. When all the signals are present, a limb is formed de novo. The ALM thus provides an opportunity to identify and characterize the signaling pathways that control blastema morphogenesis and limb regeneration. In the present study, we have utilized the ALM to identity the buttonhead-like zinc-finger transcription factor, Sp9, as being involved in the formation of the regeneration epithelium. Sp9 expression is induced in basal keratinocytes of the apical blastema epithelium in a pattern that is comparable to its expression in developing limb buds, and it thus is an important marker for dedifferentiation of the epidermis. Induction of Sp9 expression is nerve-dependent, and we have identified KGF as an endogenous nerve factor that induces expression of Sp9 in the regeneration epithelium.

Rapid encoding of relationships between spatially remote motion signals.

PubMed

Maruya, Kazushi; Holcombe, Alex O; Nishida, Shin'ya

2013-02-06

For visual processing, the temporal correlation of remote local motion signals is a strong cue to detect meaningful large-scale structures in the retinal image, because related points are likely to move together regardless of their spatial separation. While the processing of multi-element motion patterns involved in biological motion and optic flow has been studied intensively, the encoding of simpler pairwise relationships between remote motion signals remains poorly understood. We investigated this process by measuring the temporal rate limit for perceiving the relationship of two motion directions presented at the same time at different spatial locations. Compared to luminance or orientation, motion comparison was more rapid. Performance remained very high even when interstimulus separation was increased up to 100°. Motion comparison also remained rapid regardless of whether the two motion directions were similar to or different from each other. The exception was a dramatic slowing when the elements formed an orthogonal "T," in which two motions do not perceptually group together. Motion presented at task-irrelevant positions did not reduce performance, suggesting that the rapid motion comparison could not be ascribed to global optic flow processing. Our findings reveal the existence and unique nature of specialized processing that encodes long-range relationships between motion signals for quick appreciation of global dynamic scene structure.

A new mechanism for spatial pattern formation via lateral and protrusion-mediated lateral signalling

PubMed Central

Hunter, Ginger L.; Baum, Buzz

2016-01-01

Tissue organization and patterning are critical during development when genetically identical cells take on different fates. Lateral signalling plays an important role in this process by helping to generate self-organized spatial patterns in an otherwise uniform collection of cells. Recent data suggest that lateral signalling can be mediated both by junctional contacts between neighbouring cells and via cellular protrusions that allow non-neighbouring cells to interact with one another at a distance. However, it remains unclear precisely how signalling mediated by these distinct types of cell–cell contact can physically contribute to the generation of complex patterns without the assistance of diffusible morphogens or pre-patterns. To explore this question, in this work we develop a model of lateral signalling based on a single receptor/ligand pair as exemplified by Notch and Delta. We show that allowing the signalling kinetics to differ at junctional versus protrusion-mediated contacts, an assumption inspired by recent data which show that the cleavage of Notch in several systems requires both Delta binding and the application of mechanical force, permits individual cells to act to promote both lateral activation and lateral inhibition. Strikingly, under this model, in which Delta can sequester Notch, a variety of patterns resembling those typical of reaction–diffusion systems is observed, together with more unusual patterns that arise when we consider changes in signalling kinetics, and in the length and distribution of protrusions. Importantly, these patterns are self-organizing—so that local interactions drive tissue-scale patterning. Together, these data show that protrusions can, in principle, generate different types of patterns in addition to contributing to long-range signalling and to pattern refinement. PMID:27807273

Human-Machine Interface for the Control of Multi-Function Systems Based on Electrocutaneous Menu: Application to Multi-Grasp Prosthetic Hands

PubMed Central

Gonzalez-Vargas, Jose; Dosen, Strahinja; Amsuess, Sebastian; Yu, Wenwei; Farina, Dario

2015-01-01

Modern assistive devices are very sophisticated systems with multiple degrees of freedom. However, an effective and user-friendly control of these systems is still an open problem since conventional human-machine interfaces (HMI) cannot easily accommodate the system’s complexity. In HMIs, the user is responsible for generating unique patterns of command signals directly triggering the device functions. This approach can be difficult to implement when there are many functions (necessitating many command patterns) and/or the user has a considerable impairment (limited number of available signal sources). In this study, we propose a novel concept for a general-purpose HMI where the controller and the user communicate bidirectionally to select the desired function. The system first presents possible choices to the user via electro-tactile stimulation; the user then acknowledges the desired choice by generating a single command signal. Therefore, the proposed approach simplifies the user communication interface (one signal to generate), decoding (one signal to recognize), and allows selecting from a number of options. To demonstrate the new concept the method was used in one particular application, namely, to implement the control of all the relevant functions in a state of the art commercial prosthetic hand without using any myoelectric channels. We performed experiments in healthy subjects and with one amputee to test the feasibility of the novel approach. The results showed that the performance of the novel HMI concept was comparable or, for some outcome measures, better than the classic myoelectric interfaces. The presented approach has a general applicability and the obtained results point out that it could be used to operate various assistive systems (e.g., prosthesis vs. wheelchair), or it could be integrated into other control schemes (e.g., myoelectric control, brain-machine interfaces) in order to improve the usability of existing low-bandwidth HMIs. PMID:26069961

Human-Machine Interface for the Control of Multi-Function Systems Based on Electrocutaneous Menu: Application to Multi-Grasp Prosthetic Hands.

PubMed

Gonzalez-Vargas, Jose; Dosen, Strahinja; Amsuess, Sebastian; Yu, Wenwei; Farina, Dario

2015-01-01

Modern assistive devices are very sophisticated systems with multiple degrees of freedom. However, an effective and user-friendly control of these systems is still an open problem since conventional human-machine interfaces (HMI) cannot easily accommodate the system's complexity. In HMIs, the user is responsible for generating unique patterns of command signals directly triggering the device functions. This approach can be difficult to implement when there are many functions (necessitating many command patterns) and/or the user has a considerable impairment (limited number of available signal sources). In this study, we propose a novel concept for a general-purpose HMI where the controller and the user communicate bidirectionally to select the desired function. The system first presents possible choices to the user via electro-tactile stimulation; the user then acknowledges the desired choice by generating a single command signal. Therefore, the proposed approach simplifies the user communication interface (one signal to generate), decoding (one signal to recognize), and allows selecting from a number of options. To demonstrate the new concept the method was used in one particular application, namely, to implement the control of all the relevant functions in a state of the art commercial prosthetic hand without using any myoelectric channels. We performed experiments in healthy subjects and with one amputee to test the feasibility of the novel approach. The results showed that the performance of the novel HMI concept was comparable or, for some outcome measures, better than the classic myoelectric interfaces. The presented approach has a general applicability and the obtained results point out that it could be used to operate various assistive systems (e.g., prosthesis vs. wheelchair), or it could be integrated into other control schemes (e.g., myoelectric control, brain-machine interfaces) in order to improve the usability of existing low-bandwidth HMIs.

A metric for quantifying El Niño pattern diversity with implications for ENSO-mean state interaction

NASA Astrophysics Data System (ADS)

Lemmon, Danielle E.; Karnauskas, Kristopher B.

2018-04-01

Recent research on the El Niño-Southern Oscillation (ENSO) phenomenon increasingly reveals the highly complex and diverse nature of ENSO variability. A method of quantifying ENSO spatial pattern uniqueness and diversity is presented, which enables (1) formally distinguishing between unique and "canonical" El Niño events, (2) testing whether historical model simulations aptly capture ENSO diversity by comparing with instrumental observations, (3) projecting future ENSO diversity using future model simulations, (4) understanding the dynamics that give rise to ENSO diversity, and (5) analyzing the associated diversity of ENSO-related atmospheric teleconnection patterns. Here we develop a framework for measuring El Niño spatial SST pattern uniqueness and diversity for a given set of El Niño events using two indices, the El Niño Pattern Uniqueness (EPU) index and El Niño Pattern Diversity (EPD) index, respectively. By applying this framework to instrumental records, we independently confirm a recent regime shift in El Niño pattern diversity with an increase in unique El Niño event sea surface temperature patterns. However, the same regime shift is not observed in historical CMIP5 model simulations; moreover, a comparison between historical and future CMIP5 model scenarios shows no robust change in future ENSO diversity. Finally, we support recent work that asserts a link between the background cooling of the eastern tropical Pacific and changes in ENSO diversity. This robust link between an eastern Pacific cooling mode and ENSO diversity is observed not only in instrumental reconstructions and reanalysis, but also in historical and future CMIP5 model simulations.

Co-culture of osteocytes and neurons on a unique patterned surface.

PubMed

Boggs, Mary E; Thompson, William R; Farach-Carson, Mary C; Duncan, Randall L; Beebe, Thomas P

2011-12-01

Neural and skeletal communication is essential for the maintenance of bone mass and transmission of pain, yet the mechanism(s) of signal transduction between these tissues is unknown. The authors established a novel system to co-culture murine long bone osteocyte-like cells (MLO-Y4) and primary murine dorsal root ganglia (DRG) neurons. Assessment of morphology and maturation marker expression on perlecan domain IV peptide (PlnDIV) and collagen type-1 (Col1) demonstrated that PlnDIV was an optimal matrix for MLO-Y4 culture. A novel matrix-specificity competition assay was developed to expose these cells to several extracellular matrix proteins such as PlnDIV, Col1, and laminin (Ln). The competition assay showed that approximately 70% of MLO-Y4 cells preferred either PlnDIV or Col1 to Ln. To co-culture MLO-Y4 and DRG, we developed patterned surfaces using micro-contact printing to create 40 μm × 1 cm alternating stripes of PlnDIV and Ln or PlnDIV and Col1. Co-culture on PlnDIV/Ln surfaces demonstrated that these matrix molecules provided unique cues for each cell type, with MLO-Y4 preferentially attaching to the PlnDIV lanes and DRG neurons to the Ln lanes. Approximately 80% of DRG were localized to Ln. Cellular processes from MLO-Y4 were closely associated with axonal extensions of DRG neurons. Approximately 57% of neuronal processes were in close proximity to nearby MLO-Y4 cells at the PlnDIV-Ln interface. The surfaces in this new assay provided a unique model system with which to study the communication between osteocyte-like cells and neurons in an in vitro environment.

SH2 Domain Histochemistry.

PubMed

Buhs, Sophia; Nollau, Peter

2017-01-01

Among posttranslational modifications, the phosphorylation of tyrosine residues is a key modification in cell signaling. Because of its biological importance, characterization of the cellular state of tyrosine phosphorylation is of great interest. Based on the unique properties of endogenously expressed SH2 domains recognizing tyrosine phosphorylated signaling proteins with high specificity we have developed an alternative approach, coined SH2 profiling, enabling us to decipher complex patterns of tyrosine phosphorylation in various normal and cancerous tissues. So far, SH2 profiling has largely been applied for the analysis of protein extracts with the limitation that information on spatial distribution and intensity of tyrosine phosphorylation within a tissue is lost. Here, we describe a novel SH2 domain based strategy for differential characterization of the state of tyrosine phosphorylation in formaldehyde-fixed and paraffin-embedded tissues. This approach demonstrates that SH2 domains may serve as very valuable tools for the analysis of the differential state of tyrosine phosphorylation in primary tissues fixed and processed under conditions frequently applied by routine pathology laboratories.

Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci

PubMed Central

Ellinghaus, David; Jostins, Luke; Spain, Sarah L; Cortes, Adrian; Bethune, Jörn; Han, Buhm; Park, Yu Rang; Raychaudhuri, Soumya; Pouget, Jennie G; Hübenthal, Matthias; Folseraas, Trine; Wang, Yunpeng; Esko, Tonu; Metspalu, Andres; Westra, Harm-Jan; Franke, Lude; Pers, Tune H; Weersma, Rinse K; Collij, Valerie; D'Amato, Mauro; Halfvarson, Jonas; Jensen, Anders Boeck; Lieb, Wolfgang; Degenhardt, Franziska; Forstner, Andreas J; Hofmann, Andrea; Schreiber, Stefan; Mrowietz, Ulrich; Juran, Brian D; Lazaridis, Konstantinos N; Brunak, Søren; Dale, Anders M; Trembath, Richard C; Weidinger, Stephan; Weichenthal, Michael; Ellinghaus, Eva; Elder, James T; Barker, Jonathan NWN; Andreassen, Ole A; McGovern, Dermot P; Karlsen, Tom H; Barrett, Jeffrey C; Parkes, Miles; Brown, Matthew A; Franke, Andre

2016-01-01

We simultaneously investigated the genetic landscape of ankylosing spondylitis, Crohn's disease, psoriasis, primary sclerosing cholangitis and ulcerative colitis to investigate pleiotropy and the relationship between these clinically related diseases. Using high-density genotype data from more than 86,000 individuals of European-ancestry we identified 244 independent multi-disease signals including 27 novel genome-wide significant susceptibility loci and 3 unreported shared risk loci. Complex pleiotropy was supported when contrasting multi-disease signals with expression data sets from human, rat and mouse, and epigenetic and expressed enhancer profiles. The comorbidities among the five immune diseases were best explained by biological pleiotropy rather than heterogeneity (a subgroup of cases that is genetically identical to another disease, possibly due to diagnostic misclassification, molecular subtypes, or excessive comorbidity). In particular, the strong comorbidity between primary sclerosing cholangitis and inflammatory bowel disease is likely the result of a unique disease, which is genetically distinct from classical inflammatory bowel disease phenotypes. PMID:26974007

Extra-embryonic tissue spreading directs early embryo morphogenesis in killifish

PubMed Central

Reig, Germán; Cerda, Mauricio; Sepúlveda, Néstor; Flores, Daniela; Castañeda, Victor; Tada, Masazumi; Härtel, Steffen; Concha, Miguel L.

2017-01-01

The spreading of mesenchymal-like cell layers is critical for embryo morphogenesis and tissue repair, yet we know little of this process in vivo. Here we take advantage of unique developmental features of the non-conventional annual killifish embryo to study the principles underlying tissue spreading in a simple cellular environment, devoid of patterning signals and major morphogenetic cell movements. Using in vivo experimentation and physical modelling we reveal that the extra-embryonic epithelial enveloping cell layer, thought mainly to provide protection to the embryo, directs cell migration and the spreading of embryonic tissue during early development. This function relies on the ability of embryonic cells to couple their autonomous random motility to non-autonomous signals arising from the expansion of the extra-embryonic epithelium, mediated by cell membrane adhesion and tension. Thus, we present a mechanism of extra-embryonic control of embryo morphogenesis that couples the mechanical properties of adjacent tissues in the early killifish embryo. PMID:28580937

SIGNR3-dependent immune regulation by Lactobacillus acidophilus surface layer protein A in colitis

PubMed Central

Lightfoot, Yaíma L; Selle, Kurt; Yang, Tao; Goh, Yong Jun; Sahay, Bikash; Zadeh, Mojgan; Owen, Jennifer L; Colliou, Natacha; Li, Eric; Johannssen, Timo; Lepenies, Bernd; Klaenhammer, Todd R; Mohamadzadeh, Mansour

2015-01-01

Intestinal immune regulatory signals govern gut homeostasis. Breakdown of such regulatory mechanisms may result in inflammatory bowel disease (IBD). Lactobacillus acidophilus contains unique surface layer proteins (Slps), including SlpA, SlpB, SlpX, and lipoteichoic acid (LTA), which interact with pattern recognition receptors to mobilize immune responses. Here, to elucidate the role of SlpA in protective immune regulation, the NCK2187 strain, which solely expresses SlpA, was generated. NCK2187 and its purified SlpA bind to the C-type lectin SIGNR3 to exert regulatory signals that result in mitigation of colitis, maintenance of healthy gastrointestinal microbiota, and protected gut mucosal barrier function. However, such protection was not observed in Signr3−/− mice, suggesting that the SlpA/SIGNR3 interaction plays a key regulatory role in colitis. Our work presents critical insights into SlpA/SIGNR3-induced responses that are integral to the potential development of novel biological therapies for autoinflammatory diseases, including IBD. PMID:25666591

SIGNR3-dependent immune regulation by Lactobacillus acidophilus surface layer protein A in colitis.

PubMed

Lightfoot, Yaíma L; Selle, Kurt; Yang, Tao; Goh, Yong Jun; Sahay, Bikash; Zadeh, Mojgan; Owen, Jennifer L; Colliou, Natacha; Li, Eric; Johannssen, Timo; Lepenies, Bernd; Klaenhammer, Todd R; Mohamadzadeh, Mansour

2015-04-01

Intestinal immune regulatory signals govern gut homeostasis. Breakdown of such regulatory mechanisms may result in inflammatory bowel disease (IBD). Lactobacillus acidophilus contains unique surface layer proteins (Slps), including SlpA, SlpB, SlpX, and lipoteichoic acid (LTA), which interact with pattern recognition receptors to mobilize immune responses. Here, to elucidate the role of SlpA in protective immune regulation, the NCK2187 strain, which solely expresses SlpA, was generated. NCK2187 and its purified SlpA bind to the C-type lectin SIGNR3 to exert regulatory signals that result in mitigation of colitis, maintenance of healthy gastrointestinal microbiota, and protected gut mucosal barrier function. However, such protection was not observed in Signr3(-/-) mice, suggesting that the SlpA/SIGNR3 interaction plays a key regulatory role in colitis. Our work presents critical insights into SlpA/SIGNR3-induced responses that are integral to the potential development of novel biological therapies for autoinflammatory diseases, including IBD. © 2015 The Authors.

Where one hand meets the other: limb-specific and action-dependent movement plans decoded from preparatory signals in single human frontoparietal brain areas.

PubMed

Gallivan, Jason P; McLean, D Adam; Flanagan, J Randall; Culham, Jody C

2013-01-30

Planning object-directed hand actions requires successful integration of the movement goal with the acting limb. Exactly where and how this sensorimotor integration occurs in the brain has been studied extensively with neurophysiological recordings in nonhuman primates, yet to date, because of limitations of non-invasive methodologies, the ability to examine the same types of planning-related signals in humans has been challenging. Here we show, using a multivoxel pattern analysis of functional MRI (fMRI) data, that the preparatory activity patterns in several frontoparietal brain regions can be used to predict both the limb used and hand action performed in an upcoming movement. Participants performed an event-related delayed movement task whereby they planned and executed grasp or reach actions with either their left or right hand toward a single target object. We found that, although the majority of frontoparietal areas represented hand actions (grasping vs reaching) for the contralateral limb, several areas additionally coded hand actions for the ipsilateral limb. Notable among these were subregions within the posterior parietal cortex (PPC), dorsal premotor cortex (PMd), ventral premotor cortex, dorsolateral prefrontal cortex, presupplementary motor area, and motor cortex, a region more traditionally implicated in contralateral movement generation. Additional analyses suggest that hand actions are represented independently of the intended limb in PPC and PMd. In addition to providing a unique mapping of limb-specific and action-dependent intention-related signals across the human cortical motor system, these findings uncover a much stronger representation of the ipsilateral limb than expected from previous fMRI findings.

Neural activity in the reward-related brain regions predicts implicit self-esteem: A novel validity test of psychological measures using neuroimaging.

PubMed

Izuma, Keise; Kennedy, Kate; Fitzjohn, Alexander; Sedikides, Constantine; Shibata, Kazuhisa

2018-03-01

Self-esteem, arguably the most important attitudes an individual possesses, has been a premier research topic in psychology for more than a century. Following a surge of interest in implicit attitude measures in the 90s, researchers have tried to assess self-esteem implicitly to circumvent the influence of biases inherent in explicit measures. However, the validity of implicit self-esteem measures remains elusive. Critical tests are often inconclusive, as the validity of such measures is examined in the backdrop of imperfect behavioral measures. To overcome this serious limitation, we tested the neural validity of the most widely used implicit self-esteem measure, the implicit association test (IAT). Given the conceptualization of self-esteem as attitude toward the self, and neuroscience findings that the reward-related brain regions represent an individual's attitude or preference for an object when viewing its image, individual differences in implicit self-esteem should be associated with neural signals in the reward-related regions during passive-viewing of self-face (the most obvious representation of the self). Using multi-voxel pattern analysis (MVPA) on functional MRI (fMRI) data, we demonstrate that the neural signals in the reward-related regions were robustly associated with implicit (but not explicit) self-esteem, thus providing unique evidence for the neural validity of the self-esteem IAT. In addition, both implicit and explicit self-esteem were related, although differently, to neural signals in regions involved in self-processing. Our finding highlights the utility of neuroscience methods in addressing fundamental psychological questions and providing unique insights into important psychological constructs. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Muscle activation patterns and motor anatomy of Anna's hummingbirds Calypte anna and zebra finches Taeniopygia guttata.

PubMed

Donovan, Edward R; Keeney, Brooke K; Kung, Eric; Makan, Sirish; Wild, J Martin; Altshuler, Douglas L

2013-01-01

Flying animals exhibit profound transformations in anatomy, physiology, and neural architecture. Although much is known about adaptations in the avian skeleton and musculature, less is known about neuroanatomy and motor unit integration for bird flight. Hummingbirds are among the most maneuverable and specialized of vertebrate fliers, and two unusual neuromuscular features have been previously reported: (1) the pectoralis major has a unique distribution pattern of motor end plates (MEPs) compared with all other birds and (2) electromyograms (EMGs) from the hummingbird's pectoral muscles, the pectoralis major and the supracoracoideus, show activation bursts composed of one or a few spikes that appear to have a very consistent pattern. Here, we place these findings in a broader context by comparing the MEPs, EMGs, and organization of the spinal motor neuron pools of flight muscles of Anna's hummingbird Calypte anna, zebra finches Taeniopygia guttata, and, for MEPs, several other species. The previously shown MEP pattern of the hummingbird pectoralis major is not shared with its closest taxonomic relative, the swift, and appears to be unique to hummingbirds. MEP arrangements in previously undocumented wing muscles show patterns that differ somewhat from other avian muscles. In the parallel-fibered strap muscles of the shoulder, MEP patterns appear to relate to muscle length, with the smallest muscles having fibers that span the entire muscle. MEP patterns in pennate distal wing muscles were the same regardless of size, with tightly clustered bands in the middle portion of the muscle, not evenly distributed bands over the muscle's entire length. Muscle activations were examined during slow forward flight in both species, during hovering in hummingbirds, and during slow ascents in zebra finches. The EMG bursts of a wing muscle, the pronator superficialis, were highly variable in peak number, size, and distribution across wingbeats for both species. In the pectoralis major, although the individual EMG bursts were much shorter in duration in hummingbirds relative to zebra finches, the variables describing the normalized amplitude and area of the activation bursts were otherwise indistinguishable between taxa during these flight modes. However, the degree of variation in the time intervals between EMG peaks was much lower in hummingbirds, which is a plausible explanation for the "patterned" EMG signals reported previously.

New Therapeutic Window of Regenerative Opportunity in Diabetic Retinopathy by VESGEN Analysis

NASA Technical Reports Server (NTRS)

Parsons-Wingert, Patricia A.

2012-01-01

Vascular pattern may serve as a useful new biomarker principle of complex, multi-scale signaling in pathological, physiological angiogenesis and microvascular remodeling. Each angiogenesis stimulator or inhibitor we have analyzed, including VEGF, bFGF, TGF-beta1, angiostatin and triamcinolone acetonide, has induced a novel "fingerprint" or "signature" biomarker vascular pattern that is spatio-temporally unique. Remodeling vasculature thereby provides an informative read-out of dominant molecular signaling, when analyzed by innovative, fractal-based VESsel GENeration (VESGEN) Analysis software. Using VESGEN to analyze ophthalmic clinical vascular images, we recently introduced a potential paradigm shift to the understanding of early-stage progression that suggests new regenerative opportunities for human diabetic retinopathy (DR), the major blinding disease for working-aged adults. In a pilot study, we discovered that angiogenesis oscillates as a surprising, homeostatic-like regeneration of retinal vessels during early progression of DR (IOVS 51(1):498). Results suggest that the term non-proliferative DR may be a misnomer. In new studies, normalization of the vasculature will be determined from the response of vascular pattern to therapeutic monitoring and treatment. We have mapped and quantified in vivo experimental models of angiogenesis, lymphangiogenesis and intravital blood flow from cellular/molecular to higher systems levels that include a murine model of infant retinopathy of prematurity (ROP); developing and pathological coronary and placental-like vessel models; progressive intestinal inflammation, growing murine tumors, and other pathological, physiological and therapeutically treated tissues of transgenic mice and avian embryos. Vascular Alterations, Visual Impairments (VIIP) & Increased Intracranial Pressure (ICP), Immunosuppression & Bone Loss: NASA-defined risk categories for human space exploration and ISS Utilization

Individual differences in functional connectivity during naturalistic viewing conditions.

PubMed

Vanderwal, Tamara; Eilbott, Jeffrey; Finn, Emily S; Craddock, R Cameron; Turnbull, Adam; Castellanos, F Xavier

2017-08-15

Naturalistic viewing paradigms such as movies have been shown to reduce participant head motion and improve arousal during fMRI scanning relative to task-free rest, and have been used to study both functional connectivity and stimulus-evoked BOLD-signal changes. These task-based hemodynamic changes are synchronized across subjects and involve large areas of the cortex, and it is unclear whether individual differences in functional connectivity are enhanced or diminished under such naturalistic conditions. This work first aims to characterize variability in BOLD-signal based functional connectivity (FC) across 2 distinct movie conditions and eyes-open rest (n=31 healthy adults, 2 scan sessions each). We found that movies have higher within- and between-subject correlations in cluster-wise FC relative to rest. The anatomical distribution of inter-individual variability was similar across conditions, with higher variability occurring at the lateral prefrontal lobes and temporoparietal junctions. Second, we used an unsupervised test-retest matching algorithm that identifies individual subjects from within a group based on FC patterns, quantifying the accuracy of the algorithm across the three conditions. The movies and resting state all enabled identification of individual subjects based on FC matrices, with accuracies between 61% and 100%. Overall, pairings involving movies outperformed rest, and the social, faster-paced movie attained 100% accuracy. When the parcellation resolution, scan duration, and number of edges used were increased, accuracies improved across conditions, and the pattern of movies>rest was preserved. These results suggest that using dynamic stimuli such as movies enhances the detection of FC patterns that are unique at the individual level. Copyright © 2017 Elsevier Inc. All rights reserved.

Direction of Magnetoencephalography Sources Associated with Feedback and Feedforward Contributions in a Visual Object Recognition Task

PubMed Central

Ahlfors, Seppo P.; Jones, Stephanie R.; Ahveninen, Jyrki; Hämäläinen, Matti S.; Belliveau, John W.; Bar, Moshe

2014-01-01

Identifying inter-area communication in terms of the hierarchical organization of functional brain areas is of considerable interest in human neuroimaging. Previous studies have suggested that the direction of magneto- and electroencephalography (MEG, EEG) source currents depends on the layer-specific input patterns into a cortical area. We examined the direction in MEG source currents in a visual object recognition experiment in which there were specific expectations of activation in the fusiform region being driven by either feedforward or feedback inputs. The source for the early non-specific visual evoked response, presumably corresponding to feedforward driven activity, pointed outward, i.e., away from the white matter. In contrast, the source for the later, object-recognition related signals, expected to be driven by feedback inputs, pointed inward, toward the white matter. Associating specific features of the MEG/EEG source waveforms to feedforward and feedback inputs could provide unique information about the activation patterns within hierarchically organized cortical areas. PMID:25445356

Neural coding strategies in auditory cortex.

PubMed

Wang, Xiaoqin

2007-07-01

In contrast to the visual system, the auditory system has longer subcortical pathways and more spiking synapses between the peripheral receptors and the cortex. This unique organization reflects the needs of the auditory system to extract behaviorally relevant information from a complex acoustic environment using strategies different from those used by other sensory systems. The neural representations of acoustic information in auditory cortex can be characterized by three types: (1) isomorphic (faithful) representations of acoustic structures; (2) non-isomorphic transformations of acoustic features and (3) transformations from acoustical to perceptual dimensions. The challenge facing auditory neurophysiologists is to understand the nature of the latter two transformations. In this article, I will review recent studies from our laboratory regarding temporal discharge patterns in auditory cortex of awake marmosets and cortical representations of time-varying signals. Findings from these studies show that (1) firing patterns of neurons in auditory cortex are dependent on stimulus optimality and context and (2) the auditory cortex forms internal representations of sounds that are no longer faithful replicas of their acoustic structures.

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.

The shoot stem cell niche in angiosperms: expression patterns of WUS orthologues in rice and maize imply major modifications in the course of mono- and dicot evolution.

PubMed

Nardmann, Judith; Werr, Wolfgang

2006-12-01

In Arabidopsis, stem cell homeostasis in the shoot apical meristem (SAM) is controlled by a feedback loop between WUS and CLV functions. We have identified WUS orthologues in maize and rice by a detailed phylogenetic analysis of the WOX gene family and subsequent cloning. A single WUS orthologue is present in the rice genome (OsWUS), whereas the allotetraploid maize genome contains 2 WUS paralogues (ZmWUS1 and ZmWUS2). None of the isolated grass WUS orthologues displays an organizing center-type expression pattern in the vegetative SAM as in Arabidopsis. In contrast, the grass-specific expression patterns relate to the specification of new phytomers consistent with the transcriptional expression patterns of TD1 and FON1 (CLV1 orthologues of maize and rice, respectively). Moreover, the grass WUS and CLV1 orthologues are coexpressed in all reproductive meristems, where fasciation and supernumerary floral organs occur in td1 or fon1 loss-of-function mutants. The expression patterns of WUS orthologues in both grass species compared with those of dicots imply that major changes in WUS function, which are correlated with changes in CLV1 signaling, have occurred during angiosperm evolution and raise doubts about the uniqueness of the WUS/CLV antagonism in the maintenance of the shoot stem cell niche in grasses.

Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal.

PubMed

Smith, Rob; Taylor, Ryan M; Prince, John T

2015-01-01

The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts.

The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan.

PubMed

Manning, Gerard; Young, Susan L; Miller, W Todd; Zhai, Yufeng

2008-07-15

Tyrosine kinase signaling has long been considered a hallmark of intercellular communication, unique to multicellular animals. Our genomic analysis of the unicellular choanoflagellate Monosiga brevicollis discovers a remarkable count of 128 tyrosine kinases, 38 tyrosine phosphatases, and 123 phosphotyrosine (pTyr)-binding SH2 proteins, all higher counts than seen in any metazoan. This elaborate signaling network shows little orthology to metazoan counterparts yet displays many innovations reminiscent of metazoans. These include extracellular domains structurally related to those of metazoan receptor kinases, alternative methods for membrane anchoring and phosphotyrosine interaction in cytoplasmic kinases, and domain combinations that link kinases to small GTPase signaling and transcription. These proteins also display a wealth of combinations of known signaling domains. This uniquely divergent and elaborate signaling network illuminates the early evolution of pTyr signaling, explores innovative ways to traverse the cellular signaling circuitry, and shows extensive convergent evolution, highlighting pervasive constraints on pTyr signaling.

G protein signaling in plants: minus times minus equals plus.

PubMed

Stateczny, Dave; Oppenheimer, Jara; Bommert, Peter

2016-12-01

Heterotrimeric G proteins are key regulators in the transduction of extracellular signals both in animals and plants. In plants, heterotrimeric G protein signaling plays essential roles in development and in response to biotic and abiotic stress. However, over the last decade it has become clear that plants have unique mechanisms of G protein signaling. Although plants share most of the core components of heterotrimeric G proteins, some of them exhibit unusual properties compared to their animal counterparts. In addition, plants do not share functional GPCRs. Therefore the well-established paradigm of the animal G protein signaling cycle is not applicable in plants. In this review, we summarize recent insights into these unique mechanisms of G protein signaling in plants with special focus on the evident potential of G protein signaling as a target to modify developmental and physiological parameters important for yield increase. Copyright © 2016 Elsevier Ltd. All rights reserved.

Method and apparatus for automatically detecting patterns in digital point-ordered signals

DOEpatents

Brudnoy, David M.

1998-01-01

The present invention is a method and system for detecting a physical feature of a test piece by detecting a pattern in a signal representing data from inspection of the test piece. The pattern is detected by automated additive decomposition of a digital point-ordered signal which represents the data. The present invention can properly handle a non-periodic signal. A physical parameter of the test piece is measured. A digital point-ordered signal representative of the measured physical parameter is generated. The digital point-ordered signal is decomposed into a baseline signal, a background noise signal, and a peaks/troughs signal. The peaks/troughs from the peaks/troughs signal are located and peaks/troughs information indicating the physical feature of the test piece is output.

Method and apparatus for automatically detecting patterns in digital point-ordered signals

DOEpatents

Brudnoy, D.M.

1998-10-20

The present invention is a method and system for detecting a physical feature of a test piece by detecting a pattern in a signal representing data from inspection of the test piece. The pattern is detected by automated additive decomposition of a digital point-ordered signal which represents the data. The present invention can properly handle a non-periodic signal. A physical parameter of the test piece is measured. A digital point-ordered signal representative of the measured physical parameter is generated. The digital point-ordered signal is decomposed into a baseline signal, a background noise signal, and a peaks/troughs signal. The peaks/troughs from the peaks/troughs signal are located and peaks/troughs information indicating the physical feature of the test piece is output. 14 figs.

Develop advanced nonlinear signal analysis topographical mapping system

NASA Technical Reports Server (NTRS)

1994-01-01

The Space Shuttle Main Engine (SSME) has been undergoing extensive flight certification and developmental testing, which involves some 250 health monitoring measurements. Under the severe temperature, pressure, and dynamic environments sustained during operation, numerous major component failures have occurred, resulting in extensive engine hardware damage and scheduling losses. To enhance SSME safety and reliability, detailed analysis and evaluation of the measurements signal are mandatory to assess its dynamic characteristics and operational condition. Efficient and reliable signal detection techniques will reduce catastrophic system failure risks and expedite the evaluation of both flight and ground test data, and thereby reduce launch turn-around time. The basic objective of this contract are threefold: (1) develop and validate a hierarchy of innovative signal analysis techniques for nonlinear and nonstationary time-frequency analysis. Performance evaluation will be carried out through detailed analysis of extensive SSME static firing and flight data. These techniques will be incorporated into a fully automated system; (2) develop an advanced nonlinear signal analysis topographical mapping system (ATMS) to generate a Compressed SSME TOPO Data Base (CSTDB). This ATMS system will convert tremendous amount of complex vibration signals from the entire SSME test history into a bank of succinct image-like patterns while retaining all respective phase information. High compression ratio can be achieved to allow minimal storage requirement, while providing fast signature retrieval, pattern comparison, and identification capabilities; and (3) integrate the nonlinear correlation techniques into the CSTDB data base with compatible TOPO input data format. Such integrated ATMS system will provide the large test archives necessary for quick signature comparison. This study will provide timely assessment of SSME component operational status, identify probable causes of malfunction, and indicate feasible engineering solutions. The final result of this program will yield an ATMS system of nonlinear and nonstationary spectral analysis software package integrated with the Compressed SSME TOPO Data Base (CSTDB) on the same platform. This system will allow NASA engineers to retrieve any unique defect signatures and trends associated with different failure modes and anomalous phenomena over the entire SSME test history across turbo pump families.

Develop advanced nonlinear signal analysis topographical mapping system

NASA Technical Reports Server (NTRS)

Jong, Jen-Yi

1993-01-01

The SSME has been undergoing extensive flight certification and developmental testing, which involves some 250 health monitoring measurements. Under the severe temperature pressure, and dynamic environments sustained during operation, numerous major component failures have occurred, resulting in extensive engine hardware damage and scheduling losses. To enhance SSME safety and reliability, detailed analysis and evaluation of the measurements signal are mandatory to assess its dynamic characteristics and operational condition. Efficient and reliable signal detection techniques will reduce catastrophic system failure risks and expedite the evaluation of both flight and ground test data, and thereby reduce launch turn-around time. The basic objective of this contract are threefold: (1) Develop and validate a hierarchy of innovative signal analysis techniques for nonlinear and nonstationary time-frequency analysis. Performance evaluation will be carried out through detailed analysis of extensive SSME static firing and flight data. These techniques will be incorporated into a fully automated system. (2) Develop an advanced nonlinear signal analysis topographical mapping system (ATMS) to generate a Compressed SSME TOPO Data Base (CSTDB). This ATMS system will convert tremendous amounts of complex vibration signals from the entire SSME test history into a bank of succinct image-like patterns while retaining all respective phase information. A high compression ratio can be achieved to allow the minimal storage requirement, while providing fast signature retrieval, pattern comparison, and identification capabilities. (3) Integrate the nonlinear correlation techniques into the CSTDB data base with compatible TOPO input data format. Such integrated ATMS system will provide the large test archives necessary for a quick signature comparison. This study will provide timely assessment of SSME component operational status, identify probable causes of malfunction, and indicate feasible engineering solutions. The final result of this program will yield an ATMS system of nonlinear and nonstationary spectral analysis software package integrated with the Compressed SSME TOPO Data Base (CSTDB) on the same platform. This system will allow NASA engineers to retrieve any unique defect signatures and trends associated with different failure modes and anomalous phenomena over the entire SSME test history across turbo pump families.

Genomic Expression Patterns in Menstrually-Related Migraine in Adolescents

PubMed Central

Hershey, Andrew; Horn, Paul; Kabbouche, Marielle; O'Brien, Hope; Powers, Scott

2011-01-01

Background Exacerbation of migraine with menses is common in adolescent girls and women with migraine, occurring in up to 60% of females with migraine. These migraines are oftentimes longer and more disabling and may be related to estrogen levels and hormonal fluctuations. Objective This study identifies the unique genomic expression pattern of menstrually-related migraine (MRM) in comparison to migraine occurring outside the menstrual period and headache free controls. Methods Whole blood samples were obtained from female subjects having an acute migraine during their menstrual period (MRM) or outside of their menstrual period (nonMRM) and controls (C) – females having a menstrual period without any history of headache. The mRNA was isolated from these samples and genomic profile was assessed. Affymetrix Human Exon ST 1.0 arrays were used to examine the genomic expression pattern differences between these three groups. Results Blood genomic expression patterns were obtained on 56 subjects (MRM = 18, nonMRM = 18 and C = 20). Unique genomic expression patterns were observed for both MRM and nonMRM. For MRM, 77 genes were identified that were unique to MRM, while 61 genes were commonly expressed for MRM and nonMRM and 127 genes appeared to have a unique expression pattern for nonMRM. In addition, there were 279 genes that differentially expressed for MRM compared to nonMRM that were not differentially expressed for nonMRM. Gene ontology of these samples indicated many of these groups of genes were functionally related and included categories of immunomodulation/inflammation, mitochondrial function and DNA homeostasis. Conclusions Blood genomic patterns can accurately differentiate MRM from nonMRM. These results indicate that MRM involves a unique molecular biology pathway that can be identified with a specific biomarker and suggest that individuals with MRM have a different underlying genetic etiology. PMID:22220971

Macroecological factors shape local-scale spatial patterns in agriculturalist settlements.

PubMed

Tao, Tingting; Abades, Sebastián; Teng, Shuqing; Huang, Zheng Y X; Reino, Luís; Chen, Bin J W; Zhang, Yong; Xu, Chi; Svenning, Jens-Christian

2017-11-15

Macro-scale patterns of human systems ranging from population distribution to linguistic diversity have attracted recent attention, giving rise to the suggestion that macroecological rules shape the assembly of human societies. However, in which aspects the geography of our own species is shaped by macroecological factors remains poorly understood. Here, we provide a first demonstration that macroecological factors shape strong local-scale spatial patterns in human settlement systems, through an analysis of spatial patterns in agriculturalist settlements in eastern mainland China based on high-resolution Google Earth images. We used spatial point pattern analysis to show that settlement spatial patterns are characterized by over-dispersion at fine spatial scales (0.05-1.4 km), consistent with territory segregation, and clumping at coarser spatial scales beyond the over-dispersion signals, indicating territorial clustering. Statistical modelling shows that, at macroscales, potential evapotranspiration and topographic heterogeneity have negative effects on territory size, but positive effects on territorial clustering. These relationships are in line with predictions from territory theory for hunter-gatherers as well as for many animal species. Our results help to disentangle the complex interactions between intrinsic spatial processes in agriculturalist societies and external forcing by macroecological factors. While one may speculate that humans can escape ecological constraints because of unique abilities for environmental modification and globalized resource transportation, our work highlights that universal macroecological principles still shape the geography of current human agricultural societies. © 2017 The Author(s).

Tungstate-induced color-pattern modifications of butterfly wings are independent of stress response and ecdysteroid effect.

PubMed

Otaki, Joji M; Ogasawara, Tsuyoshi; Yamamoto, Haruhiko

2005-06-01

Systemic injections of sodium tungstate, a protein-tyrosine phosphatase (PTPase) inhibitor, to pupae immediately after pupation have been shown to efficiently produce characteristic color-pattern modifications on the wings of many species of butterflies. Here we demonstrated that the tungstate-induced modification pattern was entirely different from other chemically-induced ones in a species of nymphalid butterfly Junonia (Precis) orithya. In this species, the systemic injections of tungstate produced characteristic expansion of black area and shrinkage of white area together with the move of parafocal elements toward the wing base. Overall, pattern boundaries became obscure. In contrast, an entirely different modification pattern, overall darkening of wings, was observed by the injections of stress-inducing chemicals, thapsigargin, ionomycin, or geldanamycin, to pupae under the rearing conditions for the adult summer form. On the ventral wings, this darkening was due to an increase of the proportion of peppered dark scales, which was reminiscent of the natural fall form of this species. Under the same rearing conditions, the injections of ecdysteroid, which is a well-known hormone being responsible for the seasonal polyphenism of nymphalid butterflies, yielded overall expansion of orange area especially around eyespots. Taken together, we conclude that the tungstate-induced modifications are clearly distinguishable from those of stress response and ecdysteroid effect. This conclusion then suggests that the putative PTPase signaling pathway that is sensitive to tungstate uniquely contributes to the wing-wide color-pattern development in butterflies.

Simulation of range imaging-based estimation of respiratory lung motion. Influence of noise, signal dimensionality and sampling patterns.

PubMed

Wilms, M; Werner, R; Blendowski, M; Ortmüller, J; Handels, H

2014-01-01

A major problem associated with the irradiation of thoracic and abdominal tumors is respiratory motion. In clinical practice, motion compensation approaches are frequently steered by low-dimensional breathing signals (e.g., spirometry) and patient-specific correspondence models, which are used to estimate the sought internal motion given a signal measurement. Recently, the use of multidimensional signals derived from range images of the moving skin surface has been proposed to better account for complex motion patterns. In this work, a simulation study is carried out to investigate the motion estimation accuracy of such multidimensional signals and the influence of noise, the signal dimensionality, and different sampling patterns (points, lines, regions). A diffeomorphic correspondence modeling framework is employed to relate multidimensional breathing signals derived from simulated range images to internal motion patterns represented by diffeomorphic non-linear transformations. Furthermore, an automatic approach for the selection of optimal signal combinations/patterns within this framework is presented. This simulation study focuses on lung motion estimation and is based on 28 4D CT data sets. The results show that the use of multidimensional signals instead of one-dimensional signals significantly improves the motion estimation accuracy, which is, however, highly affected by noise. Only small differences exist between different multidimensional sampling patterns (lines and regions). Automatically determined optimal combinations of points and lines do not lead to accuracy improvements compared to results obtained by using all points or lines. Our results show the potential of multidimensional breathing signals derived from range images for the model-based estimation of respiratory motion in radiation therapy.

Transient rheology of the uppermost mantle beneath the Mojave Desert, California

USGS Publications Warehouse

Pollitz, F.F.

2003-01-01

Geodetic data indicate that the M7.1 Hector Mine, California, earthquake was followed by a brief period (a few weeks) of rapid deformation preceding a prolonged phase of slower deformation. We find that the signal contained in continuous and campaign global positioning system data for 2.5 years after the earthquake may be explained with a transient rheology. Quantitative modeling of these data with allowance for transient (linear biviscous) rheology in the lower crust and upper mantle demonstrates that transient rheology in the upper mantle is dominant, its material properties being typified by two characteristic relaxation times ???0.07 and ???2 years. The inferred mantle rheology is a Jeffreys solid in which the transient and steady-state shear moduli are equal. Consideration of a simpler viscoelastic model with a linear univiscous rheology (2 fewer parameters than a biviscous model) shows that it consistently underpredicts the amplitude of the first ???3 months signal, and allowance for a biviscous rheology is significant at the 99.0% confidence level. Another alternative model - deep postseismic afterslip beneath the coseismic rupture - predicts a vertical velocity pattern opposite to the observed pattern at all time periods considered. Despite its plausibility, the advocated biviscous rheology model is non-unique and should be regarded as a viable alternative to the non-linear mantle rheology model for governing postseismic flow beneath the Mojave Desert. Published by Elsevier B.V.

Ordinal patterns in epileptic brains: Analysis of intracranial EEG and simultaneous EEG-fMRI

NASA Astrophysics Data System (ADS)

Rummel, C.; Abela, E.; Hauf, M.; Wiest, R.; Schindler, K.

2013-06-01

Epileptic seizures are associated with high behavioral stereotypy of the patients. In the EEG of epilepsy patients characteristic signal patterns can be found during and between seizures. Here we use ordinal patterns to analyze EEGs of epilepsy patients and quantify the degree of signal determinism. Besides relative signal redundancy and the fraction of forbidden patterns we introduce the fraction of under-represented patterns as a new measure. Using the logistic map, parameter scans are performed to explore the sensitivity of the measures to signal determinism. Thereafter, application is made to two types of EEGs recorded in two epilepsy patients. Intracranial EEG shows pronounced determinism peaks during seizures. Finally, we demonstrate that ordinal patterns may be useful for improving analysis of non-invasive simultaneous EEG-fMRI.

Distinct neural signatures detected for ADHD subtypes after controlling for micro-movements in resting state functional connectivity MRI data

PubMed Central

Fair, Damien A.; Nigg, Joel T.; Iyer, Swathi; Bathula, Deepti; Mills, Kathryn L.; Dosenbach, Nico U. F.; Schlaggar, Bradley L.; Mennes, Maarten; Gutman, David; Bangaru, Saroja; Buitelaar, Jan K.; Dickstein, Daniel P.; Di Martino, Adriana; Kennedy, David N.; Kelly, Clare; Luna, Beatriz; Schweitzer, Julie B.; Velanova, Katerina; Wang, Yu-Feng; Mostofsky, Stewart; Castellanos, F. Xavier; Milham, Michael P.

2012-01-01

In recent years, there has been growing enthusiasm that functional magnetic resonance imaging (MRI) could achieve clinical utility for a broad range of neuropsychiatric disorders. However, several barriers remain. For example, the acquisition of large-scale datasets capable of clarifying the marked heterogeneity that exists in psychiatric illnesses will need to be realized. In addition, there continues to be a need for the development of image processing and analysis methods capable of separating signal from artifact. As a prototypical hyperkinetic disorder, and movement-related artifact being a significant confound in functional imaging studies, ADHD offers a unique challenge. As part of the ADHD-200 Global Competition and this special edition of Frontiers, the ADHD-200 Consortium demonstrates the utility of an aggregate dataset pooled across five institutions in addressing these challenges. The work aimed to (1) examine the impact of emerging techniques for controlling for “micro-movements,” and (2) provide novel insights into the neural correlates of ADHD subtypes. Using support vector machine (SVM)-based multivariate pattern analysis (MVPA) we show that functional connectivity patterns in individuals are capable of differentiating the two most prominent ADHD subtypes. The application of graph-theory revealed that the Combined (ADHD-C) and Inattentive (ADHD-I) subtypes demonstrated some overlapping (particularly sensorimotor systems), but unique patterns of atypical connectivity. For ADHD-C, atypical connectivity was prominent in midline default network components, as well as insular cortex; in contrast, the ADHD-I group exhibited atypical patterns within the dlPFC regions and cerebellum. Systematic motion-related artifact was noted, and highlighted the need for stringent motion correction. Findings reported were robust to the specific motion correction strategy employed. These data suggest that resting-state functional connectivity MRI (rs-fcMRI) data can be used to characterize individual patients with ADHD and to identify neural distinctions underlying the clinical heterogeneity of ADHD. PMID:23382713

Nontransformed, GM-CSF-dependent macrophage lines are a unique model to study tissue macrophage functions.

PubMed

Fejer, György; Wegner, Mareike Dorothee; Györy, Ildiko; Cohen, Idan; Engelhard, Peggy; Voronov, Elena; Manke, Thomas; Ruzsics, Zsolt; Dölken, Lars; Prazeres da Costa, Olivia; Branzk, Nora; Huber, Michael; Prasse, Antje; Schneider, Robert; Apte, Ron N; Galanos, Chris; Freudenberg, Marina A

2013-06-11

Macrophages are diverse cell types in the first line of antimicrobial defense. Only a limited number of primary mouse models exist to study their function. Bone marrow-derived, macrophage-CSF-induced cells with a limited life span are the most common source. We report here a simple method yielding self-renewing, nontransformed, GM-CSF/signal transducer and activator of transcription 5-dependent macrophages (Max Planck Institute cells) from mouse fetal liver, which reflect the innate immune characteristics of alveolar macrophages. Max Planck Institute cells are exquisitely sensitive to selected microbial agents, including bacterial LPS, lipopeptide, Mycobacterium tuberculosis, cord factor, and adenovirus and mount highly proinflammatory but no anti-inflammatory IL-10 responses. They show a unique pattern of innate responses not yet observed in other mononuclear phagocytes. This includes differential LPS sensing and an unprecedented regulation of IL-1α production upon LPS exposure, which likely plays a key role in lung inflammation in vivo. In conclusion, Max Planck Institute cells offer an useful tool to study macrophage biology and for biomedical science.

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.

PubMed

Wang, Zhuo; Pascual-Anaya, Juan; Zadissa, Amonida; Li, Wenqi; Niimura, Yoshihito; Huang, Zhiyong; Li, Chunyi; White, Simon; Xiong, Zhiqiang; Fang, Dongming; Wang, Bo; Ming, Yao; Chen, Yan; Zheng, Yuan; Kuraku, Shigehiro; Pignatelli, Miguel; Herrero, Javier; Beal, Kathryn; Nozawa, Masafumi; Li, Qiye; Wang, Juan; Zhang, Hongyan; Yu, Lili; Shigenobu, Shuji; Wang, Junyi; Liu, Jiannan; Flicek, Paul; Searle, Steve; Wang, Jun; Kuratani, Shigeru; Yin, Ye; Aken, Bronwen; Zhang, Guojie; Irie, Naoki

2013-06-01

The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ∼267.9-248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these turtles. Embryonic gene expression analysis identified an hourglass-like divergence of turtle and chicken embryogenesis, with maximal conservation around the vertebrate phylotypic period, rather than at later stages that show the amniote-common pattern. Wnt5a expression was found in the growth zone of the dorsal shell, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty. Our results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell.

Developing Signal-Pattern-Recognition Programs

NASA Technical Reports Server (NTRS)

Shelton, Robert O.; Hammen, David

2006-01-01

Pattern Interpretation and Recognition Application Toolkit Environment (PIRATE) is a block-oriented software system that aids the development of application programs that analyze signals in real time in order to recognize signal patterns that are indicative of conditions or events of interest. PIRATE was originally intended for use in writing application programs to recognize patterns in space-shuttle telemetry signals received at Johnson Space Center's Mission Control Center: application programs were sought to (1) monitor electric currents on shuttle ac power busses to recognize activations of specific power-consuming devices, (2) monitor various pressures and infer the states of affected systems by applying a Kalman filter to the pressure signals, (3) determine fuel-leak rates from sensor data, (4) detect faults in gyroscopes through analysis of system measurements in the frequency domain, and (5) determine drift rates in inertial measurement units by regressing measurements against time. PIRATE can also be used to develop signal-pattern-recognition software for different purposes -- for example, to monitor and control manufacturing processes.

Blue Hill Observatory Sunshine - Assessment of Climate Signals in the Longest Continuous Meteorological Record in North America

NASA Astrophysics Data System (ADS)

Magee, N. B.; Finocchio, P.; Melaas, E. K.; Iacono, M. J.

2014-12-01

The Blue Hill Meteorological Observatory occupies a unique place in the history of the American Meteorological Society and the development of atmospheric science. Through its 129-year history, the Observatory has been operated by founder Abbott Lawrence Rotch (1861-1912), Harvard University, and the National Weather Service, and it is presently run by the non-profit Blue Hill Observatory Science Center. While daily temperature and precipitation records are available through the National Climatic Data Center, they do not include the full record of sunshine duration data that were measured using a Campbell-Stokes sunshine recorder. We have recently digitized the Observatory's original daily sunshine archives, and now present the first full collection and analysis of sunshine records extending from 1889 to the present. This data set is unique and salient to modern climate research because the collection represents the earliest and longest continuous measurements of insolation outside of Western Europe. Together the record provides an unprecedented glimpse into regional climate features, as well as important links between global phenomena and regional climate. Analysis reveals long-term fluctuations of cloud-cover and solar radiation, including signals of regional industrialization, global-dimming, volcanic eruptions, the 11-Year Solar Cycle, and the El Niño Southern Oscillation. Shorter period fluctuations include evidence of an intricate annual pattern of sunshine duration and correlations with the Arctic Oscillation, North Atlantic Oscillation, and galactic cosmic rays.

The Significance of Interstitial Cells in Neurogastroenterology

PubMed Central

Blair, Peter J; Rhee, Poong-Lyul; Sanders, Kenton M; Ward, Sean M

2014-01-01

Smooth muscle layers of the gastrointestinal tract consist of a heterogeneous population of cells that include enteric neurons, several classes of interstitial cells of mesenchymal origin, a variety of immune cells and smooth muscle cells (SMCs). Over the last number of years the complexity of the interactions between these cell types has begun to emerge. For example, interstitial cells, consisting of both interstitial cells of Cajal (ICC) and platelet-derived growth factor receptor alpha-positive (PDGFRα+) cells generate pacemaker activity throughout the gastrointestinal (GI) tract and also transduce enteric motor nerve signals and mechanosensitivity to adjacent SMCs. ICC and PDGFRα+ cells are electrically coupled to SMCs possibly via gap junctions forming a multicellular functional syncytium termed the SIP syncytium. Cells that make up the SIP syncytium are highly specialized containing unique receptors, ion channels and intracellular signaling pathways that regulate the excitability of GI muscles. The unique role of these cells in coordinating GI motility is evident by the altered motility patterns in animal models where interstitial cell networks are disrupted. Although considerable advances have been made in recent years on our understanding of the roles of these cells within the SIP syncytium, the full physiological functions of these cells and the consequences of their disruption in GI muscles have not been clearly defined. This review gives a synopsis of the history of interstitial cell discovery and highlights recent advances in structural, molecular expression and functional roles of these cells in the GI tract. PMID:24948131

Entanglement near the optical instability point in damped four wave mixing systems

NASA Astrophysics Data System (ADS)

Chiangga, S.; Temnuch, W.; Frank, T. D.

2018-06-01

Entanglement of electromagnetic field modes of signal and idler photons generated by four-wave mixing (FWM) devices is a quantum phenomenon that has been examined in various experimental and theoretical studies. The focus of this theoretical study is on two aspects of this phenomenon: the emergence of signal and idler photons due to an optical instability and the entanglement of the signal and idler modes above the instability threshold. For simple FWM devices that are subjected to damping it is shown that the signal and idler modes are entangled close to the point of optical instability at which the signal and idler photons emerges. The degree of entanglement as measured by a particular entanglement function proposed earlier in the literature assumes at the point of optical instability a unique value that is independent of the model parameters of the devices. The value is slightly higher than the value reported in a FWM experiment by Boyer et al (2008 Science 321 544). Numerical simulations suggest that the aforementioned entanglement function is U-shaped such that the degree of entanglement at the instability point is the maximal possible one and represents the optimal value. A similar U-shaped pattern was observed in an FWM experiment conducted by Lawrie et al (2016 Appl. Phys. Lett. 108 151107). Our semi-analytical findings are derived within the framework of the positive P representation of quantum optical processes and are compared with the aforementioned experimental observations by Boyer et al and Lawrie et al.

Distinct requirements for signal peptidase processing and function in the stable signal peptide subunit of the Junin virus envelope glycoprotein

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

York, Joanne; Nunberg, Jack H.

2007-03-01

The arenavirus envelope glycoprotein (GP-C) retains a cleaved and stable signal peptide (SSP) as an essential subunit of the mature complex. This 58-amino-acid residue peptide serves as a signal sequence and is additionally required to enable transit of the assembled GP-C complex to the Golgi, and for pH-dependent membrane fusion activity. We have investigated the C-terminal region of the Junin virus SSP to study the role of the cellular signal peptidase (SPase) in generating SSP. Site-directed mutagenesis at the cleavage site (positions - 1 and - 3) reveals a pattern of side-chain preferences consistent with those of SPase. Although positionmore » - 2 is degenerate for SPase cleavage, this residue in the arenavirus SSP is invariably a cysteine. In the Junin virus, this cysteine is not involved in disulfide bonding. We show that replacement with alanine or serine is tolerated for SPase cleavage but prevents the mutant SSP from associating with GP-C and enabling transport to the cell surface. Conversely, an arginine mutation at position - 1 that prevents SPase cleavage is fully compatible with GP-C-mediated membrane fusion activity when the mutant SSP is provided in trans. These results point to distinct roles of SSP sequences in SPase cleavage and GP-C biogenesis. Further studies of the unique structural organization of the GP-C complex will be important in identifying novel opportunities for antiviral intervention against arenaviral hemorrhagic disease.« less

Shape matters: animal colour patterns as signals of individual quality

PubMed Central

2017-01-01

Colour patterns (e.g. irregular, spotted or barred forms) are widespread in the animal kingdom, yet their potential role as signals of quality has been mostly neglected. However, a review of the published literature reveals that pattern itself (irrespective of its size or colour intensity) is a promising signal of individual quality across species of many different taxa. We propose at least four main pathways whereby patterns may reliably reflect individual quality: (i) as conventional signals of status, (ii) as indices of developmental homeostasis, (iii) by amplifying cues of somatic integrity and (iv) by amplifying individual investment in maintenance activities. Methodological constraints have traditionally hampered research on the signalling potential of colour patterns. To overcome this, we report a series of tools (e.g. colour adjacency and pattern regularity analyses, Fourier and granularity approaches, fractal geometry, geometric morphometrics) that allow objective quantification of pattern variability. We discuss how information provided by these methods should consider the visual system of the model species and behavioural responses to pattern metrics, in order to allow biologically meaningful conclusions. Finally, we propose future challenges in this research area that will require a multidisciplinary approach, bringing together inputs from genetics, physiology, behavioural ecology and evolutionary-developmental biology. PMID:28228513

GENOMIC ORGANIZATION OF THE SP22 GENE AND A UNIQUE PATTERN OF EXPRESSION IN SPERMATOGENIC CELLS

EPA Science Inventory

GENOMIC ORGANIZATION OF THE SP22 GENE AND A UNIQUE PATTERN OF EXPRESSION IN SPERMATOGENIC CELLS.
JE Welch*, RR Barbee*, JD Suarez*, NL Roberts*, and GR Klinefelter. Reproductive Toxicology Division, NHEERL, U.S. EPA, Research Triangle Park, NC, USA.
Our laboratory has rep...

Distinctive gene expression profiles characterize donor biopsies from HCV-positive kidney donors.

PubMed

Mas, Valeria R; Archer, Kellie J; Suh, Lacey; Scian, Mariano; Posner, Marc P; Maluf, Daniel G

2010-12-15

Because of the shortage of organs for transplantation, procurement of kidneys from extended criteria donors is inevitable. Frequently, donors infected with hepatitis C virus (HCV) are used. To elucidate an initial compromise of molecular pathways in HCV graft, gene expression profiles were evaluated. Twenty-four donor allograft biopsies (n=12 HCV positive (+) and n=12 HCV negative (-)) were collected at preimplantation time and profiled using microarrays. Donors were age, race, gender, and cold and warm ischemia time matched between groups. Probe level data were read into the R programming environment using the affy Bioconductor package, and the robust multiarray average method was used to obtain probe set expression summaries. To identify probe sets exhibiting differential expression, a two sample t test was performed. Molecular and biologic functions were analyzed using Interaction Networks and Functional Analysis. Fifty-eight probe sets were differentially expressed between HCV (+) versus HCV (-) donors (P<0.001). The molecular functions associated with the two top scored networks from the analysis of the differentially expressed genes were connective tissue development and function and tissue morphology (score 34), cell death, cell signaling, cellular assembly, and organization (score 32). Among the differentially affected top canonical pathways, we found the role of RIG1-like receptors in antiviral innate immunity (P<0.001), natural killer cell signaling (P=0.007), interleukin-8 signaling (P=0.048), interferon signaling (P=0.0 11; INFA21, INFGR1, and MED14), ILK signaling (P=0.001), and apoptosis signaling. A unique gene expression pattern was identified in HCV (+) kidney grafts. Innate immune system and inflammatory pathways were the most affected.

Sequential pattern formation governed by signaling gradients

NASA Astrophysics Data System (ADS)

Jörg, David J.; Oates, Andrew C.; Jülicher, Frank

2016-10-01

Rhythmic and sequential segmentation of the embryonic body plan is a vital developmental patterning process in all vertebrate species. However, a theoretical framework capturing the emergence of dynamic patterns of gene expression from the interplay of cell oscillations with tissue elongation and shortening and with signaling gradients, is still missing. Here we show that a set of coupled genetic oscillators in an elongating tissue that is regulated by diffusing and advected signaling molecules can account for segmentation as a self-organized patterning process. This system can form a finite number of segments and the dynamics of segmentation and the total number of segments formed depend strongly on kinetic parameters describing tissue elongation and signaling molecules. The model accounts for existing experimental perturbations to signaling gradients, and makes testable predictions about novel perturbations. The variety of different patterns formed in our model can account for the variability of segmentation between different animal species.

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.

Signal replacement with an interchange.

DOT National Transportation Integrated Search

2007-08-24

The purpose of this research effort is to evaluate unique intersection designs for their suitability for use in lieu : of an existing or proposed traffic signal. Traffic signals can cause unnecessary delay and capacity restrictions : due to the opera...

The isolation of spatial patterning modes in a mathematical model of juxtacrine cell signalling.

PubMed

O'Dea, R D; King, J R

2013-06-01

Juxtacrine signalling mechanisms are known to be crucial in tissue and organ development, leading to spatial patterns in gene expression. We investigate the patterning behaviour of a discrete model of juxtacrine cell signalling due to Owen & Sherratt (1998, Mathematical modelling of juxtacrine cell signalling. Math. Biosci., 153, 125-150) in which ligand molecules, unoccupied receptors and bound ligand-receptor complexes are modelled. Feedback between the ligand and receptor production and the level of bound receptors is incorporated. By isolating two parameters associated with the feedback strength and employing numerical simulation, linear stability and bifurcation analysis, the pattern-forming behaviour of the model is analysed under regimes corresponding to lateral inhibition and induction. Linear analysis of this model fails to capture the patterning behaviour exhibited in numerical simulations. Via bifurcation analysis, we show that since the majority of periodic patterns fold subcritically from the homogeneous steady state, a wide variety of stable patterns exists at a given parameter set, providing an explanation for this failure. The dominant pattern is isolated via numerical simulation. Additionally, by sampling patterns of non-integer wavelength on a discrete mesh, we highlight a disparity between the continuous and discrete representations of signalling mechanisms: in the continuous case, patterns of arbitrary wavelength are possible, while sampling such patterns on a discrete mesh leads to longer wavelength harmonics being selected where the wavelength is rational; in the irrational case, the resulting aperiodic patterns exhibit 'local periodicity', being constructed from distorted stable shorter wavelength patterns. This feature is consistent with experimentally observed patterns, which typically display approximate short-range periodicity with defects.

Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal

PubMed Central

2015-01-01

Background The comparison of analyte mass spectrometry precursor (MS1) signal is central to many proteomic (and other -omic) workflows. Standard vocabularies for mass spectrometry exist and provide good coverage for most experimental applications yet are insufficient for concise and unambiguous description of data concepts spanning the range of signal provenance from a molecular perspective (e.g. from charged peptides down to fine isotopes). Without a standard unambiguous nomenclature, literature searches, algorithm reproducibility and algorithm evaluation for MS-omics data processing are nearly impossible. Results We show how terms from current official ontologies are too vague or ambiguous to explicitly map molecular entities to MS signals and we illustrate the inconsistency and ambiguity of current colloquially used terms. We also propose a set of terms for MS1 signal that uniquely, succinctly and intuitively describe data concepts spanning the range of signal provenance from full molecule downs to fine isotopes. We suggest that additional community discussion of these terms should precede any further standardization efforts. We propose a novel nomenclature that spans the range of the required granularity to describe MS data processing from the perspective of the molecular provenance of the MS signal. Conclusions The proposed nomenclature provides a chain of succinct and unique terms spanning the signal created by a charged molecule down through each of its constituent subsignals. We suggest that additional community discussion of these terms should precede any further standardization efforts. PMID:25952148

Calcium Signaling enhancement during oocyte maturation

NASA Astrophysics Data System (ADS)

Jung, Peter; Ullah, Ghanim; Machaca, Khaled

2006-03-01

A Ca2+ signal with a special spatial and temporal characteristic universally removes cell-cycle arrest after fertilization of a mature egg cell. The Ca2+ signal is characterized by a fast rise of intracellular Ca2+ and a slow decay on the time scale of minutes. We use computational modeling of Ca2+ release on the microscale (Ca2+ puffs) and cell-scale in conjunction with experimental knowledge of the changes in the Ca2+ signaling apparatus during oocyte maturation and changing signaling patterns to explore the relationship between organization and sensitivity of IP3 receptors and SERCA pumps and the resulting signaling patterns. We hypothesize that potentiation of the IP3 receptors during oocyte maturation is the main cause for the differentiation in the signaling patterns.

Genomics of a Metamorphic Timing QTL: met1 Maps to a Unique Genomic Position and Regulates Morph and Species-Specific Patterns of Brain Transcription

PubMed Central

Page, Robert B.; Boley, Meredith A.; Kump, David K.; Voss, Stephen R.

2013-01-01

Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect quantitative trait locus (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and determine the effect of met1 on larval growth, metamorphic timing, and gene expression in the brain. We show that met1 maps to the position of a urodele-specific chromosome rearrangement on linkage group 2 that uniquely brought functionally associated genes into linkage. Furthermore, we found that more than 200 genes were differentially expressed during larval development as a function of met1 genotype. This list of differentially expressed genes is enriched for proteins that function in the mitochondria, providing evidence of a link between met1, thyroid hormone signaling, and mitochondrial energetics associated with metamorphosis. Finally, we found that met1 significantly affected metamorphic timing in hybrids, but not early larval growth rate. Collectively, our results show that met1 regulates species and morph-specific patterns of brain transcription and life history variation. PMID:23946331

A Genome-Wide Screen Indicates Correlation between Differentiation and Expression of Metabolism Related Genes

PubMed Central

Shende, Akhilesh; Singh, Anupama; Meena, Anil; Ghosal, Ritika; Ranganathan, Madhav; Bandyopadhyay, Amitabha

2013-01-01

Differentiated tissues may be considered as materials with distinct properties. The differentiation program of a given tissue ensures that it acquires material properties commensurate with its function. It may be hypothesized that some of these properties are acquired through production of tissue-specific metabolites synthesized by metabolic enzymes. To establish correlation between metabolism and organogenesis we have carried out a genome-wide expression study of metabolism related genes by RNA in-situ hybridization. 23% of the metabolism related genes studied are expressed in a tissue-restricted but not tissue-exclusive manner. We have conducted the screen on whole mount chicken (Gallus gallus) embryos from four distinct developmental stages to correlate dynamic changes in expression patterns of metabolic enzymes with spatio-temporally unique developmental events. Our data strongly suggests that unique combinations of metabolism related genes, and not specific metabolic pathways, are upregulated during differentiation. Further, expression of metabolism related genes in well established signaling centers that regulate different aspects of morphogenesis indicates developmental roles of some of the metabolism related genes. The database of tissue-restricted expression patterns of metabolism related genes, generated in this study, should serve as a resource for systematic identification of these genes with tissue-specific functions during development. Finally, comprehensive understanding of differentiation is not possible unless the downstream genes of a differentiation cascade are identified. We propose, metabolic enzymes constitute a significant portion of these downstream target genes. Thus our study should help elucidate different aspects of tissue differentiation. PMID:23717462

A genome-wide screen indicates correlation between differentiation and expression of metabolism related genes.

PubMed

Roy, Priti; Kumar, Brijesh; Shende, Akhilesh; Singh, Anupama; Meena, Anil; Ghosal, Ritika; Ranganathan, Madhav; Bandyopadhyay, Amitabha

2013-01-01

Differentiated tissues may be considered as materials with distinct properties. The differentiation program of a given tissue ensures that it acquires material properties commensurate with its function. It may be hypothesized that some of these properties are acquired through production of tissue-specific metabolites synthesized by metabolic enzymes. To establish correlation between metabolism and organogenesis we have carried out a genome-wide expression study of metabolism related genes by RNA in-situ hybridization. 23% of the metabolism related genes studied are expressed in a tissue-restricted but not tissue-exclusive manner. We have conducted the screen on whole mount chicken (Gallus gallus) embryos from four distinct developmental stages to correlate dynamic changes in expression patterns of metabolic enzymes with spatio-temporally unique developmental events. Our data strongly suggests that unique combinations of metabolism related genes, and not specific metabolic pathways, are upregulated during differentiation. Further, expression of metabolism related genes in well established signaling centers that regulate different aspects of morphogenesis indicates developmental roles of some of the metabolism related genes. The database of tissue-restricted expression patterns of metabolism related genes, generated in this study, should serve as a resource for systematic identification of these genes with tissue-specific functions during development. Finally, comprehensive understanding of differentiation is not possible unless the downstream genes of a differentiation cascade are identified. We propose, metabolic enzymes constitute a significant portion of these downstream target genes. Thus our study should help elucidate different aspects of tissue differentiation.

Distinct signalling properties of insulin receptor substrate (IRS)-1 and IRS-2 in mediating insulin/IGF-1 action.

PubMed

Rabiee, Atefeh; Krüger, Marcus; Ardenkjær-Larsen, Jacob; Kahn, C Ronald; Emanuelli, Brice

2018-07-01

Insulin/IGF-1 action is driven by a complex and highly integrated signalling network. Loss-of-function studies indicate that the major insulin/IGF-1 receptor substrate (IRS) proteins, IRS-1 and IRS-2, mediate different biological functions in vitro and in vivo, suggesting specific signalling properties despite their high degree of homology. To identify mechanisms contributing to the differential signalling properties of IRS-1 and IRS-2 in the mediation of insulin/IGF-1 action, we performed comprehensive mass spectrometry (MS)-based phosphoproteomic profiling of brown preadipocytes from wild type, IRS-1 -/- and IRS-2 -/- mice in the basal and IGF-1-stimulated states. We applied stable isotope labeling by amino acids in cell culture (SILAC) for the accurate quantitation of changes in protein phosphorylation. We found ~10% of the 6262 unique phosphorylation sites detected to be regulated by IGF-1. These regulated sites included previously reported substrates of the insulin/IGF-1 signalling pathway, as well as novel substrates including Nuclear Factor I X and Semaphorin-4B. In silico prediction suggests the protein kinase B (PKB), protein kinase C (PKC), and cyclin-dependent kinase (CDK) as the main mediators of these phosphorylation events. Importantly, we found preferential phosphorylation patterns depending on the presence of either IRS-1 or IRS-2, which was associated with specific sets of kinases involved in signal transduction downstream of these substrates such as PDHK1, MAPK3, and PKD1 for IRS-1, and PIN1 and PKC beta for IRS-2. Overall, by generating a comprehensive phosphoproteomic profile from brown preadipocyte cells in response to IGF-1 stimulation, we reveal both common and distinct insulin/IGF-1 signalling events mediated by specific IRS proteins. Copyright © 2018 Elsevier Inc. All rights reserved.

Robustness, evolvability, and the logic of genetic regulation.

PubMed

Payne, Joshua L; Moore, Jason H; Wagner, Andreas

2014-01-01

In gene regulatory circuits, the expression of individual genes is commonly modulated by a set of regulating gene products, which bind to a gene's cis-regulatory region. This region encodes an input-output function, referred to as signal-integration logic, that maps a specific combination of regulatory signals (inputs) to a particular expression state (output) of a gene. The space of all possible signal-integration functions is vast and the mapping from input to output is many-to-one: For the same set of inputs, many functions (genotypes) yield the same expression output (phenotype). Here, we exhaustively enumerate the set of signal-integration functions that yield identical gene expression patterns within a computational model of gene regulatory circuits. Our goal is to characterize the relationship between robustness and evolvability in the signal-integration space of regulatory circuits, and to understand how these properties vary between the genotypic and phenotypic scales. Among other results, we find that the distributions of genotypic robustness are skewed, so that the majority of signal-integration functions are robust to perturbation. We show that the connected set of genotypes that make up a given phenotype are constrained to specific regions of the space of all possible signal-integration functions, but that as the distance between genotypes increases, so does their capacity for unique innovations. In addition, we find that robust phenotypes are (i) evolvable, (ii) easily identified by random mutation, and (iii) mutationally biased toward other robust phenotypes. We explore the implications of these latter observations for mutation-based evolution by conducting random walks between randomly chosen source and target phenotypes. We demonstrate that the time required to identify the target phenotype is independent of the properties of the source phenotype.

Robustness, Evolvability, and the Logic of Genetic Regulation

PubMed Central

Moore, Jason H.; Wagner, Andreas

2014-01-01

In gene regulatory circuits, the expression of individual genes is commonly modulated by a set of regulating gene products, which bind to a gene’s cis-regulatory region. This region encodes an input-output function, referred to as signal-integration logic, that maps a specific combination of regulatory signals (inputs) to a particular expression state (output) of a gene. The space of all possible signal-integration functions is vast and the mapping from input to output is many-to-one: for the same set of inputs, many functions (genotypes) yield the same expression output (phenotype). Here, we exhaustively enumerate the set of signal-integration functions that yield idential gene expression patterns within a computational model of gene regulatory circuits. Our goal is to characterize the relationship between robustness and evolvability in the signal-integration space of regulatory circuits, and to understand how these properties vary between the genotypic and phenotypic scales. Among other results, we find that the distributions of genotypic robustness are skewed, such that the majority of signal-integration functions are robust to perturbation. We show that the connected set of genotypes that make up a given phenotype are constrained to specific regions of the space of all possible signal-integration functions, but that as the distance between genotypes increases, so does their capacity for unique innovations. In addition, we find that robust phenotypes are (i) evolvable, (ii) easily identified by random mutation, and (iii) mutationally biased toward other robust phenotypes. We explore the implications of these latter observations for mutation-based evolution by conducting random walks between randomly chosen source and target phenotypes. We demonstrate that the time required to identify the target phenotype is independent of the properties of the source phenotype. PMID:23373974

Changes in the Phosphoproteome and Metabolome Link Early Signaling Events to Rearrangement of Photosynthesis and Central Metabolism in Salinity and Oxidative Stress Response in Arabidopsis1

PubMed Central

Chen, Yanmei; Hoehenwarter, Wolfgang

2015-01-01

Salinity and oxidative stress are major factors affecting and limiting the productivity of agricultural crops. The molecular and biochemical processes governing the plant response to abiotic stress have often been researched in a reductionist manner. Here, we report a systemic approach combining metabolic labeling and phosphoproteomics to capture early signaling events with quantitative metabolome analysis and enzyme activity assays to determine the effects of salt and oxidative stress on plant physiology. K+ and Na+ transporters showed coordinated changes in their phosphorylation pattern, indicating the importance of dynamic ion homeostasis for adaptation to salt stress. Unique phosphorylation sites were found for Arabidopsis (Arabidopsis thaliana) SNF1 kinase homolog10 and 11, indicating their central roles in the stress-regulated responses. Seven Sucrose Non-fermenting1-Related Protein Kinase2 kinases showed varying levels of phosphorylation at multiple serine/threonine residues in their kinase domain upon stress, showing temporally distinct modulation of the various isoforms. Salinity and oxidative stress also lead to changes in protein phosphorylation of proteins central to photosynthesis, in particular the kinase State Transition Protein7 required for state transition and light-harvesting II complex proteins. Furthermore, stress-induced changes of the phosphorylation of enzymes of central metabolism were observed. The phosphorylation patterns of these proteins were concurrent with changes in enzyme activity. This was reflected by altered levels of metabolites, such as the sugars sucrose and fructose, glycolysis intermediates, and amino acids. Together, our study provides evidence for a link between early signaling in the salt and oxidative stress response that regulates the state transition of photosynthesis and the rearrangement of primary metabolism. PMID:26471895

Multiscale Feature Analysis of Salivary Gland Branching Morphogenesis

PubMed Central

Baydil, Banu; Daley, William P.; Larsen, Melinda; Yener, Bülent

2012-01-01

Pattern formation in developing tissues involves dynamic spatio-temporal changes in cellular organization and subsequent evolution of functional adult structures. Branching morphogenesis is a developmental mechanism by which patterns are generated in many developing organs, which is controlled by underlying molecular pathways. Understanding the relationship between molecular signaling, cellular behavior and resulting morphological change requires quantification and categorization of the cellular behavior. In this study, tissue-level and cellular changes in developing salivary gland in response to disruption of ROCK-mediated signaling by are modeled by building cell-graphs to compute mathematical features capturing structural properties at multiple scales. These features were used to generate multiscale cell-graph signatures of untreated and ROCK signaling disrupted salivary gland organ explants. From confocal images of mouse submandibular salivary gland organ explants in which epithelial and mesenchymal nuclei were marked, a multiscale feature set capturing global structural properties, local structural properties, spectral, and morphological properties of the tissues was derived. Six feature selection algorithms and multiway modeling of the data was performed to identify distinct subsets of cell graph features that can uniquely classify and differentiate between different cell populations. Multiscale cell-graph analysis was most effective in classification of the tissue state. Cellular and tissue organization, as defined by a multiscale subset of cell-graph features, are both quantitatively distinct in epithelial and mesenchymal cell types both in the presence and absence of ROCK inhibitors. Whereas tensor analysis demonstrate that epithelial tissue was affected the most by inhibition of ROCK signaling, significant multiscale changes in mesenchymal tissue organization were identified with this analysis that were not identified in previous biological studies. We here show how to define and calculate a multiscale feature set as an effective computational approach to identify and quantify changes at multiple biological scales and to distinguish between different states in developing tissues. PMID:22403724

Recent (2000-2015) developments in the analysis of minor unknown natural products based on characteristic fragment information using LC-MS.

PubMed

Cai, Tian; Guo, Ze-Qin; Xu, Xiao-Ying; Wu, Zhi-Jun

2018-03-01

Liquid chromatography-Mass Spectrometry (LC-MS) has been widely used in natural product analysis. Global detection and identification of nontargeted components are desirable in natural product research, for example, in quality control of Chinese herbal medicine. Nontargeted components analysis continues to expand to exciting life science application domains such as metabonomics. With this background, the present review summarizes recent developments in the analysis of minor unknown natural products using LC-MS and mainly focuses on the determination of the molecular formulae, selection of precursor ions, and characteristic fragmentation patterns of the known compounds. This review consists of three parts. Firstly, the methods used to determine unique molecular formula of unknown compounds such as accurate mass measurements, MS n spectra, or relative isotopic abundance information, are introduced. Secondly, the methods improving signal-to-noise ratio of MS/MS spectra by manual-MS/MS or workflow targeting-only signals were elucidated; pure precursor ions can be selected by changing the precursor ion isolated window. Lastly, characteristic fragmentation patterns such as Retro-Diels-Alder (RDA), McLafferty rearrangements, "internal residue loss," and so on, occurring in the molecular ions of natural products are summarized. Classical application of characteristic fragmentation patterns in identifying unknown compounds in extracts and relevant fragmentation mechanisms are presented (RDA reactions occurring readily in the molecular ions of flavanones or isoflavanones, McLafferty-type fragmentation reactions of some natural products such as epipolythiodioxopiperazines; fragmentation by "internal residue loss" possibly involving ion-neutral complex intermediates). © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:202-216, 2018. © 2016 Wiley Periodicals, Inc.

The spatiotemporal order of signaling events unveils the logic of development signaling.

PubMed

Zhu, Hao; Owen, Markus R; Mao, Yanlan

2016-08-01

Animals from worms and insects to birds and mammals show distinct body plans; however, the embryonic development of diverse body plans with tissues and organs within is controlled by a surprisingly few signaling pathways. It is well recognized that combinatorial use of and dynamic interactions among signaling pathways follow specific logic to control complex and accurate developmental signaling and patterning, but it remains elusive what such logic is, or even, what it looks like. We have developed a computational model for Drosophila eye development with innovated methods to reveal how interactions among multiple pathways control the dynamically generated hexagonal array of R8 cells. We obtained two novel findings. First, the coupling between the long-range inductive signals produced by the proneural Hh signaling and the short-range restrictive signals produced by the antineural Notch and EGFR signaling is essential for generating accurately spaced R8s. Second, the spatiotemporal orders of key signaling events reveal a robust pattern of lateral inhibition conducted by Ato-coordinated Notch and EGFR signaling to collectively determine R8 patterning. This pattern, stipulating the orders of signaling and comparable to the protocols of communication, may help decipher the well-appreciated but poorly defined logic of developmental signaling. The model is available upon request. hao.zhu@ymail.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

The spatiotemporal order of signaling events unveils the logic of development signaling

PubMed Central

Zhu, Hao; Owen, Markus R.; Mao, Yanlan

2016-01-01

Motivation: Animals from worms and insects to birds and mammals show distinct body plans; however, the embryonic development of diverse body plans with tissues and organs within is controlled by a surprisingly few signaling pathways. It is well recognized that combinatorial use of and dynamic interactions among signaling pathways follow specific logic to control complex and accurate developmental signaling and patterning, but it remains elusive what such logic is, or even, what it looks like. Results: We have developed a computational model for Drosophila eye development with innovated methods to reveal how interactions among multiple pathways control the dynamically generated hexagonal array of R8 cells. We obtained two novel findings. First, the coupling between the long-range inductive signals produced by the proneural Hh signaling and the short-range restrictive signals produced by the antineural Notch and EGFR signaling is essential for generating accurately spaced R8s. Second, the spatiotemporal orders of key signaling events reveal a robust pattern of lateral inhibition conducted by Ato-coordinated Notch and EGFR signaling to collectively determine R8 patterning. This pattern, stipulating the orders of signaling and comparable to the protocols of communication, may help decipher the well-appreciated but poorly defined logic of developmental signaling. Availability and implementation: The model is available upon request. Contact: hao.zhu@ymail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153573

Characterization of In Vivo Resistance to Osimertinib and JNJ-61186372, an EGFR/Met Bispecific Antibody, Reveals Unique and Consensus Mechanisms of Resistance.

PubMed

Emdal, Kristina B; Dittmann, Antje; Reddy, Raven J; Lescarbeau, Rebecca S; Moores, Sheri L; Laquerre, Sylvie; White, Forest M

2017-11-01

Approximately 10% of non-small cell lung cancer (NSCLC) patients in the United States and 40% of NSCLC patients in Asia have activating epidermal growth factor receptor (EGFR) mutations and are eligible to receive targeted anti-EGFR therapy. Despite an extension of life expectancy associated with this treatment, resistance to EGFR tyrosine kinase inhibitors and anti-EGFR antibodies is almost inevitable. To identify additional signaling routes that can be cotargeted to overcome resistance, we quantified tumor-specific molecular changes that govern resistant cancer cell growth and survival. Mass spectrometry-based quantitative proteomics was used to profile in vivo signaling changes in 41 therapy-resistant tumors from four xenograft NSCLC models. We identified unique and tumor-specific tyrosine phosphorylation rewiring in tumors resistant to treatment with the irreversible third-generation EGFR-inhibitor, osimertinib, or the novel dual-targeting EGFR/Met antibody, JNJ-61186372. Tumor-specific increases in tyrosine-phosphorylated peptides from EGFR family members, Shc1 and Gab1 or Src family kinase (SFK) substrates were observed, underscoring a differential ability of tumors to uniquely escape EGFR inhibition. Although most resistant tumors within each treatment group displayed a marked inhibition of EGFR as well as SFK signaling, the combination of EGFR inhibition (osimertinib) and SFK inhibition (saracatinib or dasatinib) led to further decrease in cell growth in vitro This result suggests that residual SFK signaling mediates therapeutic resistance and that elimination of this signal through combination therapy may delay onset of resistance. Overall, analysis of individual resistant tumors captured unique in vivo signaling rewiring that would have been masked by analysis of in vitro cell population averages. Mol Cancer Ther; 16(11); 2572-85. ©2017 AACR . ©2017 American Association for Cancer Research.

Signal polymorphism under a constant environment: the odd cross in a web decorating spider

NASA Astrophysics Data System (ADS)

Walter, André; Elgar, Mark A.

2016-12-01

The quality of many animal signals varies, perhaps through their use in different contexts or by representing an adaptive response to reduce the risk of exploitation. Spiders of the orb weaver genus Argiope add linear, cruciate or circular silk structures to their orb webs, creating inter- and intra-specific polymorphic visual signals. Different decoration patterns are frequently attributed to different signal effects, but this view is contradicted by commonly observed intraspecific variation in decorating behaviour. Adults of Argiope mascordi are bimodal web decorators, building two distinct patterns, circular and cruciate silk structures. We investigated the variation of patterns under controlled, invariant laboratory conditions. Circular decorations were most frequent, but individuals often switch to the other pattern. This variation neither increased nor decreased over time, suggesting that pattern variability is primarily intrinsic rather than an exclusive response to environmental changes. Accordingly, we discuss the evolutionary implications in the light of the conservation of a single signal function through maintaining the variation of its quality and the alternative view that silk decorations may not represent adaptive signals at all.

One-year persistence of individual gait patterns identified in a follow-up study - A call for individualised diagnose and therapy.

PubMed

Horst, F; Mildner, M; Schöllhorn, W I

2017-10-01

Although a hunch about the individuality of human movements generally exists, differences in gait patterns between individuals are often neglected. To date, only a few studies distinguished individual gait patterns in terms of uniqueness and emphasised the relevance of individualised diagnoses and therapy. However, small sample sizes have been a limitation on identifying subjects based on gait patterns, and little is known about the permanence of subject-specific characteristics over time. The purpose of this study was (1) to prove the uniqueness of individual gait patterns within a larger sample and (2) to prove the long-term permanence of individual gait patterns. A sample of 128 healthy participants each walked a distance of 10m barefoot 10 times. Two force plates recorded the ground reaction forces during a double step at a self-selected walking speed. A subsample of 46 participants repeated this procedure after a period of 7-16 months. The application of support vector machines resulted in classification rates of 99.8% (1278 out of 1280) and 99.4% (914 out of 920) for the initial subject-classification and the subsample follow-up-classification, respectively. The results showed that gait patterns based on time-continuous ground reaction forces were unique to an individual and could be differentiated from those of other individuals. Support vector machines classified gait patterns to the corresponding individual almost error-free. Hence, human gait is not only different between individuals but also exhibits unique individual characteristics that are persistent over years. Our findings provide evidence for the individual nature of human walking and emphasise the need to evaluate individualised clinical approaches for diagnoses and therapy. Copyright © 2017 Elsevier B.V. All rights reserved.

Function-based Biosensor for Hazardous Waste Toxin Detection

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

James J Hickman

There is a need for new types of toxicity sensors in the DOE and other agencies that are based on biological function as the toxins encountered during decontamination or waste remediation may be previously unknown or their effects subtle. Many times the contents of the environmental waste, especially the minor components, have not been fully identified and characterized. New sensors of this type could target unknown toxins that cause death as well as intermediate levels of toxicity that impair function or cause long term impairment that may eventually lead to death. The primary question posed in this grant was tomore » create an electronically coupled neuronal cellular circuit to be used as sensor elements for a hybrid non-biological/biological toxin sensor system. A sensor based on the electrical signals transmitted between two mammalian neurons would allow the marriage of advances in solid state electronics with a functioning biological system to develop a new type of biosensor. Sensors of this type would be a unique addition to the field of sensor technology but would also be complementary to existing sensor technology that depends on knowledge of what is to be detected beforehand. We integrated physics, electronics, surface chemistry, biotechnology, and fundamental neuroscience in the development of this biosensor. Methods were developed to create artificial surfaces that enabled the patterning of discrete cells, and networks of cells, in culture; the networks were then aligned with transducers. The transducers were designed to measure electromagnetic fields (EMF) at low field strength. We have achieved all of the primary goals of the project. We can now pattern neurons routinely in our labs as well as align them with transducers. We have also shown the signals between neurons can be modulated by different biochemicals. In addition, we have made another significant advance where we have repeated the patterning results with adult hippocampal cells. Finally, we demonstrated that patterned cardiac cells on microelectrode arrays could act as sensors as well.« less

Strain distribution across magmatic margins during the breakup stage: Seismicity patterns in the Afar rift zone

NASA Astrophysics Data System (ADS)

Brown, C.; Ebinger, C. J.; Belachew, M.; Gregg, T.; Keir, D.; Ayele, A.; Aronovitz, A.; Campbell, E.

2008-12-01

Fault patterns record the strain history along passive continental margins, but geochronological constraints are, in general, too sparse to evaluate these patterns in 3D. The Afar depression in Ethiopia provides a unique setting to evaluate the time and space relations between faulting and magmatism across an incipient passive margin that formed above a mantle plume. The margin comprises a high elevation flood basalt province with thick, underplated continental crust, a narrow fault-line escarpment underlain by stretched and intruded crust, and a broad zone of highly intruded, mafic crust lying near sealevel. We analyze fault and seismicity patterns across and along the length of the Afar rift zone to determine the spatial distribution of strain during the final stages of continental breakup, and its relation to active magmatism and dike intrusions. Seismicity data include historic data and 2005-2007 data from the collaborative US-UK-Ethiopia Afar Geodynamics Project that includes the 2005-present Dabbahu rift episode. Earthquake epicenters cluster within discrete, 50 km-long magmatic segments that lack any fault linkage. Swarms also cluster along the fault-line scarp between the unstretched and highly stretched Afar rift zone; these earthquakes may signal release of stresses generated by large lateral density contrasts. We compare Coulomb static stress models with focal mechanisms and fault kinematics to discriminate between segmented magma intrusion and crank- arm models for the central Afar rift zone.

The Goldilocks Conundrum: NLR Inflammasome Modulation of Gastrointestinal Inflammation during Inflammatory Bowel Disease

PubMed Central

Ringel-Scaia, Veronica M.; McDaniel, Dylan K.; Allen, Irving C.

2017-01-01

Recent advances have revealed significant insight into Inflammatory bowel disease (IBD) pathobiology. Ulcerative colitis and Crohn's disease, the chronic relapsing clinical manifestations of IBD, are complex disorders with genetic and environmental influences. These diseases are associated with the dysregulation of immune tolerance, excessive Inflammation, and damage to the epithelial cell barrier. Increasing evidence indicates that pattern recognition receptors, including Toll-like receptors (TLRs) and nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs), function to maintain immune system homeostasis, modulate the gastrointestinal microbiome, and promote proper intestinal epithelial cell regeneration and repair. New insights have revealed that NLR family members are essential components in maintaining this immune system homeostasis. To date, the vast majority of studies associated with NLRs have focused on family members that form a multiprotein signaling platform called the Inflammasome. These signaling complexes are responsible for the cleavage and activation of the potent pleotropic cytokines IL-1β and IL-18, and they facilitate a unique form of cell death defined as pyroptosis. In this review, we summarize the current paradigms associated with NLR Inflammasome maintenance of immune system homeostasis in the gastrointestinal system. New concepts related to canonical and noncanonical Inflammasome signaling, as well as the implications of classical and alternative Inflammasomes in IBD pathogenesis, are also reviewed. PMID:28322135

Ultrasonics Equipped Crimp Tool: A New Technology for Aircraft Wiring Safety

NASA Technical Reports Server (NTRS)

Yost, William T.; Perey, Daniel F.; Cramer, Elliott

2006-01-01

We report on the development of a new measurement technique to quantitatively assess the condition of wire crimp connections. This ultrasonic (UT) method transmits high frequency sound waves through the joint under inspection. The wire-crimp region filters and scatters the ultrasonic energy as it passes through the crimp and wire. The resulting output (both time and frequency domains) provides a quantitative measure of the joint quality that is independent and unaffected by current. Crimps of poor mechanical and electrical quality will result in low temporal output and will distort the spectrum into unique and predictable patterns, depending on crimp "quality". This inexpensive, real-time measurement system can provide certification of crimps as they are made and recertification of existing wire crimps currently in service. The measurements for re-certification do not require that the wire be disconnected from its circuit. No other technology exists to measure in-situ the condition of wire joints (no electrical currents through the crimp are used in this analytical technique). We discuss the signals obtained from this instrument, and correlate these signals with destructive wire pull tests.

A Cell-Line-Specific Atlas of PARP-Mediated Protein Asp/Glu-ADP-Ribosylation in Breast Cancer.

PubMed

Zhen, Yuanli; Zhang, Yajie; Yu, Yonghao

2017-11-21

PARP1 plays a critical role in regulating many biological processes linked to cellular stress responses. Although DNA strand breaks are potent stimuli of PARP1 enzymatic activity, the context-dependent mechanism regulating PARP1 activation and signaling is poorly understood. We performed global characterization of the PARP1-dependent, Asp/Glu-ADP-ribosylated proteome in a panel of cell lines originating from benign breast epithelial cells, as well as common subtypes of breast cancer. From these analyses, we identified 503 specific ADP-ribosylation sites on 322 proteins. Despite similar expression levels, PARP1 is differentially activated in these cell lines under genotoxic conditions, which generates signaling outputs with substantial heterogeneity. By comparing protein abundances and ADP-ribosylation levels, we could dissect cell-specific PARP1 targets that are driven by unique expression patterns versus cell-specific regulatory mechanisms of PARylation. Intriguingly, PARP1 modifies many proteins in a cell-specific manner, including those involved in transcriptional regulation, mRNA metabolism, and protein translation. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Physical Unclonable Function with Multiplexing Units and its Evaluation

NASA Astrophysics Data System (ADS)

Yoshikawa, Masaya; Asai, Toshiya; Shiozaki, Mitsuru; Fujino, Takeshi

Recently, semiconductor counterfeiting has become an increasingly serious problem. Therefore, techniques to prevent the counterfeit by using random characteristic patterns that are difficult to control artificially have attracted attention. The physical unclonable function (PUF) is one of the techniques. It is a method to derive ID information peculiar to a device by detecting random physical features that cannot be controlled during the device's manufacture. Because information such as the ID information is difficult to replicate, PUF is used as a technique to prevent counterfeiting. Several studies have been reported on PUF. Arbiter PUF, which utilizes the difference in signal propagation delay between selectors, is the typical method of composing PUF using delay characteristics. This paper proposed a new PUF which is based on the arbiter PUF. The proposed PUF introduces new multiplexing selector units. It attempts to generate an effective response using the orders of three signal arrivals. Experiments using FPGAs verify the validity of the proposed PUF. Although Uniqueness is deteriorated, Correctness, Steadiness, Randomness and Resistance against the machine learning attacks are improved in comparison with conventional one.

High-resolution climate signals in the Bølling Allerød Interstadial (Greenland Interstadial 1) as reflected in European tree-ring chronologies compared to marine varves and ice-core records

NASA Astrophysics Data System (ADS)

Friedrich, Michael; Kromer, Bernd; Kaiser, Klaus F.; Spurk, Marco; Hughen, Konrad A.; Johnsen, Sigfus J.

2001-05-01

Lateglacial and Holocene tree-ring chronologies are unique archives, which provide various information on past environments on a true annual time scale. Changes in ring-width can be related to past climate anomalies and dendrodated wood provides an ideal source for radiocarbon calibration. We present a 1051 year tree-ring chronology from the Late Glacial, built from subfossil Scots pines (Pinus sylvestris) that grew in different regions of Central and Southern Europe. Through a series of high-precision radiocarbon measurements we obtained a floating radiocarbon chronology, which allowed accurate wiggle-matching to the INTCAL98 calibration curve. The trees show a coherent pattern in ring-width variations throughout Central Europe, and extending into the Mediterranean, which indicates a strong external climatic factor, most probably temperature during the growing season. We identified major growth events, which appear synchronous with events seen in isotopic and tracer signals in the Greenland ice cores and with changes in the strength of upwelling in the Cariaco Basin.

Expression pattern and signalling pathways in neutrophil like HL-60 cells after treatment with estrogen receptor selective ligands.

PubMed

Blesson, Chellakkan Selvanesan; Sahlin, Lena

2012-09-25

Estrogens play a role in the regulation of genes associated with inflammation and immunity in neutrophils. Estrogen signalling is mediated by estrogen receptor (ER)α, ERβ, and G-protein-coupled estrogen receptor-1 (GPER). The mechanisms by which estrogen regulate genes in neutrophils are poorly understood. Our aim was to identify the presence of ERs and to characterize estrogen responsive genes in terminally differentiated neutrophil like HL-60 (nHL-60) cells using estradiol and selective ER agonists. ERs were identified by Western blotting and immunocytochemistry. Microarray technique was used to screen for differentially expressed genes and the selected genes were verified by quantitative PCR. We show the presence of functional ERα, ERβ and GPER. Microarray analysis showed the presence of genes that are uniquely regulated by a single ligand and also genes that are regulated by multiple ligands. We conclude that ERs are functionally active in nHL-60 cells regulating genes involved in key physiological functions. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Gravitational radiation from rapidly rotating nascent neutron stars

NASA Technical Reports Server (NTRS)

Lai, Dong; Shapiro, Stuart L.

1995-01-01

We study the secular evolution and gravitational wave signature of a newly formed, rapidly rotating neutron star. The neutron star may arise from core collapse in a massive star or from the accretion-induced collapse of a white dwarf. After a brief dynamical phase, the nascent neutron star settles into an axisymmetric, secularly unstable state. Gravitational radiation drives the star to a nonaxisymmetric, stationary equilibrium configuration via the bar-mode instability. The emitted quasi-periodic gravitational waves have a unique signature: the wave frequency sweeps downward from a few hundred Hertz to zero, while the wave amplitude increase from zero to a maximum and then decays back to zero. Such a wave signal could detected by broadband gravitational wave interferometers currently being constructed. We also characterize two other types of gravitational wave signals that could arise in principle from a rapidly rotating, secularly unstable neutron star: a high-frequency (f greater than or approximately = 1000 Hz) wave which increases the pattern-speed of the star, and a wave that actually increases the angular momentum of the star.

Root Water Uptake and Soil Moisture Pattern Dynamics - Capturing Connections, Controls and Causalities

NASA Astrophysics Data System (ADS)

Blume, T.; Heidbuechel, I.; Hassler, S. K.; Simard, S.; Guntner, A.; Stewart, R. D.; Weiler, M.

2015-12-01

We hypothesize that there is a shift in controls on landscape scale soil moisture patterns when plants become active during the growing season. Especially during the summer soil moisture patterns are not only controlled by soils, topography and related abiotic site characteristics but also by root water uptake. Root water uptake influences soil moisture patterns both in the lateral and vertical direction. Plant water uptake from different soil depths is estimated based on diurnal fluctuations in soil moisture content and was investigated with a unique setup of 46 field sites in Luxemburg and 15 field sites in Germany. These sites cover a range of geologies, soils, topographic positions and types of vegetation. Vegetation types include pasture, pine forest (young and old) and different deciduous forest stands. Available data at all sites includes information at high temporal resolution from 3-5 soil moisture and soil temperature profiles, matrix potential, piezometers and sapflow sensors as well as standard climate data. At sites with access to a stream, discharge or water level is also recorded. The analysis of soil moisture patterns over time indicates a shift in regime depending on season. Depth profiles of root water uptake show strong differences between different forest stands, with maximum depths ranging between 50 and 200 cm. Temporal dynamics of signal strength within the profile furthermore suggest a locally shifting spatial distribution of root water uptake depending on water availability. We will investigate temporal thresholds (under which conditions spatial patterns of root water uptake become most distinct) as well as landscape controls on soil moisture and root water uptake dynamics.

Embryonic expression of endothelins and their receptors in lamprey and frog reveals stem vertebrate origins of complex Endothelin signaling

PubMed Central

Square, Tyler; Jandzik, David; Cattell, Maria; Hansen, Andrew; Medeiros, Daniel Meulemans

2016-01-01

Neural crest cells (NCCs) are highly patterned embryonic cells that migrate along stereotyped routes to give rise to a diverse array of adult tissues and cell types. Modern NCCs are thought to have evolved from migratory neural precursors with limited developmental potential and patterning. How this occurred is poorly understood. Endothelin signaling regulates several aspects of NCC development, including their migration, differentiation, and patterning. In jawed vertebrates, Endothelin signaling involves multiple functionally distinct ligands (Edns) and receptors (Ednrs) expressed in various NCC subpopulations. To test the potential role of endothelin signaling diversification in the evolution of modern, highly patterned NCC, we analyzed the expression of the complete set of endothelin ligands and receptors in the jawless vertebrate, the sea lamprey (Petromyzon marinus). To better understand ancestral features of gnathostome edn and ednr expression, we also analyzed all known Endothelin signaling components in the African clawed frog (Xenopus laevis). We found that the sea lamprey has a gnathsotome-like complement of edn and ednr duplicates, and these genes are expressed in patterns highly reminiscent of their gnathostome counterparts. Our results suggest that the duplication and specialization of vertebrate Endothelin signaling coincided with the appearance of highly patterned and multipotent NCCs in stem vertebrates. PMID:27677704

RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities

PubMed Central

Rai, Richa; Chauhan, Sudhir Kumar; Singh, Vikas Vikram; Rai, Madhukar; Rai, Geeta

2016-01-01

Systemic lupus erythematosus (SLE) patients exhibit immense heterogeneity which is challenging from the diagnostic perspective. Emerging high throughput sequencing technologies have been proved to be a useful platform to understand the complex and dynamic disease processes. SLE patients categorised based on autoantibody specificities are reported to have differential immuno-regulatory mechanisms. Therefore, we performed RNA-seq analysis to identify transcriptomics of SLE patients with distinguished autoantibody specificities. The SLE patients were segregated into three subsets based on the type of autoantibodies present in their sera (anti-dsDNA+ group with anti-dsDNA autoantibody alone; anti-ENA+ group having autoantibodies against extractable nuclear antigens (ENA) only, and anti-dsDNA+ENA+ group having autoantibodies to both dsDNA and ENA). Global transcriptome profiling for each SLE patients subsets was performed using Illumina® Hiseq-2000 platform. The biological relevance of dysregulated transcripts in each SLE subsets was assessed by ingenuity pathway analysis (IPA) software. We observed that dysregulation in the transcriptome expression pattern was clearly distinct in each SLE patients subsets. IPA analysis of transcripts uniquely expressed in different SLE groups revealed specific biological pathways to be affected in each SLE subsets. Multiple cytokine signaling pathways were specifically dysregulated in anti-dsDNA+ patients whereas Interferon signaling was predominantly dysregulated in anti-ENA+ patients. In anti-dsDNA+ENA+ patients regulation of actin based motility by Rho pathway was significantly affected. The granulocyte gene signature was a common feature to all SLE subsets; however, anti-dsDNA+ group showed relatively predominant expression of these genes. Dysregulation of Plasma cell related transcripts were higher in anti-dsDNA+ and anti-ENA+ patients as compared to anti-dsDNA+ ENA+. Association of specific canonical pathways with the uniquely expressed transcripts in each SLE subgroup indicates that specific immunological disease mechanisms are operative in distinct SLE patients’ subsets. This ‘sub-grouping’ approach could further be useful for clinical evaluation of SLE patients and devising targeted therapeutics. PMID:27835693

The alternative Medicago truncatula defense proteome of ROS—defective transgenic roots during early microbial infection

PubMed Central

Kiirika, Leonard M.; Schmitz, Udo; Colditz, Frank

2014-01-01

ROP-type GTPases of plants function as molecular switches within elementary signal transduction pathways such as the regulation of ROS synthesis via activation of NADPH oxidases (RBOH-respiratory burst oxidase homolog in plants). Previously, we reported that silencing of the Medicago truncatula GTPase MtROP9 led to reduced ROS production and suppressed induction of ROS-related enzymes in transgenic roots (MtROP9i) infected with pathogenic (Aphanomyces euteiches) and symbiotic microorganisms (Glomus intraradices, Sinorhizobium meliloti). While fungal infections were enhanced, S. meliloti infection was drastically impaired. In this study, we investigate the temporal proteome response of M. truncatula MtROP9i transgenic roots during the same microbial interactions under conditions of deprived potential to synthesize ROS. In comparison with control roots (Mtvector), we present a comprehensive proteomic analysis using sensitive MS protein identification. For four early infection time-points (1, 3, 5, 24 hpi), 733 spots were found to be different in abundance: 213 spots comprising 984 proteins (607 unique) were identified after S. meliloti infection, 230 spots comprising 796 proteins (580 unique) after G. intraradices infection, and 290 spots comprising 1240 proteins (828 unique) after A. euteiches infection. Data evaluation by GelMap in combination with a heatmap tool allowed recognition of key proteome changes during microbial interactions under conditions of hampered ROS synthesis. Overall, the number of induced proteins in MtROP9i was low as compared with controls, indicating a dual function of ROS in defense signaling as well as alternative response patterns activated during microbial infection. Qualitative analysis of induced proteins showed that enzymes linked to ROS production and scavenging were highly induced in control roots, while in MtROP9i the majority of proteins were involved in alternative defense pathways such as cell wall and protein degradation. PMID:25101099

Self-organization of spatial patterning in human embryonic stem cells

PubMed Central

Deglincerti, Alessia; Etoc, Fred; Ozair, M. Zeeshan; Brivanlou, Ali H.

2017-01-01

The developing embryo is a remarkable example of self-organization, where functional units are created in a complex spatio-temporal choreography. Recently, human embryonic stem cells (ESCs) have been used to recapitulate in vitro the self-organization programs that are executed in the embryo in vivo. This represents a unique opportunity to address self-organization in humans that is otherwise not addressable with current technologies. In this essay, we review the recent literature on self-organization of human ESCs, with a particular focus on two examples: formation of embryonic germ layers and neural rosettes. Intriguingly, both activation and elimination of TGFβ signaling can initiate self-organization, albeit with different molecular underpinnings. We discuss the mechanisms underlying the formation of these structures in vitro and explore future challenges in the field. PMID:26970615

Coding and decoding in a point-to-point communication using the polarization of the light beam.

PubMed

Kavehvash, Z; Massoumian, F

2008-05-10

A new technique for coding and decoding of optical signals through the use of polarization is described. In this technique the concept of coding is translated to polarization. In other words, coding is done in such a way that each code represents a unique polarization. This is done by implementing a binary pattern on a spatial light modulator in such a way that the reflected light has the required polarization. Decoding is done by the detection of the received beam's polarization. By linking the concept of coding to polarization we can use each of these concepts in measuring the other one, attaining some gains. In this paper the construction of a simple point-to-point communication where coding and decoding is done through polarization will be discussed.

Physical objects as vehicles of cultural transmission: maintaining harmony and uniqueness through colored geometric patterns.

PubMed

Ishii, Keiko; Miyamoto, Yuri; Rule, Nicholas O; Toriyama, Rie

2014-02-01

We examined how cultural values of harmony and uniqueness are represented and maintained through physical media (i.e., colorings of geometric patterns) and how individuals play an active role in selecting and maintaining such cultural values. We found that colorings produced by European American adults and children were judged as more unique, whereas colorings produced by Japanese adults and children were judged as more harmonious, reflecting cultural differences in values. Harmony undergirded Japanese participants' preferences for colorings, whereas uniqueness undergirded European American participants' preferences for colorings. These cultural differences led participants to prefer own-culture colorings over other-culture colorings. Moreover, bicultural participants' preferences acculturated according to their identification with their host culture. Furthermore, child rearers in Japan and Canada gave feedback about the children's colorings that were consistent with their culture's values. These findings suggest that simple geometric patterns can embody cultural values that are socialized and reinforced from an early age.

Estradiol targets T cell signaling pathways in human systemic lupus.

PubMed

Walters, Emily; Rider, Virginia; Abdou, Nabih I; Greenwell, Cindy; Svojanovsky, Stan; Smith, Peter; Kimler, Bruce F

2009-12-01

The major risk factor for developing systemic lupus erythematosus (SLE) is being female. The present study utilized gene profiles of activated T cells from females with SLE and healthy controls to identify signaling pathways uniquely regulated by estradiol that could contribute to SLE pathogenesis. Selected downstream pathway genes (+/- estradiol) were measured by real time polymerase chain amplification. Estradiol uniquely upregulated six pathways in SLE T cells that control T cell function including interferon-alpha signaling. Measurement of interferon-alpha pathway target gene expression revealed significant differences (p= 0.043) in DRIP150 (+/- estradiol) in SLE T cell samples while IFIT1 expression was bimodal and correlated moderately (r= 0.55) with disease activity. The results indicate that estradiol alters signaling pathways in activated SLE T cells that control T cell function. Differential expression of transcriptional coactivators could influence estrogen-dependent gene regulation in T cell signaling and contribute to SLE onset and disease pathogenesis.

Unique catalytic activities and scaffolding of p21 activated kinase-1 in cardiovascular signaling.

PubMed

Ke, Yunbo; Lei, Ming; Wang, Xin; Solaro, R John

2013-09-27

P21 activated kinase-1 (Pak1) has diverse functions in mammalian cells. Although a large number of phosphoproteins have been designated as Pak1 substrates from in vitro studies, emerging evidence has indicated that Pak1 may function as a signaling molecule through a unique molecular mechanism - scaffolding. By scaffolding, Pak1 delivers signals through an auto-phosphorylation-induced conformational change without transfer of a phosphate group to its immediate downstream effector(s). Here we review evidence for this regulatory mechanism based on structural and functional studies of Pak1 in different cell types and research models as well as in vitro biochemical assays. We also discuss the implications of Pak1 scaffolding in disease-related signaling processes and the potential in cardiovascular drug development.

Persistence and storage of activity patterns in spiking recurrent cortical networks: modulation of sigmoid signals by after-hyperpolarization currents and acetylcholine

PubMed Central

Palma, Jesse; Grossberg, Stephen; Versace, Massimiliano

2012-01-01

Many cortical networks contain recurrent architectures that transform input patterns before storing them in short-term memory (STM). Theorems in the 1970's showed how feedback signal functions in rate-based recurrent on-center off-surround networks control this process. A sigmoid signal function induces a quenching threshold below which inputs are suppressed as noise and above which they are contrast-enhanced before pattern storage. This article describes how changes in feedback signaling, neuromodulation, and recurrent connectivity may alter pattern processing in recurrent on-center off-surround networks of spiking neurons. In spiking neurons, fast, medium, and slow after-hyperpolarization (AHP) currents control sigmoid signal threshold and slope. Modulation of AHP currents by acetylcholine (ACh) can change sigmoid shape and, with it, network dynamics. For example, decreasing signal function threshold and increasing slope can lengthen the persistence of a partially contrast-enhanced pattern, increase the number of active cells stored in STM, or, if connectivity is distance-dependent, cause cell activities to cluster. These results clarify how cholinergic modulation by the basal forebrain may alter the vigilance of category learning circuits, and thus their sensitivity to predictive mismatches, thereby controlling whether learned categories code concrete or abstract features, as predicted by Adaptive Resonance Theory. The analysis includes global, distance-dependent, and interneuron-mediated circuits. With an appropriate degree of recurrent excitation and inhibition, spiking networks maintain a partially contrast-enhanced pattern for 800 ms or longer after stimuli offset, then resolve to no stored pattern, or to winner-take-all (WTA) stored patterns with one or multiple winners. Strengthening inhibition prolongs a partially contrast-enhanced pattern by slowing the transition to stability, while strengthening excitation causes more winners when the network stabilizes. PMID:22754524

A novel muscle LIM-only protein is generated from the paxillin gene locus in Drosophila.

PubMed

Yagi, R; Ishimaru, S; Yano, H; Gaul, U; Hanafusa, H; Sabe, H

2001-09-01

Paxillin is a protein containing four LIM domains, and functions in integrin signaling. We report here that two transcripts are generated from the paxillin gene locus in Drosophila; one encodes a protein homolog of the vertebrate Paxillin (DPxn37), and the other a protein with only three LIM domains, partly encoded by its own specific exon (PDLP). At the myotendinous junctions of Drosophila embryos where integrins play important roles, both DPxn37 and PDLP are highly expressed with different patterns; DPxn37 is predominantly concentrated at the center of the junctions, whereas PDLP is highly enriched at neighboring sides of the junction centers, primarily expressed in the mesodermal myotubes. Northern blot analysis revealed that DPxn37 is ubiquitously expressed throughout the life cycle, whereas PDLP expression exhibits a biphasic pattern during development, largely concomitant with muscle generation and remodeling. Our results collectively reveal that a unique system exists in Drosophila for the generation of a novel type of LIM-only protein, highly expressed in the embryonic musculature, largely utilizing the Paxillin LIM domains.

The switching of strong spin wave beams in patterned garnet films.

PubMed

Gieniusz, R; Gruszecki, P; Krawczyk, M; Guzowska, U; Stognij, A; Maziewski, A

2017-08-18

The application of spin waves in communication with information encoded in amplitude and phase could replace or enhance existing microelectronic and microwave devices with significantly decreased energy consumption. Spin waves (SW) are usually transported in a magnetic material shaped to act as a waveguide. However, the implementation of SW transport and switching in plane homogeneous magnetic films and running as a narrow beam with a small divergence angle still present a challenge. We propose a realization of a strong SW switchers based on a patterned yttrium iron garnet (YIG) film that could serve as a magnonic fundamental building block. Our concept relies on the creation of a narrow beam of relatively short-wavelength SW by effect of a total non-reflection, found to be tied to refraction on the decreasing internal magnetic field, near a line of antidots at YIG. Nonreciprocal SW excitation by a microstrip antenna is used for controlling the direction of the signal flow. We demonstrate unique features of the propagation of microwave-excited SW beams, provide insight into their physics and discuss their potential applications in high-frequency devices.

Embedded 3D shape measurement system based on a novel spatio-temporal coding method

NASA Astrophysics Data System (ADS)

Xu, Bin; Tian, Jindong; Tian, Yong; Li, Dong

2016-11-01

Structured light measurement has been wildly used since 1970s in industrial component detection, reverse engineering, 3D molding, robot navigation, medical and many other fields. In order to satisfy the demand for high speed, high precision and high resolution 3-D measurement for embedded system, a new patterns combining binary and gray coding principle in space are designed and projected onto the object surface orderly. Each pixel corresponds to the designed sequence of gray values in time - domain, which is treated as a feature vector. The unique gray vector is then dimensionally reduced to a scalar which could be used as characteristic information for binocular matching. In this method, the number of projected structured light patterns is reduced, and the time-consuming phase unwrapping in traditional phase shift methods is avoided. This algorithm is eventually implemented on DM3730 embedded system for 3-D measuring, which consists of an ARM and a DSP core and has a strong capability of digital signal processing. Experimental results demonstrated the feasibility of the proposed method.

Bystander signaling in C. elegans: proton microbeam studies

PubMed Central

Nelson, Gregory; Jones, Tamako; Ortloff, Leticia; Ford, John; Nuñez, Delia; Braby, Leslie

2014-01-01

Biological model: In this project, we investigated the control of radiation-induced genotoxic damage expression in somatic cells of the nematode Caenorhabditis elegans. We measured genotoxic damage in the C. elegans intestine by irradiating young larvae with 20 intestinal cells. Fourteen of these cells undergo exactly one nuclear division without cytoplasmic division leading to 14 binucleate cells. This nuclear division is synchronized and occurs at the first larval molt. Irradiation induces chromosome aberrations including dicentrics which we can quantify as stable anaphase bridges in the binucleate cells of young adult intestines. The endpoint is dose- and LET-dependent and we have demonstrated that individual intestinal cells have unique radiosensitivities. Results: The project has two components, a genetic screen for genes that control cell sensitivity and a microbeam component to directly probe individual cells. The genetic screen has identified several genes in NHEJ repair and telomere metabolism that modulate overall bridge frequency. Knockout mutants of cku-70, cku-80 and lig-4 greatly sensitize animals for anaphase bridge induction. A statistical method was used to determine whether induction of bridges was strictly random and cell autonomous and we determined that expression of bridges in pairs of cells was, in fact, non-random which suggested that signaling between cells affected the pattern of bridge expression. This allowed us to conduct an RNAi and mutation screen for genes that control the signaling (block non-random distributions) and several candidates have been identified. To directly test the notion that signaling of genotoxic damage occurs, we conducted experiments with alpha particles collimated through slits in metal foils and showed that genotoxic damage could be expressed many cell diameters away from a partial body exposure site. Thus, an in vivo bystander effect was demonstrated. Dose targeting was then improved to small regional exposures and eventually to individual cell targeting using 2 MeV protons from the microbeam facility at Texas A&M University. We now employ a green fluorescent protein (GFP)-expressing transgenic worm (rrIs1[elt-2::GFP]) to target GFP-positive gut cells via the gut-specific transcription factor elt-2. This allows alignment of the cell of interest over the microbeam aperture under appropriate fluorescence illumination. Microbeam irradiation experiments for many pairwise combinations of cell signal transmission and reception (observed as expression of anaphase bridges) have been conducted and several interesting patterns emerge. (i) The signaling pattern is cell-specific and does not simply reflect cell–cell distance or require direct contact between cell pairs. (ii) The signal range can be as far as from cell pair 2 to cell pair 8 (>100 µm). (iii) There appears to be a functional compartment boundary at the pharynx/intestine valve as even high-dose exposures to the posterior pharyngeal bulb fail to induce bridges in nearby intestinal cells. (iv) The frequency of signal transmission and reception corresponds broadly to the overall frequency of bridges observed during whole-body irradiations which suggests that direct irradiation and ‘out-of-field’ effects may be additive. These patterns have been analyzed in terms of a cellular logic circuit map for signal transmission and reception. A dose–response for a subset of microbeam-targeted cells was measured over the range of 5–20 Gy. Controlled cell pair targeting was used to test the potential additivity of signals and we found that effects were supra-additive. Finally, preliminary measurements were conducted on GFP-expressing transgenic strains that bore cku-70(tm1524) III and smk-1(mn156) V mutations which confer enhanced radiosensitivity. Cku-70 is a Ku-70 ortholog while smk-1 is orthologous to the mammalian and Dictyostelium discoideum SMEK (suppressor of MEK null) protein. In the cku-70(0/0) strain, the severity of the bridges in bystander cells was enhanced, suggesting that signal recipient cells employ NHEJ repair pathways in the expression of anaphase bridges. Clinical trial registration number: Not applicable.

Signal transduction profile of chemical sensitisers in dendritic cells: An endpoint to be included in a cell-based in vitro alternative approach to hazard identification?

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

Neves, Bruno Miguel; Centro de Neurociencias e Biologia Celular, Universidade de Coimbra, Coimbra 3004-517; Goncalo, Margarida

2011-01-15

The development of non-animal testing methods for the assessment of skin sensitisation potential is an urgent challenge within the framework of existing and forthcoming legislation. Efforts have been made to replace current animal tests, but so far no alternative methods have been developed. It is widely recognised that alternatives to animal testing cannot be accomplished with a single approach, but rather will require the integration of results obtained from different in vitro and in silico assays. The argument subjacent to the development of in vitro dendritic cell (DC)-based assays is that sensitiser-induced changes in the DC phenotype can be differentiatedmore » from those induced by irritants. This assumption is derived from the unique capacity of DC to convert environmental signals encountered at the skin into a receptor expression pattern (MHC class II molecules, co-stimulatory molecules, chemokine receptors) and a soluble mediator release profile that will stimulate T lymphocytes. Since signal transduction cascades precede changes in surface marker expression and cytokine/chemokine secretion, these phenotypic modifications are a consequence of a signal transduction profile that is specifically triggered by sensitisers and not by irritants. A limited number of studies have addressed this subject and the present review attempts to summarise and highlight all of the signalling pathways modulated by skin sensitisers and irritants. Furthermore, we conclude this review by focusing on the most promising strategies suitable for inclusion into a cell-based in vitro alternative approach to hazard identification.« less

Opto-mechanical door locking system

NASA Astrophysics Data System (ADS)

Patil, Saurabh S.; Rodrigues, Vanessa M.; Patil, Ajeetkumar; Chidangil, Santhosh

2015-09-01

We present an Opto-mechanical Door Locking System which is an optical system that combines a simple combination of a coherent light source (Laser) and a photodiode based sensor with focus toward security applications. The basic construct of the KEY comprises a Laser source in a cylindrical enclosure that slides perfectly into the LOCK. The Laser is pulsed at a fixed encrypted frequency unique to that locking system. Transistor-transistor logic (TTL) circuitry is used to achieve encryption. The casing of the key is designed in such a way that it will power the pulsing laser only when the key is inserted in the slot provided for it. The Lock includes a photo-sensor that will convert the detected light intensity to a corresponding electrical signal by decrypting the frequency. The lock also consists of a circuit with a feedback system that will carry the digital information regarding the encryption frequency code. The information received from the sensor is matched with the stored code; if found a perfect match, a signal will be sent to the servo to unlock the mechanical lock or to carry out any other operation. This technique can be incorporated in security systems for residences and safe houses, and can easily replace all conventional locks which formerly used fixed patterns to unlock. The major advantage of this proposed optomechanical system over conventional ones is that it no longer relies on a solid/imprinted pattern to perform its task and hence makes it almost impossible to tamper with.

Multiple-frequency acoustic wave devices for chemical sensing and materials characterization in both gas and liquid phase

DOEpatents

Martin, S.J.; Ricco, A.J.

1993-08-10

A chemical or intrinsic physical property sensor is described comprising: (a) a substrate; (b) an interaction region of said substrate where the presence of a chemical or physical stimulus causes a detectable change in the velocity and/or an attenuation of an acoustic wave traversing said region; and (c) a plurality of paired input and output interdigitated electrodes patterned on the surface of said substrate where each of said paired electrodes has a distinct periodicity, where each of said paired electrodes is comprised of an input and an output electrode; (d) an input signal generation means for transmitting an input signal having a distinct frequency to a specified input interdigitated electrode of said plurality so that each input electrode receives a unique input signal, whereby said electrode responds to said input signal by generating an acoustic wave of a specified frequency, thus, said plurality responds by generating a plurality of acoustic waves of different frequencies; (e) an output signal receiving means for determining an acoustic wave velocity and an amplitude of said acoustic waves at several frequencies after said waves transverses said interaction region and comparing these values to an input acoustic wave velocity and an input acoustic wave amplitude to produce values for perturbations in acoustic wave velocities and for acoustic wave attenuation as a function of frequency, where said output receiving means is individually coupled to each of said output interdigitated electrode; (f) a computer means for analyzing a data stream comprising information from said output receiving means and from said input signal generation means to differentiate a specified response due to a perturbation from a subsequent specified response due to a subsequent perturbation to determine the chemical or intrinsic physical properties desired.

CHIR99021 promotes self-renewal of mouse embryonic stem cells by modulation of protein-encoding gene and long intergenic non-coding RNA expression

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

Wu, Yongyan; Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A and F University, Yangling 712100, Shaanxi; Ai, Zhiying

2013-10-15

Embryonic stem cells (ESCs) can proliferate indefinitely in vitro and differentiate into cells of all three germ layers. These unique properties make them exceptionally valuable for drug discovery and regenerative medicine. However, the practical application of ESCs is limited because it is difficult to derive and culture ESCs. It has been demonstrated that CHIR99021 (CHIR) promotes self-renewal and enhances the derivation efficiency of mouse (m)ESCs. However, the downstream targets of CHIR are not fully understood. In this study, we identified CHIR-regulated genes in mESCs using microarray analysis. Our microarray data demonstrated that CHIR not only influenced the Wnt/β-catenin pathway bymore » stabilizing β-catenin, but also modulated several other pluripotency-related signaling pathways such as TGF-β, Notch and MAPK signaling pathways. More detailed analysis demonstrated that CHIR inhibited Nodal signaling, while activating bone morphogenetic protein signaling in mESCs. In addition, we found that pluripotency-maintaining transcription factors were up-regulated by CHIR, while several developmental-related genes were down-regulated. Furthermore, we found that CHIR altered the expression of epigenetic regulatory genes and long intergenic non-coding RNAs. Quantitative real-time PCR results were consistent with microarray data, suggesting that CHIR alters the expression pattern of protein-encoding genes (especially transcription factors), epigenetic regulatory genes and non-coding RNAs to establish a relatively stable pluripotency-maintaining network. - Highlights: • Combined use of CHIR with LIF promotes self-renewal of J1 mESCs. • CHIR-regulated genes are involved in multiple pathways. • CHIR inhibits Nodal signaling and promotes Bmp4 expression to activate BMP signaling. • Expression of epigenetic regulatory genes and lincRNAs is altered by CHIR.« less

Notch activates Wnt-4 signalling to control medio-lateral patterning of the pronephros.

PubMed

Naylor, Richard W; Jones, Elizabeth A

2009-11-01

Previous studies have highlighted a role for the Notch signalling pathway during pronephrogenesis in the amphibian Xenopus laevis, and in nephron development in the mammalian metanephros, yet a mechanism for this function remains elusive. Here, we further the understanding of how Notch signalling patterns the early X. laevis pronephros anlagen, a function that might be conserved in mammalian nephron segmentation. Our results indicate that early phase pronephric Notch signalling patterns the medio-lateral axis of the dorso-anterior pronephros anlagen, permitting the glomus and tubules to develop in isolation. We show that this novel function acts through the Notch effector gene hrt1 by upregulating expression of wnt4. Wnt-4 then patterns the proximal pronephric anlagen to establish the specific compartments that span the medio-lateral axis. We also identified pronephric expression of lunatic fringe and radical fringe that is temporally and spatially appropriate for a role in regulating Notch signalling in the dorso-anterior region of the pronephros anlagen. On the basis of these results, along with data from previous publications, we propose a mechanism by which the Notch signalling pathway regulates a Wnt-4 function that patterns the proximal pronephric anlagen.

Fibroblast growth factor receptor signaling in kidney and lower urinary tract development

PubMed Central

Walker, Kenneth A; Sims-Lucas, Sunder; Bates, Carlton M.

2015-01-01

Fibroblast growth factor receptors (FGFRs) and FGF ligands are highly expressed in the developing kidney and lower urinary tract. Several classic studies showed many effects of exogenous FGF ligands on embryonic renal tissues in vitro and in vivo. Another older landmark publication showed that mice with a dominant negative Fgfr fragment had severe renal dysplasia. Together these studies revealed the importance of FGFR signaling in kidney and lower urinary tract development. With the advent of modern gene targeting techniques, including conditional knockout approaches, several publications have revealed critical roles for FGFR signaling in many lineages of the kidney and lower urinary tract at different stages of development. FGFR signaling has been shown to be critical for early metanephric mesenchymal patterning, Wolffian duct patterning including induction of the ureteric bud, ureteric bud branching morphogenesis, nephron progenitor survival and nephrogenesis, and bladder mesenchyme patterning. FGFRs pattern these tissues by interacting with many other growth factor signaling pathways. Moreover, the many genetic Fgfr and Fgf animal models have structural defects mimicking numerous congenital anomalies of the kidney and urinary tract seen in humans. Finally, many studies have shown how FGFR signaling is critical for kidney and lower urinary tract patterning in humans. PMID:26293980

Fibroblast growth factor receptor signaling in kidney and lower urinary tract development.

PubMed

Walker, Kenneth A; Sims-Lucas, Sunder; Bates, Carlton M

2016-06-01

Fibroblast growth factor receptors (FGFRs) and FGF ligands are highly expressed in the developing kidney and lower urinary tract. Several classic studies showed many effects of exogenous FGF ligands on embryonic renal tissues in vitro and in vivo. Another older landmark publication showed that mice with a dominant negative Fgfr fragment had severe renal dysplasia. Together, these studies revealed the importance of FGFR signaling in kidney and lower urinary tract development. With the advent of modern gene targeting techniques, including conditional knockout approaches, several publications have revealed critical roles for FGFR signaling in many lineages of the kidney and lower urinary tract at different stages of development. FGFR signaling has been shown to be critical for early metanephric mesenchymal patterning, Wolffian duct patterning including induction of the ureteric bud, ureteric bud branching morphogenesis, nephron progenitor survival and nephrogenesis, and bladder mesenchyme patterning. FGFRs pattern these tissues by interacting with many other growth factor signaling pathways. Moreover, the many genetic Fgfr and Fgf animal models have structural defects mimicking numerous congenital anomalies of the kidney and urinary tract seen in humans. Finally, many studies have shown how FGFR signaling is critical for kidney and lower urinary tract patterning in humans.

Statistical analysis on the signals monitoring multiphase flow patterns in pipeline-riser system

NASA Astrophysics Data System (ADS)

Ye, Jing; Guo, Liejin

2013-07-01

The signals monitoring petroleum transmission pipeline in offshore oil industry usually contain abundant information about the multiphase flow on flow assurance which includes the avoidance of most undesirable flow pattern. Therefore, extracting reliable features form these signals to analyze is an alternative way to examine the potential risks to oil platform. This paper is focused on characterizing multiphase flow patterns in pipeline-riser system that is often appeared in offshore oil industry and finding an objective criterion to describe the transition of flow patterns. Statistical analysis on pressure signal at the riser top is proposed, instead of normal prediction method based on inlet and outlet flow conditions which could not be easily determined during most situations. Besides, machine learning method (least square supported vector machine) is also performed to classify automatically the different flow patterns. The experiment results from a small-scale loop show that the proposed method is effective for analyzing the multiphase flow pattern.

Noise assisted pattern fabrication

NASA Astrophysics Data System (ADS)

Roy, Tanushree; Agarwal, V.; Singh, B. P.; Parmananda, P.

2018-04-01

Pre-selected patterns on an n-type Si surface are fabricated by electrochemical etching in the presence of a weak optical signal. The constructive role of noise, namely, stochastic resonance (SR), is exploited for these purposes. SR is a nonlinear phenomenon wherein at an optimal amplitude of noise, the information transfer from weak input sub-threshold signals to the system output is maximal. In the present work, the amplitude of internal noise was systematically regulated by varying the molar concentration of hydrofluoric acid (HF) in the electrolyte. Pattern formation on the substrate for two different amplitudes (25 ± 2 and 11 ± 1 mW) of the optical template (sub-threshold signal) was considered. To quantify the fidelity/quality of pattern formation, the spatial cross-correlation coefficient (CCC) between the constructed pattern and the template of the applied signal was calculated. The maximum CCC is obtained for the pattern formed at an optimal HF concentration, indicating SR. Simulations, albeit using external noise, on a spatial array of coupled FitzHugh-Nagumo oscillators revealed similar results.

Separating macroecological pattern and process: comparing ecological, economic, and geological systems.

PubMed

Blonder, Benjamin; Sloat, Lindsey; Enquist, Brian J; McGill, Brian

2014-01-01

Theories of biodiversity rest on several macroecological patterns describing the relationship between species abundance and diversity. A central problem is that all theories make similar predictions for these patterns despite disparate assumptions. A troubling implication is that these patterns may not reflect anything unique about organizational principles of biology or the functioning of ecological systems. To test this, we analyze five datasets from ecological, economic, and geological systems that describe the distribution of objects across categories in the United States. At the level of functional form ('first-order effects'), these patterns are not unique to ecological systems, indicating they may reveal little about biological process. However, we show that mechanism can be better revealed in the scale-dependency of first-order patterns ('second-order effects'). These results provide a roadmap for biodiversity theory to move beyond traditional patterns, and also suggest ways in which macroecological theory can constrain the dynamics of economic systems.

Role of proton magnetic resonance spectroscopy in the diagnosis of gliomatosis cerebri: a unique pattern of normal choline but elevated Myo-inositol metabolite levels.

PubMed

Mohana-Borges, Aurea V R; Imbesi, Steven G; Dietrich, Rosalind; Alksne, John; Amjadi, Darius K

2004-01-01

A patient with histologically proven gliomatosis cerebri presented with a normal choline level but a markedly abnormal elevated myo-inositol level on magnetic resonance (MR) spectroscopy. We describe the case presentation, imaging findings (in particular, the unique MR spectroscopic pattern), and their significance regarding the diagnosis of this relatively rare neoplasm.

Separation of the global and local components in functional near-infrared spectroscopy signals using principal component spatial filtering

PubMed Central

Zhang, Xian; Noah, Jack Adam; Hirsch, Joy

2016-01-01

Abstract. Global systemic effects not specific to a task can be prominent in functional near-infrared spectroscopy (fNIRS) signals and the separation of task-specific fNIRS signals and global nonspecific effects is challenging due to waveform correlations. We describe a principal component spatial filter algorithm for separation of the global and local effects. The effectiveness of the approach is demonstrated using fNIRS signals acquired during a right finger-thumb tapping task where the response patterns are well established. Both the temporal waveforms and the spatial pattern consistencies between oxyhemoglobin and deoxyhemoglobin signals are significantly improved, consistent with the basic physiological basis of fNIRS signals and the expected pattern of activity associated with the task. PMID:26866047

Alveolar and Postalveolar Voiceless Fricative and Affricate Productions of Spanish–English Bilingual Children With Cochlear Implants

PubMed Central

Bunta, Ferenc; Tomblin, J. Bruce

2017-01-01

Purpose This study investigates the production of voiceless alveolar and postalveolar fricatives and affricates by bilingual and monolingual children with hearing loss who use cochlear implants (CIs) and their peers with normal hearing (NH). Method Fifty-four children participated in our study, including 12 Spanish–English bilingual CI users (M = 6;0 [years;months]), 12 monolingual English-speaking children with CIs (M = 6;1), 20 bilingual children with NH (M = 6;5), and 10 monolingual English-speaking children with NH (M = 5;10). Picture elicitation targeting /s/, /tʃ/, and /ʃ/ was administered. Repeated-measures analyses of variance comparing group means for frication duration, rise time, and centroid frequency were conducted for the effects of CI use and bilingualism. Results All groups distinguished the target sounds in the 3 acoustic parameters examined. Regarding frication duration and rise time, the Spanish productions of bilingual children with CIs differed from their bilingual peers with NH. English frication duration patterns for bilingual versus monolingual CI users also differed. Centroid frequency was a stronger place cue for children with NH than for children with CIs. Conclusion Patterns of fricative and affricate production display effects of bilingualism and diminished signal, yielding unique patterns for bilingual and monolingual CI users. PMID:28800372

Vocal responses of austral forest frogs to amplitude and degradation patterns of advertisement calls.

PubMed

Penna, Mario; Moreno-Gómez, Felipe N; Muñoz, Matías I; Cisternas, Javiera

2017-07-01

Degradation phenomena affecting animal acoustic signals may provide cues to assess the distance of emitters. Recognition of degraded signals has been extensively demonstrated in birds, and recently studies have also reported detection of degraded patterns in anurans that call at or above ground level. In the current study we explore the vocal responses of the syntopic burrowing male frogs Eupsophus emiliopugini and E. calcaratus from the South American temperate forest to synthetic conspecific calls differing in amplitude and emulating degraded and non-degraded signal patterns. The results show a strong dependence of vocal responses on signal amplitude, and a general lack of differential responses to signals with different pulse amplitude modulation depths in E. emiliopugini and no effect of relative amplitude of harmonics in E. calcaratus. Such limited discrimination of signal degradation patterns from non-degraded signals is likely related to the burrowing habits of these species. Shelters amplify outgoing and incoming conspecific vocalizations, but do not counteract signal degradation to an extent comparable to calling strategies used by other frogs. The limited detection abilities and resultant response permissiveness to degraded calls in these syntopic burrowing species would be advantageous for animals communicating in circumstances in which signal alteration prevails. Copyright © 2017 Elsevier B.V. All rights reserved.

Signals and circuits in the purkinje neuron.

PubMed

Abrams, Zéev R; Zhang, Xiang

2011-01-01

Purkinje neurons (PN) in the cerebellum have over 100,000 inputs organized in an orthogonal geometry, and a single output channel. As the sole output of the cerebellar cortex layer, their complex firing pattern has been associated with motor control and learning. As such they have been extensively modeled and measured using tools ranging from electrophysiology and neuroanatomy, to dynamic systems and artificial intelligence methods. However, there is an alternative approach to analyze and describe the neuronal output of these cells using concepts from electrical engineering, particularly signal processing and digital/analog circuits. By viewing the PN as an unknown circuit to be reverse-engineered, we can use the tools that provide the foundations of today's integrated circuits and communication systems to analyze the Purkinje system at the circuit level. We use Fourier transforms to analyze and isolate the inherent frequency modes in the PN and define three unique frequency ranges associated with the cells' output. Comparing the PN to a signal generator that can be externally modulated adds an entire level of complexity to the functional role of these neurons both in terms of data analysis and information processing, relying on Fourier analysis methods in place of statistical ones. We also re-describe some of the recent literature in the field, using the nomenclature of signal processing. Furthermore, by comparing the experimental data of the past decade with basic electronic circuitry, we can resolve the outstanding controversy in the field, by recognizing that the PN can act as a multivibrator circuit.

The roles of mid-myocardial and epicardial cells in T-wave alternans development: a simulation study.

PubMed

Janusek, D; Svehlikova, J; Zelinka, J; Weigl, W; Zaczek, R; Opolski, G; Tysler, M; Maniewski, R

2018-05-08

The occurrence of T-wave alternans in electrocardiographic signals was recently linked to susceptibility to ventricular arrhythmias and sudden cardiac death. Thus, by detecting and comprehending the origins of T-wave alternans, it might be possible to prevent such events. Here, we simulated T-wave alternans in a computer-generated human heart model by modulating the action potential duration and amplitude during the first part of the repolarization phase. We hypothesized that changes in the intracardiac alternans patterns of action potential properties would differentially influence T-wave alternans measurements at the body surface. Specifically, changes were simulated globally in the whole left and right ventricles to simulate concordant T-wave alternans, and locally in selected regions to simulate discordant and regional discordant, hereinafter referred to as "regional", T-wave alternans. Body surface potential maps and 12-lead electrocardiographic signals were then computed. In depth discrimination, the influence of epicardial layers on T-wave alternans development was significantly higher than that of mid-myocardial cells. Meanwhile, spatial discrimination revealed that discordant and regional action potential property changes had a higher influence on T-wave alternans amplitude than concordant changes. Notably, varying T-wave alternans sources yielded distinct body surface potential map patterns for T-wave alternans amplitude, which can be used for location of regions within hearts exhibiting impaired repolarization. The highest ability for T-wave alternans detection was achieved in lead V1. Ultimately, we proposed new parameters Vector Magnitude Alternans and Vector Angle Alternans, with higher ability for T-wave alternans detection when using multi-lead electrocardiographic signals processing than for single leads. Finally, QT alternans was found to be associated with the process of T-wave alternans generation. The distributions of the body surface T-wave alternans amplitude have been shown to have unique patterns depending on the type of alternans (concordant, discordant or regional) and the location of the disturbance in the heart. The influence of epicardial cells on T-wave alternans development is significantly higher than that of mid-myocardial cells, among which the sub-endocardial layer exerted the highest influence. QT interval alternans is identified as a phenomenon that correlate with T-wave alternans.

A STRUCTURAL THEORY FOR THE PERCEPTION OF MORSE CODE SIGNALS AND RELATED RHYTHMIC PATTERNS.

ERIC Educational Resources Information Center

WISH, MYRON

THE PRIMARY PURPOSE OF THIS DISSERTATION IS TO DEVELOP A STRUCTURAL THEORY, ALONG FACET-THEORETIC LINES, FOR THE PERCEPTION OF MORSE CODE SIGNALS AND RELATED RHYTHMIC PATTERNS. AS STEPS IN THE DEVELOPMENT OF THIS THEORY, MODELS FOR TWO SETS OF SIGNALS ARE PROPOSED AND TESTED. THE FIRST MODEL IS FOR A SET COMPRISED OF ALL SIGNALS OF THE…

Landscape pattern metrics and regional assessment

USGS Publications Warehouse

O'Neill, R. V.; Riitters, K.H.; Wickham, J.D.; Jones, K.B.

1999-01-01

The combination of remote imagery data, geographic information systems software, and landscape ecology theory provides a unique basis for monitoring and assessing large-scale ecological systems. The unique feature of the work has been the need to develop and interpret quantitative measures of spatial pattern-the landscape indices. This article reviews what is known about the statistical properties of these pattern metrics and suggests some additional metrics based on island biogeography, percolation theory, hierarchy theory, and economic geography. Assessment applications of this approach have required interpreting the pattern metrics in terms of specific environmental endpoints, such as wildlife and water quality, and research into how to represent synergystic effects of many overlapping sources of stress.

The calcium-sensing receptor and its interacting proteins

PubMed Central

Huang, Chunfa; Miller, R Tyler

2007-01-01

Abstract Seven membrane-spanning, or G protein-coupled receptors were originally thought to act through het-erotrimeric G proteins that in turn activate intracellular enzymes or ion channels, creating relatively simple, linear signalling pathways. Although this basic model remains true in that this family does act via a relatively small number of G proteins, these signalling systems are considerably more complex because the receptors interact with or are located near additional proteins that are often unique to a receptor or subset of receptors. These additional proteins give receptors their unique signalling ‘personalities’. The extracellular Ca-sensing receptor (CaR) signals via Gαi, Gαq and Gα12/13, but its effects in vivo demonstrate that the signalling pathways controlled by these subunits are not sufficient to explain all its biologic effects. Additional structural or signalling proteins that interact with the CaR may explain its behaviour more fully. Although the CaR is less well studied in this respect than other receptors, several CaR-interacting proteins such as filamin, a potential scaffolding protein, receptor activity modifying proteins (RAMPs) and potassium channels may contribute to the unique characteristics of the CaR. The CaR also appears to interact with additional proteins common to other G protein-coupled receptors such as arrestins, G protein receptor kinases, protein kinase C, caveolin and proteins in the ubiquitination pathway. These proteins probably represent a few initial members of CaR-based signalling complex. These and other proteins may not all be associated with the CaR in all tissues, but they form the basis for understanding the complete nature of CaR signalling. PMID:17979874

Unique Neural Characteristics of Atypical Lateralization of Language in Healthy Individuals

PubMed Central

Biduła, Szymon P.; Przybylski, Łukasz; Pawlak, Mikołaj A.; Króliczak, Gregory

2017-01-01

Using functional magnetic resonance imaging (fMRI) in 63 healthy participants, including left-handed and ambidextrous individuals, we tested how atypical lateralization of language—i. e., bilateral or right hemispheric language representation—differs from the typical left-hemisphere dominance. Although regardless of their handedness, all 11 participants from the atypical group engaged classical language centers, i.e., Broca's and Wernicke's areas, the right-hemisphere components of the default mode network (DMN), including the angular gyrus and middle temporal gyrus, were also critically involved during the verbal fluency task. Importantly, activity in these regions could not be explained in terms of mirroring the typical language pattern because left-hemisphere dominant individuals did not exhibit similar significant signal modulations. Moreover, when spatial extent of language-related activity across whole brain was considered, the bilateral language organization entailed more diffuse functional processing. Finally, we detected significant differences between the typical and atypical group in the resting-state connectivity at the global and local level. These findings suggest that the atypical lateralization of language has unique features, and is not a simple mirror image of the typical left hemispheric language representation. PMID:28983238

Identification of calcium-dependent protein kinase (CDPK): A multi-functional gene family in Rafflesia cantleyi

NASA Astrophysics Data System (ADS)

Amini, Safoora; Goh, Hoe-Han; Wan, Kiew-Lian

2016-11-01

Rafflesia, a parasitic plant that belongs to the Rafflesiaceae family, is notable for producing the largest flowers in the world. This study focused on identification of Calcium-dependent protein kinases (CDPKs) due to their vital roles in plant growth and development, biotic and abiotic stress responses, and hormone signaling. RNA-seq data generated from three bud stages of Rafflesia cantleyi ie BS1, BS2, and BS3 and were assembled. Based on the BLAST searches of Rafflesia unique transcripts (UTs) to Arabidopsis TAIR database, a total of 14 unique transcripts (UTs) were identified as CDPK1 to CDPK5, CDPK7 to CDPK11, CDPK16, CDPK18, CDPK19, and CDPK28. These genes are expressed at all three bud stages of R. cantleyi with up-regulation pattern at BS1 vs. BS2 and BS2 vs. BS3. This result shows that the expression of CDPK gene family increases by developmental progress in Rafflesia in order to regulate biochemical and molecular changes at the cellular level in response to exposure to environmental changes. However, CDPKs functions in plants growth and defense process still need more experimental evidence to deeply understand their biological roles in R. cantleyi.

Snowfall less sensitive to warming in Karakoram than in Himalayas due to a unique seasonal cycle

USGS Publications Warehouse

Kapnick, Sarah B.; Delworth, Thomas L.; Ashfaq, Moetasim; Malyshev, Sergey; Milly, Paul C.D.

2014-01-01

The high mountains of Asia, including the Karakoram, Himalayas and Tibetan Plateau, combine to form a region of perplexing hydroclimate changes. Glaciers have exhibited mass stability or even expansion in the Karakoram region1, 2, 3, contrasting with glacial mass loss across the nearby Himalayas and Tibetan Plateau1, 4, a pattern that has been termed the Karakoram anomaly. However, the remote location, complex terrain and multi-country fabric of high-mountain Asia have made it difficult to maintain longer-term monitoring systems of the meteorological components that may have influenced glacial change. Here we compare a set of high-resolution climate model simulations from 1861 to 2100 with the latest available observations to focus on the distinct seasonal cycles and resulting climate change signatures of Asia’s high-mountain ranges. We find that the Karakoram seasonal cycle is dominated by non-monsoonal winter precipitation, which uniquely protects it from reductions in annual snowfall under climate warming over the twenty-first century. The simulations show that climate change signals are detectable only with long and continuous records, and at specific elevations. Our findings suggest a meteorological mechanism for regional differences in the glacier response to climate warming.

The draft genomes of soft–shell turtle and green sea turtle yield insights into the development and evolution of the turtle–specific body plan

PubMed Central

Niimura, Yoshihito; Huang, Zhiyong; Li, Chunyi; White, Simon; Xiong, Zhiqiang; Fang, Dongming; Wang, Bo; Ming, Yao; Chen, Yan; Zheng, Yuan; Kuraku, Shigehiro; Pignatelli, Miguel; Herrero, Javier; Beal, Kathryn; Nozawa, Masafumi; Li, Qiye; Wang, Juan; Zhang, Hongyan; Yu, Lili; Shigenobu, Shuji; Wang, Junyi; Liu, Jiannan; Flicek, Paul; Searle, Steve; Wang, Jun; Kuratani, Shigeru; Yin, Ye; Aken, Bronwen; Zhang, Guojie; Irie, Naoki

2014-01-01

The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ~267.9–248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these turtles. Embryonic gene expression analysis identified an hourglass-like divergence of turtle and chicken embryogenesis, with maximal conservation around the vertebrate phylotypic period, rather than at later stages that show the amniote-common pattern. Wnt5a expression was found in the growth zone of the dorsal shell, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty. Our results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell. PMID:23624526

Peripheral blood gene expression profiles in metabolic syndrome, coronary artery disease and type 2 diabetes.

PubMed

Grayson, B L; Wang, L; Aune, T M

2011-07-01

To determine if individuals with metabolic disorders possess unique gene expression profiles, we compared transcript levels in peripheral blood from patients with coronary artery disease (CAD), type 2 diabetes (T2D) and their precursor state, metabolic syndrome to those of control (CTRL) subjects and subjects with rheumatoid arthritis (RA). The gene expression profile of each metabolic state was distinguishable from CTRLs and correlated with other metabolic states more than with RA. Of note, subjects in the metabolic cohorts overexpressed gene sets that participate in the innate immune response. Genes involved in activation of the pro-inflammatory transcription factor, NF-κB, were overexpressed in CAD whereas genes differentially expressed in T2D have key roles in T-cell activation and signaling. Reverse transcriptase PCR validation confirmed microarray results. Furthermore, several genes differentially expressed in human metabolic disorders have been previously shown to participate in inflammatory responses in murine models of obesity and T2D. Taken together, these data demonstrate that peripheral blood from individuals with metabolic disorders display overlapping and non-overlapping patterns of gene expression indicative of unique, underlying immune processes.

The Not-So-Global Blood Oxygen Level-Dependent Signal.

PubMed

Billings, Jacob; Keilholz, Shella

2018-04-01

Global signal regression is a controversial processing step for resting-state functional magnetic resonance imaging, partly because the source of the global blood oxygen level-dependent (BOLD) signal remains unclear. On the one hand, nuisance factors such as motion can readily introduce coherent BOLD changes across the whole brain. On the other hand, the global signal has been linked to neural activity and vigilance levels, suggesting that it contains important neurophysiological information and should not be discarded. Any widespread pattern of coordinated activity is likely to contribute appreciably to the global signal. Such patterns may include large-scale quasiperiodic spatiotemporal patterns, known also to be tied to performance on vigilance tasks. This uncertainty surrounding the separability of the global BOLD signal from concurrent neurological processes motivated an examination of the global BOLD signal's spatial distribution. The results clarify that although the global signal collects information from all tissue classes, a diverse subset of the BOLD signal's independent components contribute the most to the global signal. Further, the timing of each network's contribution to the global signal is not consistent across volunteers, confirming the independence of a constituent process that comprises the global signal.

Individually Unique Body Color Patterns in Octopus (Wunderpus photogenicus) Allow for Photoidentification

PubMed Central

Huffard, Christine L.; Caldwell, Roy L.; DeLoach, Ned; Gentry, David Wayne; Humann, Paul; MacDonald, Bill; Moore, Bruce; Ross, Richard; Uno, Takako; Wong, Stephen

2008-01-01

Studies on the longevity and migration patterns of wild animals rely heavily on the ability to track individual adults. Non-extractive sampling methods are particularly important when monitoring animals that are commercially important to ecotourism, and/or are rare. The use of unique body patterns to recognize and track individual vertebrates is well-established, but not common in ecological studies of invertebrates. Here we provide a method for identifying individual Wunderpus photogenicus using unique body color patterns. This charismatic tropical octopus is commercially important to the underwater photography, dive tourism, and home aquarium trades, but is yet to be monitored in the wild. Among the adults examined closely, the configurations of fixed white markings on the dorsal mantle were found to be unique. In two animals kept in aquaria, these fixed markings were found not to change over time. We believe another individual was photographed twice in the wild, two months apart. When presented with multiple images of W. photogenicus, volunteer observers reliably matched photographs of the same individuals. Given the popularity of W. photogenicus among underwater photographers, and the ease with which volunteers can correctly identify individuals, photo-identification appears to be a practical means to monitor individuals in the wild. PMID:19009019

Problems Associated with Statistical Pattern Recognition of Acoustic Emission Signals in a Compact Tension Fatigue Specimen

NASA Technical Reports Server (NTRS)

Hinton, Yolanda L.

1999-01-01

Acoustic emission (AE) data were acquired during fatigue testing of an aluminum 2024-T4 compact tension specimen using a commercially available AE system. AE signals from crack extension were identified and separated from noise spikes, signals that reflected from the specimen edges, and signals that saturated the instrumentation. A commercially available software package was used to train a statistical pattern recognition system to classify the signals. The software trained a network to recognize signals with a 91-percent accuracy when compared with the researcher's interpretation of the data. Reasons for the discrepancies are examined and it is postulated that additional preprocessing of the AE data to focus on the extensional wave mode and eliminate other effects before training the pattern recognition system will result in increased accuracy.

Real-time object recognition in multidimensional images based on joined extended structural tensor and higher-order tensor decomposition methods

NASA Astrophysics Data System (ADS)

Cyganek, Boguslaw; Smolka, Bogdan

2015-02-01

In this paper a system for real-time recognition of objects in multidimensional video signals is proposed. Object recognition is done by pattern projection into the tensor subspaces obtained from the factorization of the signal tensors representing the input signal. However, instead of taking only the intensity signal the novelty of this paper is first to build the Extended Structural Tensor representation from the intensity signal that conveys information on signal intensities, as well as on higher-order statistics of the input signals. This way the higher-order input pattern tensors are built from the training samples. Then, the tensor subspaces are built based on the Higher-Order Singular Value Decomposition of the prototype pattern tensors. Finally, recognition relies on measurements of the distance of a test pattern projected into the tensor subspaces obtained from the training tensors. Due to high-dimensionality of the input data, tensor based methods require high memory and computational resources. However, recent achievements in the technology of the multi-core microprocessors and graphic cards allows real-time operation of the multidimensional methods as is shown and analyzed in this paper based on real examples of object detection in digital images.

Pattern-recognition receptors: signaling pathways and dysregulation in canine chronic enteropathies-brief review.

PubMed

Heilmann, Romy M; Allenspach, Karin

2017-11-01

Pattern-recognition receptors (PRRs) are expressed by innate immune cells and recognize pathogen-associated molecular patterns (PAMPs) as well as endogenous damage-associated molecular pattern (DAMP) molecules. With a large potential for synergism or convergence between their signaling pathways, PRRs orchestrate a complex interplay of cellular mediators and transcription factors, and thus play a central role in homeostasis and host defense. Aberrant activation of PRR signaling, mutations of the receptors and/or their downstream signaling molecules, and/or DAMP/PAMP complex-mediated receptor signaling can potentially lead to chronic auto-inflammatory diseases or development of cancer. PRR signaling pathways appear to also present an interesting new avenue for the modulation of inflammatory responses and to serve as potential novel therapeutic targets. Evidence for a dysregulation of the PRR toll-like receptor (TLR)2, TLR4, TLR5, and TLR9, nucleotide-binding oligomerization domain-containing protein (NOD)2, and the receptor of advanced glycation end products (RAGE) exists in dogs with chronic enteropathies. We describe the TLR, NOD2, and RAGE signaling pathways and evaluate the current veterinary literature-in comparison to human medicine-to determine the role of TLRs, NOD2, and RAGE in canine chronic enteropathies.

Regulation of cellular responsiveness to inductive signals in the developing C. elegans nervous system.

PubMed

Waring, D A; Kenyon, C

1991-04-25

In Caenorhabditis elegans, cell-cell communication is required to form a simple pattern of sensory ray neurons and cuticular structures (alae). The C. elegans pal-1 gene initiates one developmental pathway (ray lineages) simply by blocking a cell-cell interaction that induces an alternative pathway. Here we show by mosaic analysis that pal-1+ acts by preventing specific cells from responding to inductive signals. The results indicate that although cell signals play a critical role in generating this pattern, they do not provide spatial information. Instead, signals are sent to many, if not all, of the precursor cells, and the ability to respond is spatially restricted. This patterning strategy thus differs from many well known models for pattern formation in which localized inductive signals influence a subset of cells within a field. We find that pal-1 encodes a homeodomain protein and so is likely to regulate transcription. The pal-1+ protein could block the response to cell signals either by repressing genes involved in signal transduction or by acting directly on downstream genes in a way that neutralizes the effects of the intercellular signals. Genetic experiments indicate that one candidate for such a downstream gene is the Antennapedia-like homeotic selector gene mab-5.

Probability, not linear summation, mediates the detection of concentric orientation-defined textures.

PubMed

Schmidtmann, Gunnar; Jennings, Ben J; Bell, Jason; Kingdom, Frederick A A

2015-01-01

Previous studies investigating signal integration in circular Glass patterns have concluded that the information in these patterns is linearly summed across the entire display for detection. Here we test whether an alternative form of summation, probability summation (PS), modeled under the assumptions of Signal Detection Theory (SDT), can be rejected as a model of Glass pattern detection. PS under SDT alone predicts that the exponent β of the Quick- (or Weibull-) fitted psychometric function should decrease with increasing signal area. We measured spatial integration in circular, radial, spiral, and parallel Glass patterns, as well as comparable patterns composed of Gabors instead of dot pairs. We measured the signal-to-noise ratio required for detection as a function of the size of the area containing signal, with the remaining area containing dot-pair or Gabor-orientation noise. Contrary to some previous studies, we found that the strength of summation never reached values close to linear summation for any stimuli. More importantly, the exponent β systematically decreased with signal area, as predicted by PS under SDT. We applied a model for PS under SDT and found that it gave a good account of the data. We conclude that probability summation is the most likely basis for the detection of circular, radial, spiral, and parallel orientation-defined textures.

On the uniqueness of color patterns in raptor feathers

USGS Publications Warehouse

Ellis, D.H.

2009-01-01

For this study, I compared sequentially molted feathers for a few captive raptors from year to year and symmetrically matched feathers (left/right pairs) for many raptors to see if color patterns of sequential feather pairs were identical or if symmetrical pairs were mirror-image identical. Feather pairs were found to be identical only when without color pattern (e.g., the all-white rectrices of Bald Eagles [Haliaeetus leucocephalus]). Complex patterns were not closely matched, but some simple patterns were sometimes closely matched, although not identical. Previous claims that complex color patterns in feather pairs are fingerprint-identical (and therefore that molted feathers from wild raptors can be used to identify breeding adults from year to year with certainty) were found to be untrue: each feather is unique. Although it is unwise to be certain of bird of origin using normal feathers, abnormal feathers can often be so used. ?? 2009 The Raptor Research Foundation, Inc.

Unique inhibitory cascade pattern of molars in canids contributing to their potential to evolutionary plasticity of diet

PubMed Central

Asahara, Masakazu

2013-01-01

Developmental origins that guide the evolution of dental morphology and dental formulae are fundamental subjects in mammalian evolution. In a previous study, a developmental model termed the inhibitory cascade model was established. This model could explain variations in relative molar sizes and loss of the lower third molars, which sometimes reflect diet, in murine rodents and other mammals. Here, I investigated the pattern of relative molar sizes (inhibitory cascade pattern) in canids, a taxon exhibiting a wide range of dietary habits. I found that interspecific variation in canid molars suggests a unique inhibitory cascade pattern that differs from that in murine rodents and other previously reported mammals, and that this variation reflects dietary habits. This unique variability in molars was also observed in individual variation in canid species. According to these observations, canid species have greater variability in the relative sizes of first molars (carnassials), which are functionally important for dietary adaptation in the Carnivora. In conclusion, an inhibitory cascade that differs from that in murine rodents and other mammals may have contributed to diverse dietary patterns and to their parallel evolution in canids. PMID:23467478

Tool making, hand morphology and fossil hominins.

PubMed

Marzke, Mary W

2013-11-19

Was stone tool making a factor in the evolution of human hand morphology? Is it possible to find evidence in fossil hominin hands for this capability? These questions are being addressed with increasingly sophisticated studies that are testing two hypotheses; (i) that humans have unique patterns of grip and hand movement capabilities compatible with effective stone tool making and use of the tools and, if this is the case, (ii) that there exist unique patterns of morphology in human hands that are consistent with these capabilities. Comparative analyses of human stone tool behaviours and chimpanzee feeding behaviours have revealed a distinctive set of forceful pinch grips by humans that are effective in the control of stones by one hand during manufacture and use of the tools. Comparative dissections, kinematic analyses and biomechanical studies indicate that humans do have a unique pattern of muscle architecture and joint surface form and functions consistent with the derived capabilities. A major remaining challenge is to identify skeletal features that reflect the full morphological pattern, and therefore may serve as clues to fossil hominin manipulative capabilities. Hominin fossils are evaluated for evidence of patterns of derived human grip and stress-accommodation features.

Tool making, hand morphology and fossil hominins

PubMed Central

Marzke, Mary W.

2013-01-01

Was stone tool making a factor in the evolution of human hand morphology? Is it possible to find evidence in fossil hominin hands for this capability? These questions are being addressed with increasingly sophisticated studies that are testing two hypotheses; (i) that humans have unique patterns of grip and hand movement capabilities compatible with effective stone tool making and use of the tools and, if this is the case, (ii) that there exist unique patterns of morphology in human hands that are consistent with these capabilities. Comparative analyses of human stone tool behaviours and chimpanzee feeding behaviours have revealed a distinctive set of forceful pinch grips by humans that are effective in the control of stones by one hand during manufacture and use of the tools. Comparative dissections, kinematic analyses and biomechanical studies indicate that humans do have a unique pattern of muscle architecture and joint surface form and functions consistent with the derived capabilities. A major remaining challenge is to identify skeletal features that reflect the full morphological pattern, and therefore may serve as clues to fossil hominin manipulative capabilities. Hominin fossils are evaluated for evidence of patterns of derived human grip and stress-accommodation features. PMID:24101624

Featured Article: Community Crime Exposure and Risk for Obesity in Preschool Children: Moderation by the Hypothalamic-Pituitary-Adrenal-Axis Response.

PubMed

Gartstein, Maria A; Seamon, Erich; Thompson, Stephanie F; Lengua, Liliana J

2018-05-01

Identification of early risk factors related to obesity is critical to preventative public health efforts. In this study, we investigated links between the Hypothalamic-Pituitary-Adrenal (HPA)-axis activity (diurnal cortisol pattern), geospatially operationalized exposure to neighborhood crime, and body mass index (BMI) for a sample of 5-year-old children. Greater community crime exposure and lower HPA-axis activity were hypothesized to contribute to higher BMI, with child HPA-axis moderating the association between crime exposure and BMI. Families residing within the boundaries of the City of Seattle (N = 114) provided information concerning demographic/psychosocial risk factors, used to calculate a Cumulative Risk Index, indicating the number of contextual adversities present. Child BMI and diurnal cortisol pattern (derived from assays of saliva samples) were examined, along with neighborhood crime indices computed with publically available information, based on participants' locations. Hierarchical multiple regression analyses, adjusted for covariates (cumulative risk, age, and sex), indicated that crime proximity made a unique contribution to child BMI, in the direction signaling an increase in the risk for obesity. Consistent with our hypothesis, a significant interaction was observed, indicative of moderation by diurnal cortisol pattern. Follow-up simple slope analyses demonstrated that crime exposure was significantly related to higher BMI for children with low-flat (blunted) diurnal cortisol patterns, where community crime and BMI were not significantly associated at higher levels of cortisol. Community crime exposure contributes to higher BMI as early as the preschool period, and blunted diurnal cortisol patterns may place children experiencing neighborhood adversity at greater risk for obesity.

Identification of nuclear weapons

DOEpatents

Mihalczo, J.T.; King, W.T.

1987-04-10

A method and apparatus for non-invasively indentifying different types of nuclear weapons is disclosed. A neutron generator is placed against the weapon to generate a stream of neutrons causing fissioning within the weapon. A first detects the generation of the neutrons and produces a signal indicative thereof. A second particle detector located on the opposite side of the weapon detects the fission particles and produces signals indicative thereof. The signals are converted into a detected pattern and a computer compares the detected pattern with known patterns of weapons and indicates which known weapon has a substantially similar pattern. Either a time distribution pattern or noise analysis pattern, or both, is used. Gamma-neutron discrimination and a third particle detector for fission particles adjacent the second particle detector are preferably used. The neutrons are generated by either a decay neutron source or a pulled neutron particle accelerator.

Suggested Mechanisms of Tracheal Occlusion Mediated Accelerated Fetal Lung Growth: A Case for Heterogeneous Topological Zones

PubMed Central

Marwan, Ahmed I.; Shabeka, Uladzimir; Dobrinskikh, Evgenia

2018-01-01

In this article, we report an up-to-date summary on tracheal occlusion (TO) as an approach to drive accelerated lung growth and strive to review the different maternal- and fetal-derived local and systemic signals and mechanisms that may play a significant biological role in lung growth and formation of heterogeneous topological zones following TO. Pulmonary hypoplasia is a condition whereby branching morphogenesis and embryonic pulmonary vascular development are globally affected and is classically seen in congenital diaphragmatic hernia. TO is an innovative approach aimed at driving accelerated lung growth in the most severe forms of diaphragmatic hernia and has been shown to result in improved neonatal outcomes. Currently, most research on mechanisms of TO-induced lung growth is focused on mechanical forces and is viewed from the perspective of homogeneous changes within the lung. We suggest that the key principle in understanding changes in fetal lungs after TO is taking into account formation of unique variable topological zones. Following TO, fetal lungs might temporarily look like a dynamically changing topologic mosaic with varying proliferation rates, dissimilar scale of vasculogenesis, diverse patterns of lung tissue damage, variable metabolic landscape, and different structures. The reasons for this dynamic topological mosaic pattern may include distinct degree of increased hydrostatic pressure in different parts of the lung, dissimilar degree of tissue stress/damage and responses to this damage, and incomparable patterns of altered lung zones with variable response to systemic maternal and fetal factors, among others. The local interaction between these factors and their accompanying processes in addition to the potential role of other systemic factors might lead to formation of a common vector of biological response unique to each zone. The study of the interaction between various networks formed after TO (action of mechanical forces, activation of mucosal mast cells, production and secretion of damage-associated molecular pattern substances, low-grade local pulmonary inflammation, and cardiac contraction-induced periodic agitation of lung tissue, among others) will bring us closer to an appreciation of the biological phenomenon of topological heterogeneity within the fetal lungs. PMID:29376042

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals.

PubMed

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-04-08

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems.

Multidimensional biochemical information processing of dynamical patterns

NASA Astrophysics Data System (ADS)

Hasegawa, Yoshihiko

2018-02-01

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

PubMed Central

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-01-01

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems. DOI: http://dx.doi.org/10.7554/eLife.14022.001 PMID:27058171

Multidimensional biochemical information processing of dynamical patterns.

PubMed

Hasegawa, Yoshihiko

2018-02-01

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

Extensive T-Cell Epitope Repertoire Sharing among Human Proteome, Gastrointestinal Microbiome, and Pathogenic Bacteria: Implications for the Definition of Self

PubMed Central

Bremel, Robert D.; Homan, E. Jane

2015-01-01

T-cell receptor binding to MHC-bound peptides plays a key role in discrimination between self and non-self. Only a subset, typically a pentamer, of amino acids in a MHC-bound peptide form the motif exposed to the T-cell receptor. We categorize and compare the T-cell exposed amino acid motif repertoire of the total proteomes of two groups of bacteria, comprising pathogens and gastrointestinal microbiome organisms, with the human proteome and immunoglobulins. Given the maximum 205, or 3.2 million of such motifs that bind T-cell receptors, there is considerable overlap in motif usage. We show that the human proteome, exclusive of immunoglobulins, only comprises three quarters of the possible motifs, of which 65.3% are also present in both composite bacterial proteomes. Very few motifs are unique to the human proteome. Immunoglobulin variable regions carry a broad diversity of T-cell exposed motifs (TCEMs) that provides a stratified random sample of the motifs found in pathogens, microbiome, and the human proteome. Individual bacterial genera and species vary in the content of immunoglobulin and human proteome matched motifs that they carry. Mycobacteria and Burkholderia spp carry a particularly high content of such matched motifs. Some bacteria retain a unique motif signature and motif sharing pattern with the human proteome. The implication is that distinguishing self from non-self does not depend on individual TCEMs, but on a complex and dynamic overlay of signals wherein the same TCEM may play different roles in different organisms, and the frequency with which a particular TCEM appears influences its effect. The patterns observed provide clues to bacterial immune evasion and to strategies for intervention, including vaccine design. The breadth and distinct frequency patterns of the immunoglobulin-derived peptides suggest a role of immunoglobulins in maintaining a broadly responsive T-cell repertoire. PMID:26557118

Integrated β-catenin, BMP, PTEN, and Notch signalling patterns the nephron.

PubMed

Lindström, Nils O; Lawrence, Melanie L; Burn, Sally F; Johansson, Jeanette A; Bakker, Elvira R M; Ridgway, Rachel A; Chang, C-Hong; Karolak, Michele J; Oxburgh, Leif; Headon, Denis J; Sansom, Owen J; Smits, Ron; Davies, Jamie A; Hohenstein, Peter

2015-02-03

The different segments of the nephron and glomerulus in the kidney balance the processes of water homeostasis, solute recovery, blood filtration, and metabolite excretion. When segment function is disrupted, a range of pathological features are presented. Little is known about nephron patterning during embryogenesis. In this study, we demonstrate that the early nephron is patterned by a gradient in β-catenin activity along the axis of the nephron tubule. By modifying β-catenin activity, we force cells within nephrons to differentiate according to the imposed β-catenin activity level, thereby causing spatial shifts in nephron segments. The β-catenin signalling gradient interacts with the BMP pathway which, through PTEN/PI3K/AKT signalling, antagonises β-catenin activity and promotes segment identities associated with low β-catenin activity. β-catenin activity and PI3K signalling also integrate with Notch signalling to control segmentation: modulating β-catenin activity or PI3K rescues segment identities normally lost by inhibition of Notch. Our data therefore identifies a molecular network for nephron patterning.

Generation and precise control of dynamic biochemical gradients for cellular assays

NASA Astrophysics Data System (ADS)

Saka, Yasushi; MacPherson, Murray; Giuraniuc, Claudiu V.

2017-03-01

Spatial gradients of diffusible signalling molecules play crucial roles in controlling diverse cellular behaviour such as cell differentiation, tissue patterning and chemotaxis. In this paper, we report the design and testing of a microfluidic device for diffusion-based gradient generation for cellular assays. A unique channel design of the device eliminates cross-flow between the source and sink channels, thereby stabilizing gradients by passive diffusion. The platform also enables quick and flexible control of chemical concentration that makes highly dynamic gradients in diffusion chambers. A model with the first approximation of diffusion and surface adsorption of molecules recapitulates the experimentally observed gradients. Budding yeast cells cultured in a gradient of a chemical inducer expressed a reporter fluorescence protein in a concentration-dependent manner. This microfluidic platform serves as a versatile prototype applicable to a broad range of biomedical investigations.

Production and delivery of polarized Xenon-129 for in vivo MRS/MRI.

NASA Astrophysics Data System (ADS)

Rosen, Matthew S.; Chupp, Timothy E.; Coulter, Kevin P.; Welsh, Robert C.; Swanson, Scott

1998-05-01

Laser polarized ^129Xe can be used as an entirely new magnetic tracer, and is a powerful enhancement to currently existing MRI techniques. Inert laser polarized ^129Xe is inhaled and transported via blood flow where it is detected using MR spectroscopy and imaging techniques. The time-dependent distribution patterns of ^129Xe signal intensity directly reflect local blood volume, blood flow rates, and the efficiency of perfusion and diffusive transport in tissues. We have developed a uniquely constructed laser polarized ^129Xe production and delivery system that is used in both our in vitro and in vivo imaging experiments with rats. This reliable, effective, and relatively simple production method for large volumes of laser polarized ^129Xe is the key to all other areas of research involving use of laser polarized gases.

Vibrational Profiling of Brain Tumors and Cells

PubMed Central

Nelson, Sultan L; Proctor, Dustin T; Ghasemloonia, Ahmad; Lama, Sanju; Zareinia, Kourosh; Ahn, Younghee; Al-Saiedy, Mustafa R; Green, Francis HY; Amrein, Matthias W; Sutherland, Garnette R

2017-01-01

This study reports vibration profiles of neuronal cells and tissues as well as brain tumor and neocortical specimens. A contact-free method and analysis protocol was designed to convert an atomic force microscope into an ultra-sensitive microphone with capacity to record and listen to live biological samples. A frequency of 3.4 Hz was observed for both cultured rat hippocampal neurons and tissues and vibration could be modulated pharmacologically. Malignant astrocytoma tissue samples obtained from operating room, transported in artificial cerebrospinal fluid, and tested within an hour, vibrated with a much different frequency profile and amplitude, compared to meningioma or lateral temporal cortex providing a quantifiable measurement to accurately distinguish the three tissues in real-time. Vibration signals were converted to audible sound waves by frequency modulation, thus demonstrating, acoustic patterns unique to meningioma, malignant astrocytoma and neocortex. PMID:28744324

Self-Organization of Spatial Patterning in Human Embryonic Stem Cells.

PubMed

Deglincerti, Alessia; Etoc, Fred; Ozair, M Zeeshan; Brivanlou, Ali H

2016-01-01

The developing embryo is a remarkable example of self-organization, where functional units are created in a complex spatiotemporal choreography. Recently, human embryonic stem cells (ESCs) have been used to recapitulate in vitro the self-organization programs that are executed in the embryo in vivo. This represents an unique opportunity to address self-organization in humans that is otherwise not addressable with current technologies. In this chapter, we review the recent literature on self-organization of human ESCs, with a particular focus on two examples: formation of embryonic germ layers and neural rosettes. Intriguingly, both activation and elimination of TGFβ signaling can initiate self-organization, albeit with different molecular underpinnings. We discuss the mechanisms underlying the formation of these structures in vitro and explore future challenges in the field. © 2016 Elsevier Inc. All rights reserved.

PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation.

PubMed

Belotserkovskii, Boris P; Hanawalt, Philip C

2015-11-01

Peptide Nucleic Acids (PNAs) are artificial DNA mimics with superior nucleic acid binding capabilities. T7 RNA polymerase (T7 RNAP) transcription upon encountering PNA bound to the non-template DNA strand was studied in vitro. A characteristic pattern of blockage signals was observed, extending downstream from the PNA binding site, similar to that produced by G-rich homopurine-homopyrimidine (hPu-hPy) sequences and likely caused by R-loop formation. Since blocked transcription complexes in association with stable R-loops may interfere with replication and in some cases trigger apoptosis, targeted R-loop formation might be employed to inactivate selected cells, such as those in tumors, based upon their unique complement of expressed genes. © 2014 The Authors. Molecular Carcinogenesis published by Wiley Periodicals, Inc.

Variants of windmill nystagmus.

PubMed

Choi, Kwang-Dong; Shin, Hae Kyung; Kim, Ji-Soo; Kim, Sung-Hee; Choi, Jae-Hwan; Kim, Hyo-Jung; Zee, David S

2016-07-01

Windmill nystagmus is characterized by a clock-like rotation of the beating direction of a jerk nystagmus suggesting separate horizontal and vertical oscillators, usually 90° out of phase. We report oculographic characteristics in three patients with variants of windmill nystagmus in whom the common denominator was profound visual loss due to retinal diseases. Two patients showed a clock-like pattern, while in the third, the nystagmus was largely diagonal (in phase or 180° out of phase) but also periodically changed direction by 180°. We hypothesize that windmill nystagmus is a unique manifestation of "eye movements of the blind." It emerges when the central structures, including the cerebellum, that normally keep eye movements calibrated and gaze steady can no longer perform their task, because they are deprived of the retinal image motion that signals a need for adaptive recalibration.

A security proof of the round-robin differential phase shift quantum key distribution protocol based on the signal disturbance

NASA Astrophysics Data System (ADS)

Sasaki, Toshihiko; Koashi, Masato

2017-06-01

The round-robin differential phase shift (RRDPS) quantum key distribution (QKD) protocol is a unique QKD protocol whose security has not been understood through an information-disturbance trade-off relation, and a sufficient amount of privacy amplification was given independently of signal disturbance. Here, we discuss the security of the RRDPS protocol in the asymptotic regime when a good estimate of the bit error rate is available as a measure of signal disturbance. The uniqueness of the RRDPS protocol shows up as a peculiar form of information-disturbance trade-off curve. When the length of a block of pulses used for encoding and the signal disturbance are both small, it provides a significantly better key rate than that from the original security proof. On the other hand, when the block length is large, the use of the signal disturbance makes little improvement in the key rate. Our analysis will bridge a gap between the RRDPS protocol and the conventional QKD protocols.

Identification of Mobile Phone and Analysis of Original Version of Videos through a Delay Time Analysis of Sound Signals from Mobile Phone Videos.

PubMed

Hwang, Min Gu; Har, Dong Hwan

2017-11-01

This study designs a method of identifying the camera model used to take videos that are distributed through mobile phones and determines the original version of the mobile phone video for use as legal evidence. For this analysis, an experiment was conducted to find the unique characteristics of each mobile phone. The videos recorded by mobile phones were analyzed to establish the delay time of sound signals, and the differences between the delay times of sound signals for different mobile phones were traced by classifying their characteristics. Furthermore, the sound input signals for mobile phone videos used as legal evidence were analyzed to ascertain whether they have the unique characteristics of the original version. The objective of this study was to find a method for validating the use of mobile phone videos as legal evidence using mobile phones through differences in the delay times of sound input signals. © 2017 American Academy of Forensic Sciences.

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.

Asymmetric effects of emotion on mnemonic interference

PubMed Central

Leal, Stephanie L.; Tighe, Sarah K.; Yassa, Michael A.

2014-01-01

Emotional experiences can strengthen memories so that they can be used to guide future behavior. Emotional arousal, mediated by the amygdala, is thought to modulate storage by the hippocampus, which may encode unique episodic memories via pattern separation – the process by which similar memories are stored using non-overlapping representations. While prior work has examined mnemonic interference due to similarity and emotional modulation of memory independently, examining the mechanisms by which emotion influences mnemonic interference has not been previously accomplished in humans. To this end, we developed an emotional memory task where emotional content and stimulus similarity were varied to examine the effect of emotion on fine mnemonic discrimination (a putative behavioral correlate of hippocampal pattern separation). When tested immediately after encoding, discrimination was reduced for similar emotional items compared to similar neutral items, consistent with a reduced bias towards pattern separation. After 24 h, recognition of emotional target items was preserved compared to neutral items, whereas similar emotional item discrimination was further diminished. This suggests a potential mechanism for the emotional modulation of memory with a selective remembering of gist, as well as a selective forgetting of detail, indicating an emotion-induced reduction in pattern separation. This can potentially increase the effective signal-to-noise ratio in any given situation to promote survival. Furthermore, we found that individuals with depressive symptoms hyper-discriminate negative items, which correlated with their symptom severity. This suggests that utilizing mnemonic discrimination paradigms allows us to tease apart the nuances of disorders with aberrant emotional mnemonic processing. PMID:24607286

Automated Design Tools for Integrated Mixed-Signal Microsystems (NeoCAD)

DTIC Science & Technology

2005-02-01

method, Model Order Reduction (MOR) tools, system-level, mixed-signal circuit synthesis and optimization tools, and parsitic extraction tools. A unique...Mission Area: Command and Control mixed signal circuit simulation parasitic extraction time-domain simulation IC design flow model order reduction... Extraction 1.2 Overall Program Milestones CHAPTER 2 FAST TIME DOMAIN MIXED-SIGNAL CIRCUIT SIMULATION 2.1 HAARSPICE Algorithms 2.1.1 Mathematical Background

Objective Auscultation of TCM Based on Wavelet Packet Fractal Dimension and Support Vector Machine.

PubMed

Yan, Jian-Jun; Guo, Rui; Wang, Yi-Qin; Liu, Guo-Ping; Yan, Hai-Xia; Xia, Chun-Ming; Shen, Xiaojing

2014-01-01

This study was conducted to illustrate that auscultation features based on the fractal dimension combined with wavelet packet transform (WPT) were conducive to the identification the pattern of syndromes of Traditional Chinese Medicine (TCM). The WPT and the fractal dimension were employed to extract features of auscultation signals of 137 patients with lung Qi-deficient pattern, 49 patients with lung Yin-deficient pattern, and 43 healthy subjects. With these features, the classification model was constructed based on multiclass support vector machine (SVM). When all auscultation signals were trained by SVM to decide the patterns of TCM syndromes, the overall recognition rate of model was 79.49%; when male and female auscultation signals were trained, respectively, to decide the patterns, the overall recognition rate of model reached 86.05%. The results showed that the methods proposed in this paper were effective to analyze auscultation signals, and the performance of model can be greatly improved when the distinction of gender was considered.

Objective Auscultation of TCM Based on Wavelet Packet Fractal Dimension and Support Vector Machine

PubMed Central

Yan, Jian-Jun; Wang, Yi-Qin; Liu, Guo-Ping; Yan, Hai-Xia; Xia, Chun-Ming; Shen, Xiaojing

2014-01-01

This study was conducted to illustrate that auscultation features based on the fractal dimension combined with wavelet packet transform (WPT) were conducive to the identification the pattern of syndromes of Traditional Chinese Medicine (TCM). The WPT and the fractal dimension were employed to extract features of auscultation signals of 137 patients with lung Qi-deficient pattern, 49 patients with lung Yin-deficient pattern, and 43 healthy subjects. With these features, the classification model was constructed based on multiclass support vector machine (SVM). When all auscultation signals were trained by SVM to decide the patterns of TCM syndromes, the overall recognition rate of model was 79.49%; when male and female auscultation signals were trained, respectively, to decide the patterns, the overall recognition rate of model reached 86.05%. The results showed that the methods proposed in this paper were effective to analyze auscultation signals, and the performance of model can be greatly improved when the distinction of gender was considered. PMID:24883068

Recurrence plot analysis of nonstationary data: the understanding of curved patterns.

PubMed

Facchini, A; Kantz, H; Tiezzi, E

2005-08-01

Recurrence plots of the calls of the Nomascus concolor (Western black crested gibbon) and Hylobates lar (White-handed gibbon) show characteristic circular, curved, and hyperbolic patterns superimposed to the main temporal scale of the signal. It is shown that these patterns are related to particular nonstationarities in the signal. Some of them can be reproduced by artificial signals like frequency modulated sinusoids and sinusoids with time divergent frequency. These modulations are too faint to be resolved by conventional time-frequency analysis with similar precision. Therefore, recurrence plots act as a magnifying glass for the detection of multiple temporal scales in slightly modulated signals. The detected phenomena in these acoustic signals can be explained in the biomechanical context by taking in account the role of the muscles controlling the vocal folds.

Coherent correlator and equalizer using a reconfigurable all-optical tapped delay line.

PubMed

Chitgarha, Mohammad Reza; Khaleghi, Salman; Yilmaz, Omer F; Tur, Moshe; Haney, Michael W; Langrock, Carsten; Fejer, Martin M; Willner, Alan E

2013-07-01

We experimentally demonstrate a reconfigurable optical tapped delay line in conjunction with coherent detection to search multiple patterns among quadrature phase shift keying (QPSK) symbols in 20 Gbaud data channel and also to equalize 20 and 31 Gbaud QPSK, 20 Gbaud 8 phase shift keying (PSK), and 16 QAM signals. Multiple patterns are searched successfully on QPSK signals, and correlation peaks are obtained at the matched patterns. QPSK, 8 PSK, and 16 QAM signals are also successfully recovered after 25 km of SMF-28 with average EVMs of 8.3%, 8.9%, and 7.8%. A penalty of <1 dB optical signal to noise penalty is achieved for a 20 Gbaud QPSK signal distorted by up to 400  ps/nm dispersion.

Caspase-2 Is Localized at the Golgi Complex and Cleaves Golgin-160 during Apoptosis

PubMed Central

Mancini, Marie; Machamer, Carolyn E.; Roy, Sophie; Nicholson, Donald W.; Thornberry, Nancy A.; Casciola-Rosen, Livia A.; Rosen, Antony

2000-01-01

Caspases are an extended family of cysteine proteases that play critical roles in apoptosis. Animals deficient in caspases-2 or -3, which share very similar tetrapeptide cleavage specificities, exhibit very different phenotypes, suggesting that the unique features of individual caspases may account for distinct regulation and specialized functions. Recent studies demonstrate that unique apoptotic stimuli are transduced by distinct proteolytic pathways, with multiple components of the proteolytic machinery clustering at distinct subcellular sites. We demonstrate here that, in addition to its nuclear distribution, caspase-2 is localized to the Golgi complex, where it cleaves golgin-160 at a unique site not susceptible to cleavage by other caspases with very similar tetrapeptide specificities. Early cleavage at this site precedes cleavage at distal sites by other caspases. Prevention of cleavage at the unique caspase-2 site delays disintegration of the Golgi complex after delivery of a pro-apoptotic signal. We propose that the Golgi complex, like mitochondria, senses and integrates unique local conditions, and transduces pro-apoptotic signals through local caspases, which regulate local effectors. PMID:10791974

System and technique for retrieving depth information about a surface by projecting a composite image of modulated light patterns

NASA Technical Reports Server (NTRS)

Hassebrook, Laurence G. (Inventor); Lau, Daniel L. (Inventor); Guan, Chun (Inventor)

2010-01-01

A technique, associated system and program code, for retrieving depth information about at least one surface of an object, such as an anatomical feature. Core features include: projecting a composite image comprising a plurality of modulated structured light patterns, at the anatomical feature; capturing an image reflected from the surface; and recovering pattern information from the reflected image, for each of the modulated structured light patterns. Pattern information is preferably recovered for each modulated structured light pattern used to create the composite, by performing a demodulation of the reflected image. Reconstruction of the surface can be accomplished by using depth information from the recovered patterns to produce a depth map/mapping thereof. Each signal waveform used for the modulation of a respective structured light pattern, is distinct from each of the other signal waveforms used for the modulation of other structured light patterns of a composite image; these signal waveforms may be selected from suitable types in any combination of distinct signal waveforms, provided the waveforms used are uncorrelated with respect to each other. The depth map/mapping to be utilized in a host of applications, for example: displaying a 3-D view of the object; virtual reality user-interaction interface with a computerized device; face--or other animal feature or inanimate object--recognition and comparison techniques for security or identification purposes; and 3-D video teleconferencing/telecollaboration.

System and technique for retrieving depth information about a surface by projecting a composite image of modulated light patterns

NASA Technical Reports Server (NTRS)

Guan, Chun (Inventor); Hassebrook, Laurence G. (Inventor); Lau, Daniel L. (Inventor)

2008-01-01

A technique, associated system and program code, for retrieving depth information about at least one surface of an object. Core features include: projecting a composite image comprising a plurality of modulated structured light patterns, at the object; capturing an image reflected from the surface; and recovering pattern information from the reflected image, for each of the modulated structured light patterns. Pattern information is preferably recovered for each modulated structured light pattern used to create the composite, by performing a demodulation of the reflected image. Reconstruction of the surface can be accomplished by using depth information from the recovered patterns to produce a depth map/mapping thereof. Each signal waveform used for the modulation of a respective structured light pattern, is distinct from each of the other signal waveforms used for the modulation of other structured light patterns of a composite image; these signal waveforms may be selected from suitable types in any combination of distinct signal waveforms, provided the waveforms used are uncorrelated with respect to each other. The depth map/mapping to be utilized in a host of applications, for example: displaying a 3-D view of the object; virtual reality user-interaction interface with a computerized device; face--or other animal feature or inanimate object--recognition and comparison techniques for security or identification purposes; and 3-D video teleconferencing/telecollaboration.

A new molecular logic for BMP-mediated dorsoventral patterning in the leech Helobdella.

PubMed

Kuo, Dian-Han; Weisblat, David A

2011-08-09

Bone morphogenetic protein (BMP) signaling is broadly implicated in dorsoventral (DV) patterning of bilaterally symmetric animals [1-3], and its role in axial patterning apparently predates the birth of Bilateria [4-7]. In fly and vertebrate embryos, BMPs and their antagonists (primarily Sog/chordin) diffuse and interact to generate signaling gradients that pattern fields of cells [8-10]. Work in other species reveals diversity in essential facets of this ancient patterning process, however. Here, we report that BMP signaling patterns the DV axis of segmental ectoderm in the leech Helobdella, a clitellate annelid (superphylum Lophotrochozoa) featuring stereotyped developmental cell lineages, but the detailed mechanisms of DV patterning in Helobdella differ markedly from fly and vertebrates. In Helobdella, BMP2/4s are expressed broadly, rather than in dorsal territory, whereas a dorsally expressed BMP5-8 specifies dorsal fate by short-range signaling. A BMP antagonist, gremlin, is upregulated by BMP5-8 in dorsolateral, rather than ventral territory, and yet the BMP-antagonizing activity of gremlin is required for normal ventral cell fates. Gremlin promotes ventral fates without disrupting dorsal fates by selectively inhibiting BMP2/4s, not BMP5-8. Thus, DV patterning in the development of the leech revealed unexpected evolutionary plasticity of the conserved BMP patterning system, presumably reflecting its adaptation to different modes of embryogenesis. Copyright © 2011 Elsevier Ltd. All rights reserved.

Usefullness of palatal rugae patterns in establishing identity: Preliminary results from Bengaluru city, India.

PubMed

Indira, Ap; Gupta, Manish; David, Maria Priscilla

2012-01-01

Palatal rugoscopy is the name given to the study of palatal rugae. Rugae pattern are widely considered to remain unchanged during an individual's lifetime. The rugae pattern has the potential to remain intact by virtue of their internal position in the head when most other anatomical structures are destroyed or burned. Moreover, rugae pattern are considered to be unique similar to fingerprints and are advocated in personal identification. The purpose of the study is to establish, individual identity using palatal rugae patterns. The study group consisted of 100 study models all of whom were subjects above 14 years old. Martin dos Santos' classification was followed based on form and position to assess the individuality of rugae pattern. Each individual had different rugae patterns including dizygous twins and the rugae patterns were not symmetrical, both in number and in its distribution. The preliminary study undertaken here shows no two palates are alike in terms of their rugae pattern. Palatal rugae possess unique characteristics as they are absolutely individualistic and therefore, can be used as a personal soft-tissue 'oral' print for identification in forensic cases.

Control of the ZnO nanowires nucleation site using microfluidic channels.

PubMed

Lee, Sang Hyun; Lee, Hyun Jung; Oh, Dongcheol; Lee, Seog Woo; Goto, Hiroki; Buckmaster, Ryan; Yasukawa, Tomoyuki; Matsue, Tomokazu; Hong, Soon-Ku; Ko, HyunChul; Cho, Meoung-Whan; Yao, Takafumi

2006-03-09

We report on the growth of uniquely shaped ZnO nanowires with high surface area and patterned over large areas by using a poly(dimethylsiloxane) (PDMS) microfluidic channel technique. The synthesis uses first a patterned seed template fabricated by zinc acetate solution flowing though a microfluidic channel and then growth of ZnO nanowire at the seed using thermal chemical vapor deposition on a silicon substrate. Variations the ZnO nanowire by seed pattern formed within the microfluidic channel were also observed for different substrates and concentrations of the zinc acetate solution. The photocurrent properties of the patterned ZnO nanowires with high surface area, due to their unique shape, were also investigated. These specialized shapes and patterning technique increase the possibility of realizing one-dimensional nanostructure devices such as sensors and optoelectric devices.

Modeling left-turn crash occurrence at signalized intersections by conflicting patterns.

PubMed

Wang, Xuesong; Abdel-Aty, Mohamed

2008-01-01

In order to better understand the underlying crash mechanisms, left-turn crashes occurring at 197 four-legged signalized intersections over 6 years were classified into nine patterns based on vehicle maneuvers and then were assigned to intersection approaches. Crash frequency of each pattern was modeled at the approach level by mainly using Generalized Estimating Equations (GEE) with the Negative Binomial as the link function to account for the correlation among the crash data. GEE with a binomial logit link function was also applied for patterns with fewer crashes. The Cumulative Residuals test shows that, for correlated left-turn crashes, GEE models usually outperformed basic Negative Binomial models. The estimation results show that there are obvious differences in the factors that cause the occurrence of different left-turn collision patterns. For example, for each pattern, the traffic flows to which the colliding vehicles belong are identified to be significant. The width of the crossing distance (represented by the number of through lanes on the opposing approach of the left-turning traffic) is associated with more left-turn traffic colliding with opposing through traffic (Pattern 5), but with less left-turning traffic colliding with near-side crossing through traffic (Pattern 8). The safety effectiveness of the left-turning signal is not consistent for different crash patterns; "protected" phasing is correlated with fewer Pattern 5 crashes, but with more Pattern 8 crashes. The study indicates that in order to develop efficient countermeasures for left-turn crashes and improve safety at signalized intersections, left-turn crashes should be considered in different patterns.

Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health.

PubMed

Koch, Carl D; Gladwin, Mark T; Freeman, Bruce A; Lundberg, Jon O; Weitzberg, Eddie; Morris, Alison

2017-04-01

Recent insights into the bioactivation and signaling actions of inorganic, dietary nitrate and nitrite now suggest a critical role for the microbiome in the development of cardiac and pulmonary vascular diseases. Once thought to be the inert, end-products of endothelial-derived nitric oxide (NO) heme-oxidation, nitrate and nitrite are now considered major sources of exogenous NO that exhibit enhanced vasoactive signaling activity under conditions of hypoxia and stress. The bioavailability of nitrate and nitrite depend on the enzymatic reduction of nitrate to nitrite by a unique set of bacterial nitrate reductase enzymes possessed by specific bacterial populations in the mammalian mouth and gut. The pathogenesis of pulmonary hypertension (PH), obesity, hypertension and CVD are linked to defects in NO signaling, suggesting a role for commensal oral bacteria to shape the development of PH through the formation of nitrite, NO and other bioactive nitrogen oxides. Oral supplementation with inorganic nitrate or nitrate-containing foods exert pleiotropic, beneficial vascular effects in the setting of inflammation, endothelial dysfunction, ischemia-reperfusion injury and in pre-clinical models of PH, while traditional high-nitrate dietary patterns are associated with beneficial outcomes in hypertension, obesity and CVD. These observations highlight the potential of the microbiome in the development of novel nitrate- and nitrite-based therapeutics for PH, CVD and their risk factors. Copyright © 2017 Elsevier Inc. All rights reserved.

Detection and classification of concealed weapons using a magnetometer-based portal

NASA Astrophysics Data System (ADS)

Kotter, Dale K.; Roybal, Lyle G.; Polk, Robert E.

2002-08-01

A concealed weapons detection technology was developed through the support of the National Institute of Justice (NIJ) to provide a non intrusive means for rapid detection, location, and archiving of data (including visual) of potential suspects and weapon threats. This technology, developed by the Idaho National Engineering and Environmental Laboratory (INEEL), has been applied in a portal style weapons detection system using passive magnetic sensors as its basis. This paper will report on enhancements to the weapon detection system to enable weapon classification and to discriminate threats from non-threats. Advanced signal processing algorithms were used to analyze the magnetic spectrum generated when a person passes through a portal. These algorithms analyzed multiple variables including variance in the magnetic signature from random weapon placement and/or orientation. They perform pattern recognition and calculate the probability that the collected magnetic signature correlates to a known database of weapon versus non-weapon responses. Neural networks were used to further discriminate weapon type and identify controlled electronic items such as cell phones and pagers. False alarms were further reduced by analyzing the magnetic detector response by using a Joint Time Frequency Analysis digital signal processing technique. The frequency components and power spectrum for a given sensor response were derived. This unique fingerprint provided additional information to aid in signal analysis. This technology has the potential to produce major improvements in weapon detection and classification.

Human Fetal Membranes at Term: Dead Tissue or Signalers of Parturition?

PubMed Central

MENON, Ramkumar

2017-01-01

Various endocrine, immune, and mechanical factors produced by feto-maternal compartments at term increase intrauterine inflammatory loads to induce labor. The role of fetal (placental) membranes (amniochorion) as providers of parturition signals has not been well investigated. Fetal membranes line the intrauterine cavity and grow with and protect the fetus. Fetal membranes exist as an entity between the mother and fetus and perform unique functions during pregnancy. Membranes undergo a telomere-dependent p38 MAPK-induced senescence and demonstrate a decline in functional and mechanical abilities at term, showing signs of aging. Fetal membrane senescence is also allied with completion of fetal maturation at term as the fetus readies for delivery, which may also indicate the end of independent life and longevity of fetal membranes as their functional role concludes. Fetal membrane senescence is accelerated at term because of oxidative stress and increased stretching. Senescent fetal membranes cells produce senescence-associated secretory phenotype (SASP-inflammation) and also release proinflammatory damage-associated molecular patterns (DAMPs), namely HMGB1 and cell-free fetal telomere fragments. In a feedback loop, SASP and DAMPs increase senescence and enhance the inflammatory load to promote labor. Membranes increase the inflammatory load to disrupt homeostatic balance to transition quiescent uterine tissues toward a labor phenotype. Therefore, along with other well-described labor-promoting signals, senescent fetal membranes may also contribute to human term parturition. PMID:27452431

Human fetal membranes at term: Dead tissue or signalers of parturition?

PubMed

Menon, Ramkumar

2016-08-01

Various endocrine, immune, and mechanical factors produced by feto-maternal compartments at term increase intrauterine inflammatory loads to induce labor. The role of fetal (placental) membranes (amniochorion) as providers of parturition signals has not been well investigated. Fetal membranes line the intrauterine cavity and grow with and protect the fetus. Fetal membranes exist as an entity between the mother and fetus and perform unique functions during pregnancy. Membranes undergo a telomere-dependent p38 MAPK-induced senescence and demonstrate a decline in functional and mechanical abilities at term, showing signs of aging. Fetal membrane senescence is also allied with completion of fetal maturation at term as the fetus readies for delivery, which may also indicate the end of independent life and longevity of fetal membranes as their functional role concludes. Fetal membrane senescence is accelerated at term because of oxidative stress and increased stretching. Senescent fetal membranes cells produce senescence-associated secretory phenotype (SASP-inflammation) and also release proinflammatory damage-associated molecular patterns (DAMPs), namely HMGB1 and cell-free fetal telomere fragments. In a feedback loop, SASP and DAMPs increase senescence and enhance the inflammatory load to promote labor. Membranes increase the inflammatory load to disrupt homeostatic balance to transition quiescent uterine tissues toward a labor phenotype. Therefore, along with other well-described labor-promoting signals, senescent fetal membranes may also contribute to human term parturition. Copyright © 2016 Elsevier Ltd. All rights reserved.

Antagonizing retinoic acid and FGF/MAPK pathways control posterior body patterning in the invertebrate chordate Ciona intestinalis.

PubMed

Pasini, Andrea; Manenti, Raoul; Rothbächer, Ute; Lemaire, Patrick

2012-01-01

Vertebrate embryos exploit the mutual inhibition between the RA and FGF signalling pathways to coordinate the proliferative elongation of the main body axis with the progressive patterning and differentiation of its neuroectodermal and paraxial mesodermal structures. The evolutionary history of this patterning system is still poorly understood. Here, we investigate the role played by the RA and FGF/MAPK signals during the development of the tail structures in the tunicate Ciona intestinalis, an invertebrate chordate belonging to the sister clade of vertebrates, in which the prototypical chordate body plan is established through very derived morphogenetic processes. Ciona embryos are constituted of few cells and develop according to a fixed lineage; elongation of the tail occurs largely by rearrangement of postmitotic cells; mesoderm segmentation and somitogenesis are absent. We show that in the Ciona embryo, the antagonism of the RA and FGF/MAPK signals is required to control the anteroposterior patterning of the tail epidermis. We also demonstrate that the RA, FGF/MAPK and canonical Wnt pathways control the anteroposterior patterning of the tail peripheral nervous system, and reveal the existence of distinct subpopulations of caudal epidermal neurons with different responsiveness to the RA, FGF/MAPK and canonical Wnt signals. Our data provide the first demonstration that the use of the antagonism between the RA and FGF signals to pattern the main body axis predates the emergence of vertebrates and highlight the evolutionary plasticity of this patterning strategy, showing that in different chordates it can be used to pattern different tissues within the same homologous body region.

Multiple Shh signaling centers participate in fungiform papilla and taste bud formation and maintenance

PubMed Central

Liu, H-X; Ermilov, A; Grachtchouk, M; Li, L; Gumucio, DL; Dlugosz, AA; Mistretta, CM

2014-01-01

The adult fungiform taste papilla is a complex of specialized cell types residing in the stratified squamous tongue epithelium. This unique sensory organ includes taste buds, papilla epithelium and lateral walls that extend into underlying connective tissue to surround a core of lamina propria cells. Fungiform papillae must contain long-lived, sustaining or stem cells and short-lived, maintaining or transit amplifying cells that support the papilla and specialized taste buds. Shh signaling has established roles in supporting fungiform induction, development and patterning. However, for a full understanding of how Shh transduced signals act in tongue, papilla and taste bud formation and maintenance, it is necessary to know where and when the Shh ligand and pathway components are positioned. We used immunostaining, in situ hybridization and mouse reporter strains for Shh, Ptch1, Gli1 and Gli2-expression and proliferation markers to identify cells that participate in hedgehog signaling. Whereas there is a progressive restriction in location of Shh ligand-expressing cells, from placode and apical papilla cells to taste bud cells only, a surrounding population of Ptch1 and Gli1 responding cells is maintained in signaling centers throughout papilla and taste bud development and differentiation. The Shh signaling targets are in regions of active cell proliferation. Using genetic-inducible lineage tracing for Gli1-expression, we found that Shh-responding cells contribute not only to maintenance of filiform and fungiform papillae, but also to taste buds. A requirement for normal Shh signaling in fungiform papilla, taste bud and filiform papilla maintenance was shown by Gli2 constitutive activation. We identified proliferation niches where Shh signaling is active and suggest that epithelial and mesenchymal compartments harbor potential stem and/or progenitor cell zones. In all, we report a set of hedgehog signaling centers that regulate development and maintenance of taste organs, the fungiform papilla and taste bud, and surrounding lingual cells. Shh signaling has roles in forming and maintaining fungiform papillae and taste buds, most likely via stage-specific autocrine and/or paracrine mechanisms, and by engaging epithelial/mesenchymal interactions. PMID:23916850

Multiple Shh signaling centers participate in fungiform papilla and taste bud formation and maintenance.

PubMed

Liu, Hong Xiang; Ermilov, Alexandre; Grachtchouk, Marina; Li, Libo; Gumucio, Deborah L; Dlugosz, Andrzej A; Mistretta, Charalotte M

2013-10-01

The adult fungiform taste papilla is a complex of specialized cell types residing in the stratified squamous tongue epithelium. This unique sensory organ includes taste buds, papilla epithelium and lateral walls that extend into underlying connective tissue to surround a core of lamina propria cells. Fungiform papillae must contain long-lived, sustaining or stem cells and short-lived, maintaining or transit amplifying cells that support the papilla and specialized taste buds. Shh signaling has established roles in supporting fungiform induction, development and patterning. However, for a full understanding of how Shh transduced signals act in tongue, papilla and taste bud formation and maintenance, it is necessary to know where and when the Shh ligand and pathway components are positioned. We used immunostaining, in situ hybridization and mouse reporter strains for Shh, Ptch1, Gli1 and Gli2-expression and proliferation markers to identify cells that participate in hedgehog signaling. Whereas there is a progressive restriction in location of Shh ligand-expressing cells, from placode and apical papilla cells to taste bud cells only, a surrounding population of Ptch1 and Gli1 responding cells is maintained in signaling centers throughout papilla and taste bud development and differentiation. The Shh signaling targets are in regions of active cell proliferation. Using genetic-inducible lineage tracing for Gli1-expression, we found that Shh-responding cells contribute not only to maintenance of filiform and fungiform papillae, but also to taste buds. A requirement for normal Shh signaling in fungiform papilla, taste bud and filiform papilla maintenance was shown by Gli2 constitutive activation. We identified proliferation niches where Shh signaling is active and suggest that epithelial and mesenchymal compartments harbor potential stem and/or progenitor cell zones. In all, we report a set of hedgehog signaling centers that regulate development and maintenance of taste organs, the fungiform papilla and taste bud, and surrounding lingual cells. Shh signaling has roles in forming and maintaining fungiform papillae and taste buds, most likely via stage-specific autocrine and/or paracrine mechanisms, and by engaging epithelial/mesenchymal interactions. © 2013 Elsevier Inc. All rights reserved.

Short-time windowed covariance: A metric for identifying non-stationary, event-related covariant cortical sites

PubMed Central

Blakely, Timothy; Ojemann, Jeffrey G.; Rao, Rajesh P.N.

2014-01-01

Background Electrocorticography (ECoG) signals can provide high spatio-temporal resolution and high signal to noise ratio recordings of local neural activity from the surface of the brain. Previous studies have shown that broad-band, spatially focal, high-frequency increases in ECoG signals are highly correlated with movement and other cognitive tasks and can be volitionally modulated. However, significant additional information may be present in inter-electrode interactions, but adding additional higher order inter-electrode interactions can be impractical from a computational aspect, if not impossible. New method In this paper we present a new method of calculating high frequency interactions between electrodes called Short-Time Windowed Covariance (STWC) that builds on mathematical techniques currently used in neural signal analysis, along with an implementation that accelerates the algorithm by orders of magnitude by leveraging commodity, off-the-shelf graphics processing unit (GPU) hardware. Results Using the hardware-accelerated implementation of STWC, we identify many types of event-related inter-electrode interactions from human ECoG recordings on global and local scales that have not been identified by previous methods. Unique temporal patterns are observed for digit flexion in both low- (10 mm spacing) and high-resolution (3 mm spacing) electrode arrays. Comparison with existing methods Covariance is a commonly used metric for identifying correlated signals, but the standard covariance calculations do not allow for temporally varying covariance. In contrast STWC allows and identifies event-driven changes in covariance without identifying spurious noise correlations. Conclusions: STWC can be used to identify event-related neural interactions whose high computational load is well suited to GPU capabilities. PMID:24211499

Redox-signals and macrophage biology (for the upcoming issue of molecular aspects of medicine on signaling by reactive oxygen species).

PubMed

Weigert, Andreas; von Knethen, Andreas; Fuhrmann, Dominik; Dehne, Nathalie; Brüne, Bernhard

2018-01-11

Macrophages are known for their versatile role in biology. They sense and clear structures that contain exogenous or endogenous pathogen-associated molecular patterns. This process is tightly linked to the production of a mixture of potentially harmful oxidants and cytokines. Their inherent destructive behavior is directed against foreign material or structures of 'altered self', which explains the role of macrophages during innate immune reactions and inflammation. However, there is also another side of macrophages when they turn into a tissue regenerative, pro-resolving, and healing phenotype. Phenotype changes of macrophages are termed macrophage polarization, representing a continuum between classical and alternative activation. Macrophages as the dominating producers of superoxide/hydrogen peroxide and nitric oxide are not only prone to oxidative modifications but also to more subtle signaling properties of redox-active molecules conveying redox regulation. We review basic concepts of the enzymatic nitric oxide and superoxide production within macrophages, refer to their unique chemical reactions and outline biological consequences not only for macrophage biology but also for their communication with cells in the microenvironment. These considerations link hypoxia to the NO system, addressing feedforward as well as feedback circuits. Moreover, we summarize the role of redox-signaling affecting epigenetics and reflect the central role of mitochondrial-derived oxygen species in inflammation. To better understand the diverse functions of macrophages during initiation as well as resolution of inflammation and to decode their versatile roles during innate and adaptive immunity with the entire spectrum of cell protective towards cell destructive activities we need to appreciate the signaling properties of redox-active species. Herein we discuss macrophage responses in terms of nitric oxide and superoxide formation with the modulating impact of hypoxia. Copyright © 2018. Published by Elsevier Ltd.

What Is the Evidence for Inter-laminar Integration in a Prefrontal Cortical Minicolumn?

PubMed

Opris, Ioan; Chang, Stephano; Noga, Brian R

2017-01-01

The objective of this perspective article is to examine columnar inter-laminar integration during the executive control of behavior. The integration hypothesis posits that perceptual and behavioral signals are integrated within the prefrontal cortical inter-laminar microcircuits. Inter-laminar minicolumnar activity previously recorded from the dorsolateral prefrontal cortex (dlPFC) of nonhuman primates, trained in a visual delay match-to-sample (DMS) task, was re-assessed from an integrative perspective. Biomorphic multielectrode arrays (MEAs) played a unique role in the in vivo recording of columnar cell firing in the dlPFC layers 2/3 and 5/6. Several integrative aspects stem from these experiments: 1. Functional integration of perceptual and behavioral signals across cortical layers during executive control. The integrative effect of dlPFC minicolumns was shown by: (i) increased correlated firing on correct vs. error trials; (ii) decreased correlated firing when the number of non-matching images increased; and (iii) similar spatial firing preference across cortical-striatal cells during spatial-trials, and less on object-trials. 2. Causal relations to integration of cognitive signals by the minicolumnar turbo-engines. The inter-laminar integration between the perceptual and executive circuits was facilitated by stimulating the infra-granular layers with firing patterns obtained from supra-granular layers that enhanced spatial preference of percent correct performance on spatial trials. 3. Integration across hierarchical levels of the brain. The integration of intention signals (visual spatial, direction) with movement preparation (timing, velocity) in striatum and with the motor command and posture in midbrain is also discussed. These findings provide evidence for inter-laminar integration of executive control signals within brain's prefrontal cortical microcircuits.

Readout characteristics of a minute aperture-mounted optical head slider flying above a submicron wide metal patterned medium track

NASA Astrophysics Data System (ADS)

Ohkubo, Toshifumi; Hirota, Terunao; Oumi, Manabu; Hirata, Masakazu; Nakajima, Kunio

2004-10-01

Advances in a digital network society require both higher densities and higher transfer rates in all sorts of storage devices. In optical recording, the trend toward higher recording density and larger storage capacity requires novel surface recording technologies that would drastically improve recording density. To satisfy these severe requirements, we have already proposed a compact integrated optical head slider assembly for proximity optical recording based on the "near field principle". Using the optical head slider, we have successfully demonstrated readout signals from 200 to 150-nm-long bit patterns at frequency bands up to approximately 10 MHz. However, from the practical point of view, it is quite necessary to evaluate readout signals from patterns of smaller (sub-micron to sub-sub-micron) track width in order to prove high-density recording potential. In this paper, we have investigated tracking accuracy characteristics utilizing sub-micron sized alternate patterns of 1-mm length formed in a straight line in the circumferential direction of the medium. Arranging precisely the head's relative position to these recorded patterns, we have successfully obtained readout signals just crossing the sub-micron line-and-space pattern's boundaries. Assuming that an aperture runs along an accurate trajectory of the arc of a circle, readout signal amplitude variations when crossing the pattern edge at a right angle have precisely predicted. Also, the influences of track width on maximum readout signal intensity and tracking sensitivity are discussed in detail.

UHF Signal Processing and Pattern Recognition of Partial Discharge in Gas-Insulated Switchgear Using Chromatic Methodology

PubMed Central

Wang, Xiaohua; Li, Xi; Rong, Mingzhe; Xie, Dingli; Ding, Dan; Wang, Zhixiang

2017-01-01

The ultra-high frequency (UHF) method is widely used in insulation condition assessment. However, UHF signal processing algorithms are complicated and the size of the result is large, which hinders extracting features and recognizing partial discharge (PD) patterns. This article investigated the chromatic methodology that is novel in PD detection. The principle of chromatic methodologies in color science are introduced. The chromatic processing represents UHF signals sparsely. The UHF signals obtained from PD experiments were processed using chromatic methodology and characterized by three parameters in chromatic space (H, L, and S representing dominant wavelength, signal strength, and saturation, respectively). The features of the UHF signals were studied hierarchically. The results showed that the chromatic parameters were consistent with conventional frequency domain parameters. The global chromatic parameters can be used to distinguish UHF signals acquired by different sensors, and they reveal the propagation properties of the UHF signal in the L-shaped gas-insulated switchgear (GIS). Finally, typical PD defect patterns had been recognized by using novel chromatic parameters in an actual GIS tank and good performance of recognition was achieved. PMID:28106806

UHF Signal Processing and Pattern Recognition of Partial Discharge in Gas-Insulated Switchgear Using Chromatic Methodology.

PubMed

Wang, Xiaohua; Li, Xi; Rong, Mingzhe; Xie, Dingli; Ding, Dan; Wang, Zhixiang

2017-01-18

The ultra-high frequency (UHF) method is widely used in insulation condition assessment. However, UHF signal processing algorithms are complicated and the size of the result is large, which hinders extracting features and recognizing partial discharge (PD) patterns. This article investigated the chromatic methodology that is novel in PD detection. The principle of chromatic methodologies in color science are introduced. The chromatic processing represents UHF signals sparsely. The UHF signals obtained from PD experiments were processed using chromatic methodology and characterized by three parameters in chromatic space ( H , L , and S representing dominant wavelength, signal strength, and saturation, respectively). The features of the UHF signals were studied hierarchically. The results showed that the chromatic parameters were consistent with conventional frequency domain parameters. The global chromatic parameters can be used to distinguish UHF signals acquired by different sensors, and they reveal the propagation properties of the UHF signal in the L-shaped gas-insulated switchgear (GIS). Finally, typical PD defect patterns had been recognized by using novel chromatic parameters in an actual GIS tank and good performance of recognition was achieved.

Parathyroid hormone-dependent signaling pathways regulating genes in bone cells

NASA Technical Reports Server (NTRS)

Swarthout, John T.; D'Alonzo, Richard C.; Selvamurugan, Nagarajan; Partridge, Nicola C.

2002-01-01

Parathyroid hormone (PTH) is an 84-amino-acid polypeptide hormone functioning as a major mediator of bone remodeling and as an essential regulator of calcium homeostasis. PTH and PTH-related protein (PTHrP) indirectly activate osteoclasts resulting in increased bone resorption. During this process, PTH changes the phenotype of the osteoblast from a cell involved in bone formation to one directing bone resorption. In addition to these catabolic effects, PTH has been demonstrated to be an anabolic factor in skeletal tissue and in vitro. As a result, PTH has potential medical application to the treatment of osteoporosis, since intermittent administration of PTH stimulates bone formation. Activation of osteoblasts by PTH results in expression of genes important for the degradation of the extracellular matrix, production of growth factors, and stimulation and recruitment of osteoclasts. The ability of PTH to drive changes in gene expression is dependent upon activation of transcription factors such as the activator protein-1 family, RUNX2, and cAMP response element binding protein (CREB). Much of the regulation of these processes by PTH is protein kinase A (PKA)-dependent. However, while PKA is linked to many of the changes in gene expression directed by PTH, PKA activation has been shown to inhibit mitogen-activated protein kinase (MAPK) and proliferation of osteoblasts. It is now known that stimulation of MAPK and proliferation by PTH at low concentrations is protein kinase C (PKC)-dependent in both osteoblastic and kidney cells. Furthermore, PTH has been demonstrated to regulate components of the cell cycle. However, whether this regulation requires PKC and/or extracellular signal-regulated kinases or whether PTH is able to stimulate other components of the cell cycle is unknown. It is possible that stimulation of this signaling pathway by PTH mediates a unique pattern of gene expression resulting in proliferation in osteoblastic and kidney cells; however, specific examples of this are still unknown. This review will focus on what is known about PTH-mediated cell signaling, and discuss the established or putative PTH-regulated pattern of gene expression in osteoblastic cells following treatment with catabolic (high) or anabolic (low) concentrations of the hormone.

Regulation of Facial Morphogenesis by Endothelin Signaling: Insights from Mice and Fish

PubMed Central

Clouthier, David E.; Garcia, Elvin; Schilling, Thomas F.

2010-01-01

Craniofacial morphogenesis is accomplished through a complex set of developmental events, most of which are initiated in neural crest cells within the pharyngeal arches. Local patterning cues from the surrounding environment induce gene expression within neural crest cells, leading to formation of a diverse set of skeletal elements. Endothelin-1 (Edn1) is one of the primary signals that establish the identities of neural crest cells within the mandibular portion of the first pharyngeal arch. Signaling through its cognate receptor, the endothelin-A receptor, is critical for patterning the ventral/distal portion of the arch (lower jaw) and also participates with Hox genes in patterning more posterior arches. Edn1/Ednra signaling is highly conserved between mouse and zebrafish, and genetic analyses in these two species have provided complementary insights into the patterning cues responsible for establishing the craniofacial complex as well as the genetic basis of facial birth defect syndromes. PMID:20684004

Fourier transform magnitudes are unique pattern recognition templates.

PubMed

Gardenier, P H; McCallum, B C; Bates, R H

1986-01-01

Fourier transform magnitudes are commonly used in the generation of templates in pattern recognition applications. We report on recent advances in Fourier phase retrieval which are relevant to pattern recognition. We emphasise in particular that the intrinsic form of a finite, positive image is, in general, uniquely related to the magnitude of its Fourier transform. We state conditions under which the Fourier phase can be reconstructed from samples of the Fourier magnitude, and describe a method of achieving this. Computational examples of restoration of Fourier phase (and hence, by Fourier transformation, the intrinsic form of the image) from samples of the Fourier magnitude are also presented.

Requirement for Jagged1-Notch2 signaling in patterning the bones of the mouse and human middle ear.

PubMed

Teng, Camilla S; Yen, Hai-Yun; Barske, Lindsey; Smith, Bea; Llamas, Juan; Segil, Neil; Go, John; Sanchez-Lara, Pedro A; Maxson, Robert E; Crump, J Gage

2017-05-31

Whereas Jagged1-Notch2 signaling is known to pattern the sensorineural components of the inner ear, its role in middle ear development has been less clear. We previously reported a role for Jagged-Notch signaling in shaping skeletal elements derived from the first two pharyngeal arches of zebrafish. Here we show a conserved requirement for Jagged1-Notch2 signaling in patterning the stapes and incus middle ear bones derived from the equivalent pharyngeal arches of mammals. Mice lacking Jagged1 or Notch2 in neural crest-derived cells (NCCs) of the pharyngeal arches display a malformed stapes. Heterozygous Jagged1 knockout mice, a model for Alagille Syndrome (AGS), also display stapes and incus defects. We find that Jagged1-Notch2 signaling functions early to pattern the stapes cartilage template, with stapes malformations correlating with hearing loss across all frequencies. We observe similar stapes defects and hearing loss in one patient with heterozygous JAGGED1 loss, and a diversity of conductive and sensorineural hearing loss in nearly half of AGS patients, many of which carry JAGGED1 mutations. Our findings reveal deep conservation of Jagged1-Notch2 signaling in patterning the pharyngeal arches from fish to mouse to man, despite the very different functions of their skeletal derivatives in jaw support and sound transduction.

[Biology and immunotherapy advance of interleukin 2 and interleukin 15-review].

PubMed

Chen, Guang-Hua; Wu, De-Pei

2009-08-01

IL-2 and IL-15 play an important roles in regulating the lymphocyte function and homeostasis. Advances in understanding of the cellular and molecular biology of IL-2 and IL-15 and their receptor complex have provided rationale to better utilize them to expand and activate immune effectors in patients with cancer. These two cytokines stimulate similar responses from lymphocytes in vitro, but play markedly distinct roles in lymphoid biology in vivo. Their distinct physiological functions can be ascribed to distinct signaling pathways initiated by distinct cytokine receptor subunits, differential expression patterns of their receptors. Recently, the discovery of a novel mechanism of IL-15 cytokine signaling, trans-presentation, has provided insights into the divergent ways of these cytokine function. Although their heterotrimeric receptors have two receptor subunits in common, these two cytokines have contrasting roles in adaptive immune responses. The unique role of interleukin 2 is in the elimination of self-reactive T cells to prevent autoimmunity. By contrast, interleukin 15 is dedicated to the prolonged maintenance of memory T-cell responses to pathogens. As discussed in this article, the biology of IL-2 and IL-15 two cytokines will affect the development of novel treatment for malignancies and autoimmune diseases.

Axonal degeneration in Alzheimer’s disease: When signaling abnormalities meet the axonal transport system

PubMed Central

Kanaan, Nicholas M.; Pigino, Gustavo F.; Brady, Scott T.; Lazarov, Orly; Binder, Lester I.; Morfini, Gerardo A.

2012-01-01

Alzheimer’s disease (AD) is characterized by progressive, age-dependent degeneration of neurons in the central nervous system. A large body of evidence indicates that neurons affected in AD follow a dying-back pattern of degeneration, where abnormalities in synaptic function and axonal connectivity long precede somatic cell death. Mechanisms underlying dying-back degeneration of neurons in AD remain elusive but several have been proposed, including deficits in fast axonal transport (FAT). Accordingly, genetic evidence linked alterations in FAT to dying-back degeneration of neurons, and FAT defects have been widely documented in various AD models. In light of these findings, we discuss experimental evidence linking several AD-related pathogenic polypeptides to aberrant activation of signaling pathways involved in the phosphoregulation of microtubule-based motor proteins. While each pathway appears to affect FAT in a unique manner, in the context of AD, many of these pathways might work synergistically to compromise the delivery of molecular components critical for the maintenance and function of synapses and axons. Therapeutic approaches aimed at preventing FAT deficits by normalizing the activity of specific protein kinases may help prevent degeneration of vulnerable neurons in AD. PMID:22721767

Multi-band infrared camera systems

NASA Astrophysics Data System (ADS)

Davis, Tim; Lang, Frank; Sinneger, Joe; Stabile, Paul; Tower, John

1994-12-01

The program resulted in an IR camera system that utilizes a unique MOS addressable focal plane array (FPA) with full TV resolution, electronic control capability, and windowing capability. Two systems were delivered, each with two different camera heads: a Stirling-cooled 3-5 micron band head and a liquid nitrogen-cooled, filter-wheel-based, 1.5-5 micron band head. Signal processing features include averaging up to 16 frames, flexible compensation modes, gain and offset control, and real-time dither. The primary digital interface is a Hewlett-Packard standard GPID (IEEE-488) port that is used to upload and download data. The FPA employs an X-Y addressed PtSi photodiode array, CMOS horizontal and vertical scan registers, horizontal signal line (HSL) buffers followed by a high-gain preamplifier and a depletion NMOS output amplifier. The 640 x 480 MOS X-Y addressed FPA has a high degree of flexibility in operational modes. By changing the digital data pattern applied to the vertical scan register, the FPA can be operated in either an interlaced or noninterlaced format. The thermal sensitivity performance of the second system's Stirling-cooled head was the best of the systems produced.

New advances in targeted gastric cancer treatment

PubMed Central

Lazăr, Daniela Cornelia; Tăban, Sorina; Cornianu, Marioara; Faur, Alexandra; Goldiş, Adrian

2016-01-01

Despite a decrease in incidence over past decades, gastric cancer remains a major global health problem. In the more recent period, survival has shown only minor improvement, despite significant advances in diagnostic techniques, surgical and chemotherapeutic approaches, the development of novel therapeutic agents and treatment by multidisciplinary teams. Because multiple genetic mutations, epigenetic alterations, and aberrant molecular signalling pathways are involved in the development of gastric cancers, recent research has attempted to determine the molecular heterogeneity responsible for the processes of carcinogenesis, spread and metastasis. Currently, some novel agents targeting a part of these dysfunctional molecular signalling pathways have already been integrated into the standard treatment of gastric cancer, whereas others remain in phases of investigation within clinical trials. It is essential to identify the unique molecular patterns of tumours and specific biomarkers to develop treatments targeted to the individual tumour behaviour. This review analyses the global impact of gastric cancer, as well as the role of Helicobacter pylori infection and the efficacy of bacterial eradication in preventing gastric cancer development. Furthermore, the paper discusses the currently available targeted treatments and future directions of research using promising novel classes of molecular agents for advanced tumours. PMID:27570417

The Identification and Tracking of Uterine Contractions Using Template Based Cross-Correlation.

PubMed

McDonald, Sarah C; Brooker, Graham; Phipps, Hala; Hyett, Jon

2017-09-01

The purpose of this paper is to outline a novel method of using template based cross-correlation to identify and track uterine contractions during labour. A purpose built six-channel Electromyography (EMG) device was used to collect data from consenting women during labour and birth. A range of templates were constructed for the purpose of identifying and tracking uterine activity when cross-correlated with the EMG signal. Peak finding techniques were applied on the cross-correlated result to simplify and automate the identification and tracking of contractions. The EMG data showed a unique pattern when a woman was contracting with key features of the contraction signal remaining consistent and identifiable across subjects. Contraction profiles across subjects were automatically identified using template based cross-correlation. Synthetic templates from a rectangular function with a duration of between 5 and 10 s performed best at identifying and tracking uterine activity across subjects. The successful application of this technique provides opportunity for both simple and accurate real-time analysis of contraction data while enabling investigations into the application of techniques such as machine learning which could enable automated learning from contraction data as part of real-time monitoring and post analysis.

Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy

PubMed Central

Johnson, Douglas B.; Estrada, Monica V.; Salgado, Roberto; Sanchez, Violeta; Doxie, Deon B.; Opalenik, Susan R.; Vilgelm, Anna E.; Feld, Emily; Johnson, Adam S.; Greenplate, Allison R.; Sanders, Melinda E.; Lovly, Christine M.; Frederick, Dennie T.; Kelley, Mark C.; Richmond, Ann; Irish, Jonathan M.; Shyr, Yu; Sullivan, Ryan J.; Puzanov, Igor; Sosman, Jeffrey A.; Balko, Justin M.

2016-01-01

Anti-PD-1 therapy yields objective clinical responses in 30–40% of advanced melanoma patients. Since most patients do not respond, predictive biomarkers to guide treatment selection are needed. We hypothesize that MHC-I/II expression is required for tumour antigen presentation and may predict anti-PD-1 therapy response. In this study, across 60 melanoma cell lines, we find bimodal expression patterns of MHC-II, while MHC-I expression was ubiquitous. A unique subset of melanomas are capable of expressing MHC-II under basal or IFNγ-stimulated conditions. Using pathway analysis, we show that MHC-II(+) cell lines demonstrate signatures of ‘PD-1 signalling', ‘allograft rejection' and ‘T-cell receptor signalling', among others. In two independent cohorts of anti-PD-1-treated melanoma patients, MHC-II positivity on tumour cells is associated with therapeutic response, progression-free and overall survival, as well as CD4+ and CD8+ tumour infiltrate. MHC-II+ tumours can be identified by melanoma-specific immunohistochemistry using commercially available antibodies for HLA-DR to improve anti-PD-1 patient selection. PMID:26822383

Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection.

PubMed

Chang, Hsiao-Han; Hartl, Daniel L

2015-02-01

Detecting signals of selection in the genome of malaria parasites is a key to identify targets for drug and vaccine development. Malaria parasites have a unique life cycle alternating between vector and host organism with a population bottleneck at each transition. These recurrent bottlenecks could influence the patterns of genetic diversity and the power of existing population genetic tools to identify sites under positive selection. We therefore simulated the site-frequency spectrum of a beneficial mutant allele through time under the malaria life cycle. We investigated the power of current population genetic methods to detect positive selection based on the site-frequency spectrum as well as temporal changes in allele frequency. We found that a within-host selective advantage is difficult to detect using these methods. Although a between-host transmission advantage could be detected, the power is decreased when compared with the classical Wright-Fisher (WF) population model. Using an adjusted null site-frequency spectrum that takes the malaria life cycle into account, the power of tests based on the site-frequency spectrum to detect positive selection is greatly improved. Our study demonstrates the importance of considering the life cycle in genetic analysis, especially in parasites with complex life cycles.

Mechanisms and evolution of plant resistance to aphids.

PubMed

Züst, Tobias; Agrawal, Anurag A

2016-01-06

Aphids are important herbivores of both wild and cultivated plants. Plants rely on unique mechanisms of recognition, signalling and defence to cope with the specialized mode of phloem feeding by aphids. Aspects of the molecular mechanisms underlying aphid-plant interactions are beginning to be understood. Recent advances include the identification of aphid salivary proteins involved in host plant manipulation, and plant receptors involved in aphid recognition. However, a complete picture of aphid-plant interactions requires consideration of the ecological outcome of these mechanisms in nature, and the evolutionary processes that shaped them. Here we identify general patterns of resistance, with a special focus on recognition, phytohormonal signalling, secondary metabolites and induction of plant resistance. We discuss how host specialization can enable aphids to co-opt both the phytohormonal responses and defensive compounds of plants for their own benefit at a local scale. In response, systemically induced resistance in plants is common and often involves targeted responses to specific aphid species or even genotypes. As co-evolutionary adaptation between plants and aphids is ongoing, the stealthy nature of aphid feeding makes both the mechanisms and outcomes of these interactions highly distinct from those of other herbivore-plant interactions.

New advances in targeted gastric cancer treatment.

PubMed

Lazăr, Daniela Cornelia; Tăban, Sorina; Cornianu, Marioara; Faur, Alexandra; Goldiş, Adrian

2016-08-14

Despite a decrease in incidence over past decades, gastric cancer remains a major global health problem. In the more recent period, survival has shown only minor improvement, despite significant advances in diagnostic techniques, surgical and chemotherapeutic approaches, the development of novel therapeutic agents and treatment by multidisciplinary teams. Because multiple genetic mutations, epigenetic alterations, and aberrant molecular signalling pathways are involved in the development of gastric cancers, recent research has attempted to determine the molecular heterogeneity responsible for the processes of carcinogenesis, spread and metastasis. Currently, some novel agents targeting a part of these dysfunctional molecular signalling pathways have already been integrated into the standard treatment of gastric cancer, whereas others remain in phases of investigation within clinical trials. It is essential to identify the unique molecular patterns of tumours and specific biomarkers to develop treatments targeted to the individual tumour behaviour. This review analyses the global impact of gastric cancer, as well as the role of Helicobacter pylori infection and the efficacy of bacterial eradication in preventing gastric cancer development. Furthermore, the paper discusses the currently available targeted treatments and future directions of research using promising novel classes of molecular agents for advanced tumours.

Pattern-Recognition Algorithm for Locking Laser Frequency

NASA Technical Reports Server (NTRS)

Karayan, Vahag; Klipstein, William; Enzer, Daphna; Yates, Philip; Thompson, Robert; Wells, George

2006-01-01

A computer program serves as part of a feedback control system that locks the frequency of a laser to one of the spectral peaks of cesium atoms in an optical absorption cell. The system analyzes a saturation absorption spectrum to find a target peak and commands a laser-frequency-control circuit to minimize an error signal representing the difference between the laser frequency and the target peak. The program implements an algorithm consisting of the following steps: Acquire a saturation absorption signal while scanning the laser through the frequency range of interest. Condition the signal by use of convolution filtering. Detect peaks. Match the peaks in the signal to a pattern of known spectral peaks by use of a pattern-recognition algorithm. Add missing peaks. Tune the laser to the desired peak and thereafter lock onto this peak. Finding and locking onto the desired peak is a challenging problem, given that the saturation absorption signal includes noise and other spurious signal components; the problem is further complicated by nonlinearity and shifting of the voltage-to-frequency correspondence. The pattern-recognition algorithm, which is based on Hausdorff distance, is what enables the program to meet these challenges.

Gaussian process based independent analysis for temporal source separation in fMRI.

PubMed

Hald, Ditte Høvenhoff; Henao, Ricardo; Winther, Ole

2017-05-15

Functional Magnetic Resonance Imaging (fMRI) gives us a unique insight into the processes of the brain, and opens up for analyzing the functional activation patterns of the underlying sources. Task-inferred supervised learning with restrictive assumptions in the regression set-up, restricts the exploratory nature of the analysis. Fully unsupervised independent component analysis (ICA) algorithms, on the other hand, can struggle to detect clear classifiable components on single-subject data. We attribute this shortcoming to inadequate modeling of the fMRI source signals by failing to incorporate its temporal nature. fMRI source signals, biological stimuli and non-stimuli-related artifacts are all smooth over a time-scale compatible with the sampling time (TR). We therefore propose Gaussian process ICA (GPICA), which facilitates temporal dependency by the use of Gaussian process source priors. On two fMRI data sets with different sampling frequency, we show that the GPICA-inferred temporal components and associated spatial maps allow for a more definite interpretation than standard temporal ICA methods. The temporal structures of the sources are controlled by the covariance of the Gaussian process, specified by a kernel function with an interpretable and controllable temporal length scale parameter. We propose a hierarchical model specification, considering both instantaneous and convolutive mixing, and we infer source spatial maps, temporal patterns and temporal length scale parameters by Markov Chain Monte Carlo. A companion implementation made as a plug-in for SPM can be downloaded from https://github.com/dittehald/GPICA. Copyright © 2017 Elsevier Inc. All rights reserved.

Cytological and Proteomic Analyses of Osmunda cinnamomea Germinating Spores Reveal Characteristics of Fern Spore Germination and Rhizoid Tip Growth.

PubMed

Suo, Jinwei; Zhao, Qi; Zhang, Zhengxiu; Chen, Sixue; Cao, Jian'guo; Liu, Guanjun; Wei, Xing; Wang, Tai; Yang, Chuanping; Dai, Shaojun

2015-09-01

Fern spore is a good single-cell model for studying the sophisticated molecular networks in asymmetric cell division, differentiation, and polar growth. Osmunda cinnamomea L. var. asiatica is one of the oldest fern species with typical separate-growing trophophyll and sporophyll. The chlorophyllous spores generated from sporophyll can germinate without dormancy. In this study, the spore ultrastructure, antioxidant enzyme activities, as well as protein and gene expression patterns were analyzed in the course of spore germination at five typical stages (i.e. mature spores, rehydrated spores, double-celled spores, germinated spores, and spores with protonemal cells). Proteomic analysis revealed 113 differentially expressed proteins, which were mainly involved in photosynthesis, reserve mobilization, energy supplying, protein synthesis and turnover, reactive oxygen species scavenging, signaling, and cell structure modulation. The presence of multiple proteoforms of 25 differentially expressed proteins implies that post-translational modification may play important roles in spore germination. The dynamic patterns of proteins and their encoding genes exhibited specific characteristics in the processes of cell division and rhizoid tip growth, which include heterotrophic and autotrophic metabolisms, de novo protein synthesis and active protein turnover, reactive oxygen species and hormone (brassinosteroid and ethylene) signaling, and vesicle trafficking and cytoskeleton dynamic. In addition, the function skew of proteins in fern spores highlights the unique and common mechanisms when compared with evolutionarily divergent spermatophyte pollen. These findings provide an improved understanding of the typical single-celled asymmetric division and polar growth during fern spore germination. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Biases in rhythmic sensorimotor coordination: effects of modality and intentionality.

PubMed

Debats, Nienke B; Ridderikhoff, Arne; de Boer, Betteco J; Peper, C Lieke E

2013-08-01

Sensorimotor biases were examined for intentional (tracking task) and unintentional (distractor task) rhythmic coordination. The tracking task involved unimanual tracking of either an oscillating visual signal or the passive movements of the contralateral hand (proprioceptive signal). In both conditions the required coordination patterns (isodirectional and mirror-symmetric) were defined relative to the body midline and the hands were not visible. For proprioceptive tracking the two patterns did not differ in stability, whereas for visual tracking the isodirectional pattern was performed more stably than the mirror-symmetric pattern. However, when visual feedback about the unimanual hand movements was provided during visual tracking, the isodirectional pattern ceased to be dominant. Together these results indicated that the stability of the coordination patterns did not depend on the modality of the target signal per se, but on the combination of sensory signals that needed to be processed (unimodal vs. cross-modal). The distractor task entailed rhythmic unimanual movements during which a rhythmic visual or proprioceptive distractor signal had to be ignored. The observed biases were similar as for intentional coordination, suggesting that intentionality did not affect the underlying sensorimotor processes qualitatively. Intentional tracking was characterized by active sensory pursuit, through muscle activity in the passively moved arm (proprioceptive tracking task) and rhythmic eye movements (visual tracking task). Presumably this pursuit afforded predictive information serving the coordination process. Copyright © 2013 Elsevier B.V. All rights reserved.

RNA-Seq reveals common and unique PXR- and CAR-target gene signatures in the mouse liver transcriptome.

PubMed

Cui, Julia Yue; Klaassen, Curtis D

2016-09-01

The pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are well-known xenobiotic-sensing nuclear receptors with overlapping functions. However, there lacks a quantitative characterization to distinguish between the PXR and CAR target genes and signaling pathways in the liver. The present study performed a transcriptomic comparison of the PXR- and CAR-targets using RNA-Seq in livers of adult wild-type mice that were treated with the prototypical PXR ligand PCN (200mg/kg, i.p. once daily for 4days in corn oil) or the prototypical CAR ligand TCPOBOP (3mg/kg, i.p., once daily for 4days in corn oil). At the given doses, TCPOBOP differentially regulated many more genes (2125) than PCN (212), and 147 of the same genes were differentially regulated by both chemicals. As expected, the top pathways differentially regulated by both PCN and TCPOBOP were involved in xenobiotic metabolism, and they also up-regulated genes involved in retinoid metabolism, but down-regulated genes involved in inflammation and iron homeostasis. Regarding unique pathways, PXR activation appeared to overlap with the aryl hydrocarbon receptor signaling, whereas CAR activation appeared to overlap with the farnesoid X receptor signaling, acute-phase response, and mitochondrial dysfunction. The mRNAs of differentially regulated drug-processing genes (DPGs) partitioned into three patterns, namely TCPOBOP-induced, PCN-induced, as well as TCPOBOP-suppressed gene clusters. The cumulative mRNAs of the differentially regulated DPGs, phase-I and -II enzymes, as well as efflux transporters were all up-regulated by both PCN and TCPOBOPOP, whereas the cumulative mRNAs of the uptake transporters were down-regulated only by TCPOBOP. The absolute mRNA abundance in control and receptor-activated conditions was examined in each DPG category to predict the contribution of specific DPG genes in the PXR/CAR-mediated pharmacokinetic responses. The preferable differential regulation by TCPOBOP in the entire hepatic transcriptome correlated with a marked change in the expression of many DNA and histone epigenetic modifiers. In conclusion, the present study has revealed known and novel, as well as common and unique targets of PXR and CAR in mouse liver following pharmacological activation using their prototypical ligands. Results from this study will further support the role of these receptors in regulating the homeostasis of xenobiotic and intermediary metabolism in the liver, and aid in distinguishing between PXR and CAR signaling at various physiological and pathophysiological conditions. This article is part of a Special Issue entitled: Xenobiotic nuclear receptors: New Tricks for An Old Dog, edited by Dr. Wen Xie. Copyright © 2016 Elsevier B.V. All rights reserved.

Signalling Signalhood and the Emergence of Communication

ERIC Educational Resources Information Center

Scott-Phillips, Thomas C.; Kirby, Simon; Ritchie, Graham R. S.

2009-01-01

A unique hallmark of human language is that it uses signals that are both learnt and symbolic. The emergence of such signals was therefore a defining event in human cognitive evolution, yet very little is known about how such a process occurs. Previous work provides some insights on how meaning can become attached to form, but a more foundational…

The Development of a Greeting Signal in Wild Chimpanzees

ERIC Educational Resources Information Center

Laporte, Marion N. C.; Zuberbuhler, Klaus

2011-01-01

Adult chimpanzees produce a unique vocal signal, the pant-grunt, when encountering higher-ranking group members. The behaviour is typically directed to a specific receiver and has thus been interpreted as a "greeting" signal. The alpha male obtains a large share of these calls, followed by the other adult males of the group. In this study, we…

Molecular classification of patients with grade II/III glioma using quantitative MRI characteristics.

PubMed

Bahrami, Naeim; Hartman, Stephen J; Chang, Yu-Hsuan; Delfanti, Rachel; White, Nathan S; Karunamuni, Roshan; Seibert, Tyler M; Dale, Anders M; Hattangadi-Gluth, Jona A; Piccioni, David; Farid, Nikdokht; McDonald, Carrie R

2018-06-02

Molecular markers of WHO grade II/III glioma are known to have important prognostic and predictive implications and may be associated with unique imaging phenotypes. The purpose of this study is to determine whether three clinically relevant molecular markers identified in gliomas-IDH, 1p/19q, and MGMT status-show distinct quantitative MRI characteristics on FLAIR imaging. Sixty-one patients with grade II/III gliomas who had molecular data and MRI available prior to radiation were included. Quantitative MRI features were extracted that measured tissue heterogeneity (homogeneity and pixel correlation) and FLAIR border distinctiveness (edge contrast; EC). T-tests were conducted to determine whether patients with different genotypes differ across the features. Logistic regression with LASSO regularization was used to determine the optimal combination of MRI and clinical features for predicting molecular subtypes. Patients with IDH wildtype tumors showed greater signal heterogeneity (p = 0.001) and lower EC (p = 0.008) within the FLAIR region compared to IDH mutant tumors. Among patients with IDH mutant tumors, 1p/19q co-deleted tumors had greater signal heterogeneity (p = 0.002) and lower EC (p = 0.005) compared to 1p/19q intact tumors. MGMT methylated tumors showed lower EC (p = 0.03) compared to the unmethylated group. The combination of FLAIR border distinctness, heterogeneity, and pixel correlation optimally classified tumors by IDH status. Quantitative imaging characteristics of FLAIR heterogeneity and border pattern in grade II/III gliomas may provide unique information for determining molecular status at time of initial diagnostic imaging, which may then guide subsequent surgical and medical management.

Periodic regulation of expression of genes for kisspeptin, gonadotropin-inhibitory hormone and their receptors in the grass puffer: Implications in seasonal, daily and lunar rhythms of reproduction.

PubMed

Ando, Hironori; Shahjahan, Md; Kitahashi, Takashi

2018-04-03

The seasonal, daily and lunar control of reproduction involves photoperiodic, circadian and lunar changes in the activity of kisspeptin, gonadotropin-inhibitory hormone (GnIH) and gonadotropin-releasing hormone (GnRH) neurons. These changes are brought through complex networks of light-, time- and non-photic signal-dependent control mechanisms, which are mostly unknown at present. The grass puffer, Takifugu alboplumbeus, a semilunar spawner, provides a unique and excellent animal model to assess this question because its spawning is synchronized with seasonal, daily and lunar cycles. In the diencephalon, the genes for kisspeptin, GnIH and their receptors showed similar expression patterns with clear seasonal and daily oscillations, suggesting that they are regulated by common mechanisms involving melatonin, circadian clock and water temperature. For implications in semilunar-synchronized spawning rhythm, melatonin receptor genes showed ultradian oscillations in expression with the period of 14.0-15.4 h in the pineal gland. This unique ultradian rhythm might be driven by circatidal clock. The possible circatidal clock and circadian clock in the pineal gland may cooperate to drive circasemilunar rhythm to regulate the expression of the kisspeptin, GnIH and their receptor genes. On the other hand, high temperature (over 28 °C) conditions, under which the expression of the kisspeptin and its receptor genes is markedly suppressed, may provide an environmental signal that terminates reproduction at the end of breeding period. Taken together, the periodic regulation of the kisspeptin, GnIH and their receptor genes by melatonin, circadian clock and water temperature may be important in the precisely-timed spawning of the grass puffer. Copyright © 2018 Elsevier Inc. All rights reserved.

Ionospheric Scintillation Explorer (ISX)

NASA Astrophysics Data System (ADS)

Iuliano, J.; Bahcivan, H.

2015-12-01

NSF has recently selected Ionospheric Scintillation Explorer (ISX), a 3U Cubesat mission to explore the three-dimensional structure of scintillation-scale ionospheric irregularities associated with Equatorial Spread F (ESF). ISX is a collaborative effort between SRI International and Cal Poly. This project addresses the science question: To what distance along a flux tube does an irregularity of certain transverse-scale extend? It has been difficult to measure the magnetic field-alignment of scintillation-scale turbulent structures because of the difficulty of sampling a flux tube at multiple locations within a short time. This measurement is now possible due to the worldwide transition to DTV, which presents unique signals of opportunity for remote sensing of ionospheric irregularities from numerous vantage points. DTV spectra, in various formats, contain phase-stable, narrowband pilot carrier components that are transmitted simultaneously. A 4-channel radar receiver will simultaneously record up to 4 spatially separated transmissions from the ground. Correlations of amplitude and phase scintillation patterns corresponding to multiple points on the same flux tube will be a measure of the spatial extent of the structures along the magnetic field. A subset of geometries where two or more transmitters are aligned with the orbital path will be used to infer the temporal development of the structures. ISX has the following broad impact. Scintillation of space-based radio signals is a space weather problem that is intensively studied. ISX is a step toward a CubeSat constellation to monitor worldwide TEC variations and radio wave distortions on thousands of ionospheric paths. Furthermore, the rapid sampling along spacecraft orbits provides a unique dataset to deterministically reconstruct ionospheric irregularities at scintillation-scale resolution using diffraction radio tomography, a technique that enables prediction of scintillations at other radio frequencies, and potentially, mitigation of phase distortions.

Performance-informed EEG analysis reveals mixed evidence for EEG signatures unique to the processing of time.

PubMed

Schlichting, Nadine; de Jong, Ritske; van Rijn, Hedderik

2018-06-20

Certain EEG components (e.g., the contingent negative variation, CNV, or beta oscillations) have been linked to the perception of temporal magnitudes specifically. However, it is as of yet unclear whether these EEG components are really unique to time perception or reflect the perception of magnitudes in general. In the current study we recorded EEG while participants had to make judgments about duration (time condition) or numerosity (number condition) in a comparison task. This design allowed us to directly compare EEG signals between the processing of time and number. Stimuli consisted of a series of blue dots appearing and disappearing dynamically on a black screen. Each stimulus was characterized by its duration and the total number of dots that it consisted of. Because it is known that tasks like these elicit perceptual interference effects that we used a maximum-likelihood estimation (MLE) procedure to determine, for each participant and dimension separately, to what extent time and numerosity information were taken into account when making a judgement in an extensive post hoc analysis. This approach enabled us to capture individual differences in behavioral performance and, based on the MLE estimates, to select a subset of participants who suppressed task-irrelevant information. Even for this subset of participants, who showed no or only small interference effects and thus were thought to truly process temporal information in the time condition and numerosity information in the number condition, we found CNV patterns in the time-domain EEG signals for both tasks that was more pronounced in the time-task. We found no substantial evidence for differences between the processing of temporal and numerical information in the time-frequency domain.

Salicylic Acid and Jasmonic Acid Pathways are Activated in Spatially Different Domains Around the Infection Site During Effector-Triggered Immunity in Arabidopsis thaliana.

PubMed

Betsuyaku, Shigeyuki; Katou, Shinpei; Takebayashi, Yumiko; Sakakibara, Hitoshi; Nomura, Nobuhiko; Fukuda, Hiroo

2018-01-01

The innate immune response is, in the first place, elicited at the site of infection. Thus, the host response can be different among the infected cells and the cells surrounding them. Effector-triggered immunity (ETI), a form of innate immunity in plants, is triggered by specific recognition between pathogen effectors and their corresponding plant cytosolic immune receptors, resulting in rapid localized cell death known as hypersensitive response (HR). HR cell death is usually limited to a few cells at the infection site, and is surrounded by a few layers of cells massively expressing defense genes such as Pathogenesis-Related Gene 1 (PR1). This virtually concentric pattern of the cellular responses in ETI is proposed to be regulated by a concentration gradient of salicylic acid (SA), a phytohormone accumulated around the infection site. Recent studies demonstrated that jasmonic acid (JA), another phytohormone known to be mutually antagonistic to SA in many cases, is also accumulated in and required for ETI, suggesting that ETI is a unique case. However, the molecular basis for this uniqueness remained largely to be solved. Here, we found that, using intravital time-lapse imaging, the JA signaling pathway is activated in the cells surrounding the central SA-active cells around the infection sites in Arabidopsis thaliana. This distinct spatial organization explains how these two phythormone pathways in a mutually antagonistic relationship can be activated simultaneously during ETI. Our results re-emphasize that the spatial consideration is a key strategy to gain mechanistic insights into the apparently complex signaling cross-talk in immunity. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

What determines the relationship between color naming, unique hues, and sensory singularities: Illuminations, surfaces, or photoreceptors?

PubMed

Witzel, Christoph; Cinotti, François; O'Regan, J Kevin

2015-01-01

The relationship between the sensory signal of the photoreceptors on one hand and color appearance and language on the other hand is completely unclear. A recent finding established a surprisingly accurate correlation between focal colors, unique hues, and so-called singularities in the laws governing how sensory signals for different surfaces change across illuminations. This article examines how this correlation with singularities depends on reflectances, illuminants, and cone sensitivities. Results show that this correlation holds for a large range of illuminants and for a large range of sensors, including sensors that are fundamentally different from human photoreceptors. In contrast, the spectral characteristics of the reflectance spectra turned out to be the key factor that determines the correlation between focal colors, unique hues, and sensory singularities. These findings suggest that the origins of color appearance and color language may be found in particular characteristics of the reflectance spectra that correspond to focal colors and unique hues.

Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction.

PubMed

Dimasi, Nazzareno

2007-01-01

The Grb2-like adaptor protein GADS is essential for tyrosine kinase-dependent signaling in T lymphocytes. Following T cell receptor ligation, GADS interacts through its C-terminal SH3 domain with the adaptors SLP-76 and LAT, to form a multiprotein signaling complex that is crucial for T cell activation. To understand the structural basis for the selective recognition of GADS by SLP-76, herein is reported the crystal structure at 1.54 Angstrom of the C-terminal SH3 domain of GADS bound to the SLP-76 motif 233-PSIDRSTKP-241, which represents the minimal binding site. In addition to the unique structural features adopted by the bound SLP-76 peptide, the complex structure reveals a unique SH3-SH3 interaction. This homophilic interaction, which is observed in presence of the SLP-76 peptide and is present in solution, extends our understanding of the molecular mechanisms that could be employed by modular proteins to increase their signaling transduction specificity.

Normalization of TAM post-receptor signaling reveals a cell invasive signature for Axl tyrosine kinase.

PubMed

Kimani, Stanley G; Kumar, Sushil; Davra, Viralkumar; Chang, Yun-Juan; Kasikara, Canan; Geng, Ke; Tsou, Wen-I; Wang, Shenyan; Hoque, Mainul; Boháč, Andrej; Lewis-Antes, Anita; De Lorenzo, Mariana S; Kotenko, Sergei V; Birge, Raymond B

2016-09-06

Tyro3, Axl, and Mertk (TAMs) are a family of three conserved receptor tyrosine kinases that have pleiotropic roles in innate immunity and homeostasis and when overexpressed in cancer cells can drive tumorigenesis. In the present study, we engineered EGFR/TAM chimeric receptors (EGFR/Tyro3, EGFR/Axl, and EGF/Mertk) with the goals to interrogate post-receptor functions of TAMs, and query whether TAMs have unique or overlapping post-receptor activation profiles. Stable expression of EGFR/TAMs in EGFR-deficient CHO cells afforded robust EGF inducible TAM receptor phosphorylation and activation of downstream signaling. Using a series of unbiased screening approaches, that include kinome-view analysis, phosphor-arrays, RNAseq/GSEA analysis, as well as cell biological and in vivo readouts, we provide evidence that each TAM has unique post-receptor signaling platforms and identify an intrinsic role for Axl that impinges on cell motility and invasion compared to Tyro3 and Mertk. These studies demonstrate that TAM show unique post-receptor signatures that impinge on distinct gene expression profiles and tumorigenic outcomes.

The canonical Wnt signaling activator, R-spondin2, regulates craniofacial patterning and morphogenesis within the branchial arch through ectodermal-mesenchymal interaction

PubMed Central

Jin, Yong-Ri; Turcotte, Taryn J.; Crocker, Alison L.; Han, Xiang Hua; Yoon, Jeong Kyo

2011-01-01

R-spondins are a recently characterized family of secreted proteins that activate Wnt/β-catenin signaling. Herein, we determine R-spondin2 (Rspo2) function in craniofacial development in mice. Mice lacking a functional Rspo2 gene exhibit craniofacial abnormalities such as mandibular hypoplasia, maxillary and mandibular skeletal deformation, and cleft palate. We found that loss of the mouse Rspo2 gene significantly disrupted Wnt/β-catenin signaling and gene expression within the first branchial arch (BA1). Rspo2, which is normally expressed in BA1 mesenchymal cells, regulates gene expression through a unique ectoderm-mesenchyme interaction loop. The Rspo2 protein, potentially in combination with ectoderm-derived Wnt ligands, up-regulates Msx1 and Msx2 expression within mesenchymal cells. In contrast, Rspo2 regulates expression of the Dlx5, Dlx6, and Hand2 genes in mesenchymal cells via inducing expression of their upstream activator, Endothelin1 (Edn1), within ectodermal cells. Loss of Rspo2 also causes increased cell apoptosis, especially within the aboral (or caudal) domain of the BA1, resulting in hypoplasia of the BA1. Severely reduced expression of Fgf8, a survival factor for mesenchymal cells, in the ectoderm of Rspo2−/− embryos is likely responsible for increased cell apoptosis. Additionally, we found that cleft palate in Rspo2−/− mice is not associated with defects intrinsic to the palatal shelves. A possible cause of cleft palate is a delay of proper palatal shelf elevation that may result from the small mandible and a failure of lowering the tongue. Thus, our study identifies Rspo2 as a mesenchyme-derived factor that plays critical roles in regulating BA1 patterning and morphogenesis through ectodermal-mesenchymal interaction and a novel genetic factor for cleft palate. PMID:21237142

Evidence for a physical linkage between galactic cosmic rays and regional climate time series

USGS Publications Warehouse

Perry, C.A.

2007-01-01

The effects of solar variability on regional climate time series were examined using a sequence of physical connections between total solar irradiance (TSI) modulated by galactic cosmic rays (GCRs), and ocean and atmospheric patterns that affect precipitation and streamflow. The solar energy reaching the Earth's surface and its oceans is thought to be controlled through an interaction between TSI and GCRs, which are theorized to ionize the atmosphere and increase cloud formation and its resultant albedo. High (low) GCR flux may promote cloudiness (clear skies) and higher (lower) albedo at the same time that TSI is lowest (highest) in the solar cycle which in turn creates cooler (warmer) ocean temperature anomalies. These anomalies have been shown to affect atmospheric flow patterns and ultimately affect precipitation over the Midwestern United States. This investigation identified a relation among TSI and geomagnetic index aa (GI-AA), and streamflow in the Mississippi River Basin for the period 1878-2004. The GI-AA was used as a proxy for GCRs. The lag time between the solar signal and streamflow in the Mississippi River at St. Louis, Missouri is approximately 34 years. The current drought (1999-2007) in the Mississippi River Basin appears to be caused by a period of lower solar activity that occurred between 1963 and 1977. There appears to be a solar "fingerprint" that can be detected in climatic time series in other regions of the world, with each series having a unique lag time between the solar signal and the hydroclimatic response. A progression of increasing lag times can be spatially linked to the ocean conveyor belt, which may transport the solar signal over a time span of several decades. The lag times for any one region vary slightly and may be linked to the fluctuations in the velocity of the ocean conveyor belt.

LAMP2GO

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

Priye, Aashish

2017-06-08

The app is a unique image analysis software and acts as a fluorescence reader for multiplexed nucleic acid amplification reactions. If the reaction is positive, a bright fluorescent signal is emitted from the solution depending on the choice of fluorophore molecule. The app reads the Red, blue and green (RGB) channels of the emitted signal and transforms it to yield the chromaticity (x and y) and luminance of the signal. This new representation of signal is far superior to the RGB system in determining the signal color and intensity.

In-lab versus at-home activity recognition in ambulatory subjects with incomplete spinal cord injury.

PubMed

Albert, Mark V; Azeze, Yohannes; Courtois, Michael; Jayaraman, Arun

2017-02-06

Although commercially available activity trackers can aid in tracking therapy and recovery of patients, most devices perform poorly for patients with irregular movement patterns. Standard machine learning techniques can be applied on recorded accelerometer signals in order to classify the activities of ambulatory subjects with incomplete spinal cord injury in a way that is specific to this population and the location of the recording-at home or in the clinic. Subjects were instructed to perform a standardized set of movements while wearing a waist-worn accelerometer in the clinic and at-home. Activities included lying, sitting, standing, walking, wheeling, and stair climbing. Multiple classifiers and validation methods were used to quantify the ability of the machine learning techniques to distinguish the activities recorded in-lab or at-home. In the lab, classifiers trained and tested using within-subject cross-validation provided an accuracy of 91.6%. When the classifier was trained on data collected in the lab but tested on at home data, the accuracy fell to 54.6% indicating distinct movement patterns between locations. However, the accuracy of the at-home classifications, when training the classifier with at-home data, improved to 85.9%. Individuals with unique movement patterns can benefit from using tailored activity recognition algorithms easily implemented using modern machine learning methods on collected movement data.

Signaling hierarchy regulating human endothelial cell development

USDA-ARS?s Scientific Manuscript database

Our present knowledge of the regulation of mammalian endothelial cell differentiation has been largely derived from studies of mouse embryonic development. However, unique mechanisms and hierarchy of signals that govern human endothelial cell development are unknown and, thus, explored in these stud...

Systematic analysis of gene expression pattern in has-miR-197 over-expressed human uterine leiomyoma cells.

PubMed

Ling, Jing; Wu, Xiaoli; Fu, Ziyi; Tan, Jie; Xu, Qing

2015-10-01

Our previous study showed that the expression of miR-197 in leiomyoma was down-regulated compared with myometrium. Further, miR-197 has been identified to affect uterine leiomyoma cell proliferation, apoptosis, and metastasis ability, though the responsible molecular mechanism has not been well elucidated. In this study, we sought to determine the expression patterns of miR-197 targeted genes and to explore their potential functions, participating Pathways and the networks that are involved in the biological behavior of human uterine leiomyoma. After transfection of human uterine leiomyoma cells with miR-197, we confirmed the expression level of miR-197 using quantitative real-time PCR (qRT-PCR), and we detected the gene expression profiles after miR-197 over-expression through DNA microarray analysis. Further, we performed GO and Pathway analysis. The dominantly dys-regulated genes, which were up- or down-regulated by more than 10-fold, compared with parental cells, were confirmed using qRT-PCR technology. Compared with the control group, miR-197 was up-regulated by 30-fold after miR-197 lentiviral transfection. The microarray data showed that 872 genes were dys-regulated by more than 2-fold in human uterine leiomyoma cells after miR-197 overexpression, including 537 up-regulated and 335 down-regulated genes. The GO analysis indicated that the dys-regulated genes were primarily involved in response to stimuli, multicellular organ processes, and the signaling of biological progression. Further, Pathway analysis data showed that these genes participated in regulating several signaling Pathways, including the JAK/STAT signaling Pathway, the Toll-like receptor signaling Pathway, and cytokine-cytokine receptor interaction. The qRT-PCR results confirmed that 17 of the 66 selected genes, which were up- or down-regulated more than 10-fold by miR-197, were consistent with the microarray results, including tumorigenesis-related genes, such as DRT7, SLC549, SFMBT2, FLJ37956, FBLN2, C10orf35, HOXD12, CACNG7, and LOC100134279. Our study explored gene expression patterns after miR-197 overexpression and confirmed 17 dominantly dys-regulated genes, which could expand the insights into the function of miR-197 and the molecular mechanisms during the development and progression of uterine leiomyomas. This study might afford new clues for understanding the pathogenesis of uterine leiomyomas, and it could likely provide a unique method for diagnosing or predicting prognosis in the clinical treatment of leiomyoma. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Integrated β-catenin, BMP, PTEN, and Notch signalling patterns the nephron

PubMed Central

Lindström, Nils O; Lawrence, Melanie L; Burn, Sally F; Johansson, Jeanette A; Bakker, Elvira RM; Ridgway, Rachel A; Chang, C-Hong; Karolak, Michele J; Oxburgh, Leif; Headon, Denis J; Sansom, Owen J; Smits, Ron; Davies, Jamie A; Hohenstein, Peter

2015-01-01

The different segments of the nephron and glomerulus in the kidney balance the processes of water homeostasis, solute recovery, blood filtration, and metabolite excretion. When segment function is disrupted, a range of pathological features are presented. Little is known about nephron patterning during embryogenesis. In this study, we demonstrate that the early nephron is patterned by a gradient in β-catenin activity along the axis of the nephron tubule. By modifying β-catenin activity, we force cells within nephrons to differentiate according to the imposed β-catenin activity level, thereby causing spatial shifts in nephron segments. The β-catenin signalling gradient interacts with the BMP pathway which, through PTEN/PI3K/AKT signalling, antagonises β-catenin activity and promotes segment identities associated with low β-catenin activity. β-catenin activity and PI3K signalling also integrate with Notch signalling to control segmentation: modulating β-catenin activity or PI3K rescues segment identities normally lost by inhibition of Notch. Our data therefore identifies a molecular network for nephron patterning. DOI: http://dx.doi.org/10.7554/eLife.04000.001 PMID:25647637

Vascular pattern of the dentate gyrus is regulated by neural progenitors.

PubMed

Pombero, Ana; Garcia-Lopez, Raquel; Estirado, Alicia; Martinez, Salvador

2018-05-01

Neurogenesis is a vital process that begins during early embryonic development and continues until adulthood, though in the latter case, it is restricted to the subventricular zone and the subgranular zone of the dentate gyrus (DG). In particular, the DG's neurogenic properties are structurally and functionally unique, which may be related to its singular vascular pattern. Neurogenesis and angiogenesis share molecular signals and act synergistically, supporting the concept of a neurogenic niche as a functional unit between neural precursors cells and their environment, in which the blood vessels play an important role. Whereas it is well known that vascular development controls neural proliferation in the embryonary and in the adult brain, by releasing neurotrophic factors; the potential influence of neural cells on vascular components during angiogenesis is largely unknown. We have demonstrated that the reduction of neural progenitors leads to a significant impairment of vascular development. Since VEGF is a potential regulator in the neurogenesis-angiogenesis crosstalk, we were interested in assessing the possible role of this molecule in the hippocampal neurovascular development. Our results showed that VEGF is the molecule involved in the regulation of vascular development by neural progenitor cells in the DG.

Visualizing fossilization using laser ablation-inductively coupled plasma-mass spectrometry maps of trace elements in Late Cretaceous bones

USGS Publications Warehouse

Koenig, A.E.; Rogers, R.R.; Trueman, C.N.

2009-01-01

Elemental maps generated by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) provide a previously unavailable high-resolution visualization of the complex physicochemical conditions operating within individual bones during the early stages of diagenesis and fossilization. A selection of LA-ICP-MS maps of bones collected from the Late Cretaceous of Montana (United States) and Madagascar graphically illustrate diverse paths to recrystallization, and reveal unique insights into geochemical aspects of taphonomic history. Some bones show distinct gradients in concentrations of rare earth elements and uranium, with highest concentrations at external bone margins. Others exhibit more intricate patterns of trace element uptake related to bone histology and its control on the flow paths of pore waters. Patterns of element uptake as revealed by LA-ICP-MS maps can be used to guide sampling strategies, and call into question previous studies that hinge upon localized bulk samples of fossilized bone tissue. LA-ICP-MS maps also allow for comparison of recrystallization rates among fossil bones, and afford a novel approach to identifying bones or regions of bones potentially suitable for extracting intact biogeochemical signals. ?? 2009 Geological Society of America.

Data-driven inference of network connectivity for modeling the dynamics of neural codes in the insect antennal lobe

PubMed Central

Shlizerman, Eli; Riffell, Jeffrey A.; Kutz, J. Nathan

2014-01-01

The antennal lobe (AL), olfactory processing center in insects, is able to process stimuli into distinct neural activity patterns, called olfactory neural codes. To model their dynamics we perform multichannel recordings from the projection neurons in the AL driven by different odorants. We then derive a dynamic neuronal network from the electrophysiological data. The network consists of lateral-inhibitory neurons and excitatory neurons (modeled as firing-rate units), and is capable of producing unique olfactory neural codes for the tested odorants. To construct the network, we (1) design a projection, an odor space, for the neural recording from the AL, which discriminates between distinct odorants trajectories (2) characterize scent recognition, i.e., decision-making based on olfactory signals and (3) infer the wiring of the neural circuit, the connectome of the AL. We show that the constructed model is consistent with biological observations, such as contrast enhancement and robustness to noise. The study suggests a data-driven approach to answer a key biological question in identifying how lateral inhibitory neurons can be wired to excitatory neurons to permit robust activity patterns. PMID:25165442

Enhancement of Stereo Imagery by Artificial Texture Projection Generated Using a LIDAR

NASA Astrophysics Data System (ADS)

Veitch-Michaelis, Joshua; Muller, Jan-Peter; Walton, David; Storey, Jonathan; Foster, Michael; Crutchley, Benjamin

2016-06-01

Passive stereo imaging is capable of producing dense 3D data, but image matching algorithms generally perform poorly on images with large regions of homogenous texture due to ambiguous match costs. Stereo systems can be augmented with an additional light source that can project some form of unique texture onto surfaces in the scene. Methods include structured light, laser projection through diffractive optical elements, data projectors and laser speckle. Pattern projection using lasers has the advantage of producing images with a high signal to noise ratio. We have investigated the use of a scanning visible-beam LIDAR to simultaneously provide enhanced texture within the scene and to provide additional opportunities for data fusion in unmatched regions. The use of a LIDAR rather than a laser alone allows us to generate highly accurate ground truth data sets by scanning the scene at high resolution. This is necessary for evaluating different pattern projection schemes. Results from LIDAR generated random dots are presented and compared to other texture projection techniques. Finally, we investigate the use of image texture analysis to intelligently project texture where it is required while exploiting the texture available in the ambient light image.

Hot on the Trail of Genes that Shape Our Fingerprints.

PubMed

Walsh, Susan; Pośpiech, Ewelina; Branicki, Wojciech

2016-04-01

Fingerprint patterns have been associated with their ability to identify an individual uniquely, but can uniqueness be understood genetically? Ho et al. point out some key variants that may be responsible for some of the concentric patterns that are observed in digital skin. Furthermore, they propose that one highly associated gene, ADAMTS9-AS2, has a role in epigenetic regulation, a role that may be important in early-stage digit development. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Behavioral and Single-Neuron Sensitivity to Millisecond Variations in Temporally Patterned Communication Signals

PubMed Central

Baker, Christa A.; Ma, Lisa; Casareale, Chelsea R.

2016-01-01

In many sensory pathways, central neurons serve as temporal filters for timing patterns in communication signals. However, how a population of neurons with diverse temporal filtering properties codes for natural variation in communication signals is unknown. Here we addressed this question in the weakly electric fish Brienomyrus brachyistius, which varies the time intervals between successive electric organ discharges to communicate. These fish produce an individually stereotyped signal called a scallop, which consists of a distinctive temporal pattern of ∼8–12 electric pulses. We manipulated the temporal structure of natural scallops during behavioral playback and in vivo electrophysiology experiments to probe the temporal sensitivity of scallop encoding and recognition. We found that presenting time-reversed, randomized, or jittered scallops increased behavioral response thresholds, demonstrating that fish's electric signaling behavior was sensitive to the precise temporal structure of scallops. Next, using in vivo intracellular recordings and discriminant function analysis, we found that the responses of interval-selective midbrain neurons were also sensitive to the precise temporal structure of scallops. Subthreshold changes in membrane potential recorded from single neurons discriminated natural scallops from time-reversed, randomized, and jittered sequences. Pooling the responses of multiple neurons improved the discriminability of natural sequences from temporally manipulated sequences. Finally, we found that single-neuron responses were sensitive to interindividual variation in scallop sequences, raising the question of whether fish may analyze scallop structure to gain information about the sender. Collectively, these results demonstrate that a population of interval-selective neurons can encode behaviorally relevant temporal patterns with millisecond precision. SIGNIFICANCE STATEMENT The timing patterns of action potentials, or spikes, play important roles in representing information in the nervous system. However, how these temporal patterns are recognized by downstream neurons is not well understood. Here we use the electrosensory system of mormyrid weakly electric fish to investigate how a population of neurons with diverse temporal filtering properties encodes behaviorally relevant input timing patterns, and how this relates to behavioral sensitivity. We show that fish are behaviorally sensitive to millisecond variations in natural, temporally patterned communication signals, and that the responses of individual midbrain neurons are also sensitive to variation in these patterns. In fact, the output of single neurons contains enough information to discriminate stereotyped communication signals produced by different individuals. PMID:27559179

Behavioral and Single-Neuron Sensitivity to Millisecond Variations in Temporally Patterned Communication Signals.

PubMed

Baker, Christa A; Ma, Lisa; Casareale, Chelsea R; Carlson, Bruce A

2016-08-24

In many sensory pathways, central neurons serve as temporal filters for timing patterns in communication signals. However, how a population of neurons with diverse temporal filtering properties codes for natural variation in communication signals is unknown. Here we addressed this question in the weakly electric fish Brienomyrus brachyistius, which varies the time intervals between successive electric organ discharges to communicate. These fish produce an individually stereotyped signal called a scallop, which consists of a distinctive temporal pattern of ∼8-12 electric pulses. We manipulated the temporal structure of natural scallops during behavioral playback and in vivo electrophysiology experiments to probe the temporal sensitivity of scallop encoding and recognition. We found that presenting time-reversed, randomized, or jittered scallops increased behavioral response thresholds, demonstrating that fish's electric signaling behavior was sensitive to the precise temporal structure of scallops. Next, using in vivo intracellular recordings and discriminant function analysis, we found that the responses of interval-selective midbrain neurons were also sensitive to the precise temporal structure of scallops. Subthreshold changes in membrane potential recorded from single neurons discriminated natural scallops from time-reversed, randomized, and jittered sequences. Pooling the responses of multiple neurons improved the discriminability of natural sequences from temporally manipulated sequences. Finally, we found that single-neuron responses were sensitive to interindividual variation in scallop sequences, raising the question of whether fish may analyze scallop structure to gain information about the sender. Collectively, these results demonstrate that a population of interval-selective neurons can encode behaviorally relevant temporal patterns with millisecond precision. The timing patterns of action potentials, or spikes, play important roles in representing information in the nervous system. However, how these temporal patterns are recognized by downstream neurons is not well understood. Here we use the electrosensory system of mormyrid weakly electric fish to investigate how a population of neurons with diverse temporal filtering properties encodes behaviorally relevant input timing patterns, and how this relates to behavioral sensitivity. We show that fish are behaviorally sensitive to millisecond variations in natural, temporally patterned communication signals, and that the responses of individual midbrain neurons are also sensitive to variation in these patterns. In fact, the output of single neurons contains enough information to discriminate stereotyped communication signals produced by different individuals. Copyright © 2016 the authors 0270-6474/16/368985-16$15.00/0.

Hedgehog signaling regulates segment formation in the annelid Platynereis.

PubMed

Dray, Nicolas; Tessmar-Raible, Kristin; Le Gouar, Martine; Vibert, Laura; Christodoulou, Foteini; Schipany, Katharina; Guillou, Aurélien; Zantke, Juliane; Snyman, Heidi; Béhague, Julien; Vervoort, Michel; Arendt, Detlev; Balavoine, Guillaume

2010-07-16

Annelids and arthropods share a similar segmented organization of the body whose evolutionary origin remains unclear. The Hedgehog signaling pathway, prominent in arthropod embryonic segment patterning, has not been shown to have a similar function outside arthropods. We show that the ligand Hedgehog, the receptor Patched, and the transcription factor Gli are all expressed in striped patterns before the morphological appearance of segments in the annelid Platynereis dumerilii. Treatments with small molecules antagonistic to Hedgehog signaling disrupt segment formation. Platynereis Hedgehog is not necessary to establish early segment patterns but is required to maintain them. The molecular similarity of segment patterning functions of the Hedgehog pathway in an annelid and in arthropods supports a common origin of segmentation in protostomes.

Investigating Patterns for Self-Induced Emotion Recognition from EEG Signals.

PubMed

Zhuang, Ning; Zeng, Ying; Yang, Kai; Zhang, Chi; Tong, Li; Yan, Bin

2018-03-12

Most current approaches to emotion recognition are based on neural signals elicited by affective materials such as images, sounds and videos. However, the application of neural patterns in the recognition of self-induced emotions remains uninvestigated. In this study we inferred the patterns and neural signatures of self-induced emotions from electroencephalogram (EEG) signals. The EEG signals of 30 participants were recorded while they watched 18 Chinese movie clips which were intended to elicit six discrete emotions, including joy, neutrality, sadness, disgust, anger and fear. After watching each movie clip the participants were asked to self-induce emotions by recalling a specific scene from each movie. We analyzed the important features, electrode distribution and average neural patterns of different self-induced emotions. Results demonstrated that features related to high-frequency rhythm of EEG signals from electrodes distributed in the bilateral temporal, prefrontal and occipital lobes have outstanding performance in the discrimination of emotions. Moreover, the six discrete categories of self-induced emotion exhibit specific neural patterns and brain topography distributions. We achieved an average accuracy of 87.36% in the discrimination of positive from negative self-induced emotions and 54.52% in the classification of emotions into six discrete categories. Our research will help promote the development of comprehensive endogenous emotion recognition methods.

Investigating Patterns for Self-Induced Emotion Recognition from EEG Signals

PubMed Central

Zeng, Ying; Yang, Kai; Tong, Li; Yan, Bin

2018-01-01

Most current approaches to emotion recognition are based on neural signals elicited by affective materials such as images, sounds and videos. However, the application of neural patterns in the recognition of self-induced emotions remains uninvestigated. In this study we inferred the patterns and neural signatures of self-induced emotions from electroencephalogram (EEG) signals. The EEG signals of 30 participants were recorded while they watched 18 Chinese movie clips which were intended to elicit six discrete emotions, including joy, neutrality, sadness, disgust, anger and fear. After watching each movie clip the participants were asked to self-induce emotions by recalling a specific scene from each movie. We analyzed the important features, electrode distribution and average neural patterns of different self-induced emotions. Results demonstrated that features related to high-frequency rhythm of EEG signals from electrodes distributed in the bilateral temporal, prefrontal and occipital lobes have outstanding performance in the discrimination of emotions. Moreover, the six discrete categories of self-induced emotion exhibit specific neural patterns and brain topography distributions. We achieved an average accuracy of 87.36% in the discrimination of positive from negative self-induced emotions and 54.52% in the classification of emotions into six discrete categories. Our research will help promote the development of comprehensive endogenous emotion recognition methods. PMID:29534515

Variable environmental effects on a multicomponent sexually selected trait.

PubMed

Cole, Gemma L; Endler, John A

2015-04-01

Multicomponent signals are made up of interacting elements that generate a functional signaling unit. The interactions between signal components and their effects on individual fitness are not well understood, and the effect of environment is even less so. It is usually assumed that color patterns appear the same in all light environments and that the effects of each color are additive. Using guppies, Poecilia reticulata, we investigated the effect of water color on the interactions between components of sexually selected male coloration. Through behavioral mate choice trials in four different water colors, we estimated the attractiveness of male color patterns, using multivariate fitness estimates and overall signal contrast. Our results show that females exhibit preferences that favor groups of colors rather than individual colors independently and that each environment favors different color combinations. We found that these effects are consistent with female guppies selecting entire color patterns on the basis of overall visual contrast. This suggests that both individuals and populations inhabiting different light environments will be subject to divergent, multivariate selection. Although the appearance of color patterns changes with light environment, achromatic components change little, suggesting that these could function in species recognition or other aspects of communication that must work across environments. Consequently, we predict different phylogenetic patterns between chromatic and achromatic signals within the same clades.

Method and Apparatus for Reducing Noise from Near Ocean Surface Sources

DTIC Science & Technology

2001-10-01

reducing the acoustic noise from near-surface 4 sources using an array processing technique that utilizes 5 Multiple Signal Classification ( MUSIC ...sources without 13 degrading the signal level and quality of the TOI. The present 14 invention utilizes a unique application of the MUSIC beamforming...specific algorithm that utilizes a 5 MUSIC technique and estimates the direction of arrival (DOA) of 6 the acoustic signal signals and generates output

An equilibrium-point model of electromyographic patterns during single-joint movements based on experimentally reconstructed control signals.

PubMed

Latash, M L; Goodman, S R

1994-01-01

The purpose of this work has been to develop a model of electromyographic (EMG) patterns during single-joint movements based on a version of the equilibrium-point hypothesis, a method for experimental reconstruction of the joint compliant characteristics, the dual-strategy hypothesis, and a kinematic model of movement trajectory. EMG patterns are considered emergent properties of hypothetical control patterns that are equally affected by the control signals and peripheral feedback reflecting actual movement trajectory. A computer model generated the EMG patterns based on simulated movement kinematics and hypothetical control signals derived from the reconstructed joint compliant characteristics. The model predictions have been compared to published recordings of movement kinematics and EMG patterns in a variety of movement conditions, including movements over different distances, at different speeds, against different-known inertial loads, and in conditions of possible unexpected decrease in the inertial load. Changes in task parameters within the model led to simulated EMG patterns qualitatively similar to the experimentally recorded EMG patterns. The model's predictive power compares it favourably to the existing models of the EMG patterns. Copyright © 1994. Published by Elsevier Ltd.

Usefullness of palatal rugae patterns in establishing identity: Preliminary results from Bengaluru city, India

PubMed Central

Indira, AP; Gupta, Manish; David, Maria Priscilla

2012-01-01

Introduction: Palatal rugoscopy is the name given to the study of palatal rugae. Rugae pattern are widely considered to remain unchanged during an individual's lifetime. The rugae pattern has the potential to remain intact by virtue of their internal position in the head when most other anatomical structures are destroyed or burned. Moreover, rugae pattern are considered to be unique similar to fingerprints and are advocated in personal identification. Objectives: The purpose of the study is to establish, individual identity using palatal rugae patterns. Materials and Methods: The study group consisted of 100 study models all of whom were subjects above 14 years old. Martin dos Santos’ classification was followed based on form and position to assess the individuality of rugae pattern. Results: Each individual had different rugae patterns including dizygous twins and the rugae patterns were not symmetrical, both in number and in its distribution. Conclusion: The preliminary study undertaken here shows no two palates are alike in terms of their rugae pattern. Palatal rugae possess unique characteristics as they are absolutely individualistic and therefore, can be used as a personal soft-tissue ‘oral’ print for identification in forensic cases. PMID:23087574

β-catenin-mediated Wnt signaling regulates neurogenesis in the ventral telencephalon

PubMed Central

Gulacsi, Alexandra A.; Anderson, Stewart A.

2009-01-01

Development of the telencephalon involves the coordinated growth of diversely patterned brain structures. Previous studies have demonstrated the importance of β-catenin-mediated Wnt signaling in proliferation and fate determination during cerebral cortical development. In this paper, we present novel evidence that β-catenin-mediated Wnt signaling also critically maintains progenitor proliferation in the subcortical (pallidal) telencephalon of mice. Targeted deletion of β-catenin severely impairs proliferation in the medial ganglionic eminence without grossly altering differentiated fate. Several lines of evidence suggest that this phenotype is primarily due to loss of canonical Wnt signaling. As previous studies have suggested that the ventral patterning factor Shh also stimulates dorsal telencephalic proliferation, we propose a model whereby Wnt and Shh signaling promote distinct dorsal-ventral patterning, while also having broader effects on proliferation that serve to coordinate the growth of telencephalic subregions. PMID:18997789

APEX_SCOPE: A graphical user interface for visualization of multi-modal data in inter-disciplinary studies.

PubMed

Kanbar, Lara J; Shalish, Wissam; Precup, Doina; Brown, Karen; Sant'Anna, Guilherme M; Kearney, Robert E

2017-07-01

In multi-disciplinary studies, different forms of data are often collected for analysis. For example, APEX, a study on the automated prediction of extubation readiness in extremely preterm infants, collects clinical parameters and cardiorespiratory signals. A variety of cardiorespiratory metrics are computed from these signals and used to assign a cardiorespiratory pattern at each time. In such a situation, exploratory analysis requires a visualization tool capable of displaying these different types of acquired and computed signals in an integrated environment. Thus, we developed APEX_SCOPE, a graphical tool for the visualization of multi-modal data comprising cardiorespiratory signals, automated cardiorespiratory metrics, automated respiratory patterns, manually classified respiratory patterns, and manual annotations by clinicians during data acquisition. This MATLAB-based application provides a means for collaborators to view combinations of signals to promote discussion, generate hypotheses and develop features.

Signaling mechanisms underlying the robustness and tunability of the plant immune network

PubMed Central

Kim, Yungil; Tsuda, Kenichi; Igarashi, Daisuke; Hillmer, Rachel A.; Sakakibara, Hitoshi; Myers, Chad L.; Katagiri, Fumiaki

2014-01-01

Summary How does robust and tunable behavior emerge in a complex biological network? We sought to understand this for the signaling network controlling pattern-triggered immunity (PTI) in Arabidopsis. A dynamic network model containing four major signaling sectors, the jasmonate, ethylene, PAD4, and salicylate sectors, which together explain up to 80% of the PTI level, was built using data for dynamic sector activities and PTI levels under exhaustive combinatorial sector perturbations. Our regularized multiple regression model had a high level of predictive power and captured known and unexpected signal flows in the network. The sole inhibitory sector in the model, the ethylene sector, was central to the network robustness via its inhibition of the jasmonate sector. The model's multiple input sites linked specific signal input patterns varying in strength and timing to different network response patterns, indicating a mechanism enabling tunability. PMID:24439900

Nodal patterning without Lefty inhibitory feedback is functional but fragile

PubMed Central

Gagnon, James A; Pauli, Andrea; Zimmerman, Steven; Aksel, Deniz C; Reyon, Deepak; Tsai, Shengdar Q; Joung, J Keith

2017-01-01

Developmental signaling pathways often activate their own inhibitors. Such inhibitory feedback has been suggested to restrict the spatial and temporal extent of signaling or mitigate signaling fluctuations, but these models are difficult to rigorously test. Here, we determine whether the ability of the mesendoderm inducer Nodal to activate its inhibitor Lefty is required for development. We find that zebrafish lefty mutants exhibit excess Nodal signaling and increased specification of mesendoderm, resulting in embryonic lethality. Strikingly, development can be fully restored without feedback: Lethal patterning defects in lefty mutants can be rescued by ectopic expression of lefty far from its normal expression domain or by spatially and temporally uniform exposure to a Nodal inhibitor drug. While drug-treated mutants are less tolerant of mild perturbations to Nodal signaling levels than wild type embryos, they can develop into healthy adults. These results indicate that patterning without inhibitory feedback is functional but fragile. PMID:29215332

Signal detection by means of orthogonal decomposition

NASA Astrophysics Data System (ADS)

Hajdu, C. F.; Dabóczi, T.; Péceli, G.; Zamantzas, C.

2018-03-01

Matched filtering is a well-known method frequently used in digital signal processing to detect the presence of a pattern in a signal. In this paper, we suggest a time variant matched filter, which, unlike a regular matched filter, maintains a given alignment between the input signal and the template carrying the pattern, and can be realized recursively. We introduce a method to synchronize the two signals for presence detection, usable in case direct synchronization between the signal generator and the receiver is not possible or not practical. We then propose a way of realizing and extending the same filter by modifying a recursive spectral observer, which gives rise to orthogonal filter channels and also leads to another way to synchronize the two signals.

Tactile Sensing with Whiskers of Various Shapes: Determining the Three-Dimensional Location of Object Contact Based on Mechanical Signals at the Whisker Base.

PubMed

Huet, Lucie A; Rudnicki, John W; Hartmann, Mitra J Z

2017-06-01

Almost all mammals use their mystacial vibrissae (whiskers) as important tactile sensors. There are no sensors along the length of a whisker: all sensing is performed by mechanoreceptors at the whisker base. To use artificial whiskers as a sensing tool in robotics, it is essential to be able to determine the three-dimensional (3D) location at which a whisker has made contact with an object. With the assumption of quasistatic, frictionless, single-point contact, previous work demonstrated that the 3D contact point can be uniquely determined if all six components of force and moment are measured at the whisker base, but these measurements require a six-axis load cell. Here, we perform simulations to investigate the extent to which each of the 20 possible "triplet" combinations of the six mechanical signals at the whisker base uniquely determine 3D contact point location. We perform this analysis for four different whisker profiles (shapes): tapered with and without intrinsic curvature, and cylindrical with and without intrinsic curvature. We show that whisker profile has a strong influence on the particular triplet(s) of signals that uniquely map to the 3D contact point. The triplet of bending moment, bending moment direction, and axial force produces unique mappings for tapered whiskers. Four different mappings are unique for a cylindrical whisker without intrinsic curvature, but only when large deflections are excluded. These results inform the neuroscience of vibrissotactile sensing and represent an important step toward the development of artificial whiskers for robotic applications.

The STAT3-Ser/Hes3 signaling axis: an emerging regulator of endogenous regeneration and cancer growth

PubMed Central

Poser, Steven W.; Park, Deric M.; Androutsellis-Theotokis, Andreas

2013-01-01

Stem cells, by definition, are able to both self-renew (give rise to more cells of their own kind) and demonstrate multipotential (the ability to differentiate into multiple cell types). To accommodate this unique dual ability, stem cells interpret signal transduction pathways in specialized ways. Notable examples include canonical and non-canonical branches of the Notch signaling pathway, with each controlling different downstream targets (e.g., Hes1 vs. Hes3) and promoting either differentiation or self-renewal. Similarly, stem cells utilize STAT3 signaling uniquely. Most mature cells studied thus far rely on tyrosine phosphorylation (STAT3-Tyr) to promote survival and growth; in contrast, STAT3-Tyr induces the differentiation of neural stem cells (NSCs). NSCs use an alternative phosphorylation site, STAT3-Ser, to regulate survival and growth, a site that is largely redundant for this function in most other cell types. STAT3-Ser regulates Hes3, and together they form a convergence point for several signals, including Notch, Tie2, and insulin receptor activation. Disregulation and manipulation of the STAT3-Ser/Hes3 signaling pathway is important in both tumorigenesis and regenerative medicine, and worthy of extensive study. PMID:24101906

Notch-signalling is required for head regeneration and tentacle patterning in Hydra.

PubMed

Münder, Sandra; Tischer, Susanne; Grundhuber, Maresa; Büchels, Nathalie; Bruckmeier, Nadine; Eckert, Stefanie; Seefeldt, Carolin A; Prexl, Andrea; Käsbauer, Tina; Böttger, Angelika

2013-11-01

Local self-activation and long ranging inhibition provide a mechanism for setting up organising regions as signalling centres for the development of structures in the surrounding tissue. The adult hydra hypostome functions as head organiser. After hydra head removal it is newly formed and complete heads can be regenerated. The molecular components of this organising region involve Wnt-signalling and β-catenin. However, it is not known how correct patterning of hypostome and tentacles are achieved in the hydra head and whether other signals in addition to HyWnt3 are needed for re-establishing the new organiser after head removal. Here we show that Notch-signalling is required for re-establishing the organiser during regeneration and that this is due to its role in restricting tentacle activation. Blocking Notch-signalling leads to the formation of irregular head structures characterised by excess tentacle tissue and aberrant expression of genes that mark the tentacle boundaries. This indicates a role for Notch-signalling in defining the tentacle pattern in the hydra head. Moreover, lateral inhibition by HvNotch and its target HyHes are required for head regeneration and without this the formation of the β-catenin/Wnt dependent head organiser is impaired. Work on prebilaterian model organisms has shown that the Wnt-pathway is important for setting up signalling centres for axial patterning in early multicellular animals. Our data suggest that the integration of Wnt-signalling with Notch-Delta activity was also involved in the evolution of defined body plans in animals. © 2013 Elsevier Inc. All rights reserved.

Analysis of 14-3-3 Family Member Function in Xenopus Embryos by Microinjection of Antisense Morpholino Oligos

NASA Astrophysics Data System (ADS)

Lau, Jeffrey M. C.; Muslin, Anthony J.

The 14-3-3 intracellular phosphoserine/threonine-binding proteins are adapter molecules that regulate signal transduction, cell cycle, nutrient sensing, apoptotic, and cytoskeletal pathways. There are seven 14-3-3 family members, encoded by separate genes, in vertebrate organisms. To evaluate the role of individual 14-3-3 proteins in vertebrate embryonic development, we utilized an antisense morpholino oligo microinjection technique in Xenopus laevis embryos. By use of this method, we showed that embryos lacking specific 14-3-3 proteins displayed unique phenotypic abnormalities. Specifically, embryos lacking 14-3-3 τ exhibited gastrulation and axial patterning defects, but embryos lacking 14-3-3 γ exhibited eye defects without other abnormalities, and embryos lacking 14-3-3 ζ appeared completely normal. These and other results demonstrate the power and specificity of the morpholino antisense oligo microinjection technique.

Category-dependent and category-independent goal-value codes in human ventromedial prefrontal cortex

PubMed Central

McNamee, Daniel; Rangel, Antonio; O’Doherty, John P

2013-01-01

To choose between manifestly distinct options, it is suggested that the brain assigns values to goals using a common currency. Although previous studies have reported activity in ventromedial prefrontal cortex (vmPFC) correlating with the value of different goal stimuli, it remains unclear whether such goal-value representations are independent of the associated stimulus categorization, as required by a common currency. Using multivoxel pattern analyses on functional magnetic resonance imaging (fMRI) data, we found a region of medial prefrontal cortex to contain a distributed goal-value code that is independent of stimulus category. More ventrally in the vmPFC, we found spatially distinct areas of the medial orbitofrontal cortex to contain unique category-dependent distributed value codes for food and consumer items. These results implicate the medial prefrontal cortex in the implementation of a common currency and suggest a ventral versus dorsal topographical organization of value signals in the vmPFC. PMID:23416449

Two-Dimensional Titanium Carbide (MXene) as Surface-Enhanced Raman Scattering Substrate

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

Sarycheva, Asia; Makaryan, Taron; Maleski, Kathleen

Here, noble metal (gold or silver) nanoparticles or patterned films are typically used as substrates for surface-enhanced Raman spectroscopy (SERS). Two-dimensional (2D) carbides and nitrides (MXenes) exhibit unique electronic and optical properties, including metallic conductivity and plasmon resonance in the visible or near-infrared range, making them promising candidates for a wide variety of applications. Herein, we show that 2D titanium carbide, Ti 3C 2T x, enhances Raman signal from organic dyes on a substrate and in solution. As a proof of concept, MXene SERS substrates were manufactured by spray-coating and used to detect several common dyes, with calculated enhancement factorsmore » reaching ~10 6. Titanium carbide MXene demonstrates SERS effect in aqueous colloidal solutions, suggesting the potential for biomedical or environmental applications, where MXene can selectively enhance positively charged molecules.« less

Framing the nicotine debate: a cultural approach to risk.

PubMed

Murphy, P

2001-01-01

This study examined Congressional testimony concerning regulation of tobacco advertising by 3 policy factions representing industry, government, and lay activists. On the basis of the cultural theory of risk, policy disputants were divided into entrepreneurial, bureaucratic, and egalitarian communities, each with a distinct cosmology that impedes discourse among the groups. The authors examined ways in which the 3 policy factions framed the tobacco advertising issues to see the extent to which such unique cosmologies were expressed or whether mutual frames might signal opportunities for negotiation among the interest groups. Major themes in the testimony were identified through semantic network analysis and clustering of associated words that revealed discourse patterns peculiar to each group and reflective of their cultural biases toward health risk. Semantic network analysis can be a tool to clarify these presuppositions and unmask relations among factions, thereby bridging policy solutions across interest groups.

Identification of embryonic pancreatic genes using Xenopus DNA microarrays.

PubMed

Hayata, Tadayoshi; Blitz, Ira L; Iwata, Nahoko; Cho, Ken W Y

2009-06-01

The pancreas is both an exocrine and endocrine endodermal organ involved in digestion and glucose homeostasis. During embryogenesis, the anlagen of the pancreas arise from dorsal and ventral evaginations of the foregut that later fuse to form a single organ. To better understand the molecular genetics of early pancreas development, we sought to isolate markers that are uniquely expressed in this tissue. Microarray analysis was performed comparing dissected pancreatic buds, liver buds, and the stomach region of tadpole stage Xenopus embryos. A total of 912 genes were found to be differentially expressed between these organs during early stages of organogenesis. K-means clustering analysis predicted 120 of these genes to be specifically enriched in the pancreas. Of these, we report on the novel expression patterns of 24 genes. Our analyses implicate the involvement of previously unsuspected signaling pathways during early pancreas development. Developmental Dynamics 238:1455-1466, 2009. (c) 2009 Wiley-Liss, Inc.

Simultaneous overlay and CD measurement for double patterning: scatterometry and RCWA approach

NASA Astrophysics Data System (ADS)

Li, Jie; Liu, Zhuan; Rabello, Silvio; Dasari, Prasad; Kritsun, Oleg; Volkman, Catherine; Park, Jungchul; Singh, Lovejeet

2009-03-01

As optical lithography advances to 32 nm technology node and beyond, double patterning technology (DPT) has emerged as an attractive solution to circumvent the fundamental optical limitations. DPT poses unique demands on critical dimension (CD) uniformity and overlay control, making the tolerance decrease much faster than the rate at which critical dimension shrinks. This, in turn, makes metrology even more challenging. In the past, multi-pad diffractionbased overlay (DBO) using empirical approach has been shown to be an effective approach to measure overlay error associated with double patterning [1]. In this method, registration errors for double patterning were extracted from specially designed diffraction targets (three or four pads for each direction); CD variation is assumed negligible within each group of adjacent pads and not addressed in the measurement. In another paper, encouraging results were reported with a first attempt at simultaneously extracting overlay and CD parameters using scatterometry [2]. In this work, we apply scatterometry with a rigorous coupled wave analysis (RCWA) approach to characterize two double-patterning processes: litho-etch-litho-etch (LELE) and litho-freeze-litho-etch (LFLE). The advantage of performing rigorous modeling is to reduce the number of pads within each measurement target, thus reducing space requirement and improving throughput, and simultaneously extract CD and overlay information. This method measures overlay errors and CDs by fitting the optical signals with spectra calculated from a model of the targets. Good correlation is obtained between the results from this method and that of several reference techniques, including empirical multi-pad DBO, CD-SEM, and IBO. We also perform total measurement uncertainty (TMU) analysis to evaluate the overall performance. We demonstrate that scatterometry provides a promising solution to meet the challenging overlay metrology requirement in DPT.

The Intersection of the Extrinsic Hedgehog and WNT/Wingless Signals with the Intrinsic Hox Code Underpins Branching Pattern and Tube Shape Diversity in the Drosophila Airways

PubMed Central

Matsuda, Ryo; Hosono, Chie; Saigo, Kaoru; Samakovlis, Christos

2015-01-01

The tubular networks of the Drosophila respiratory system and our vasculature show distinct branching patterns and tube shapes in different body regions. These local variations are crucial for organ function and organismal fitness. Organotypic patterns and tube geometries in branched networks are typically controlled by variations of extrinsic signaling but the impact of intrinsic factors on branch patterns and shapes is not well explored. Here, we show that the intersection of extrinsic hedgehog(hh) and WNT/wingless (wg) signaling with the tube-intrinsic Hox code of distinct segments specifies the tube pattern and shape of the Drosophila airways. In the cephalic part of the airways, hh signaling induces expression of the transcription factor (TF) knirps (kni) in the anterior dorsal trunk (DTa1). kni represses the expression of another TF spalt major (salm), making DTa1 a narrow and long tube. In DTa branches of more posterior metameres, Bithorax Complex (BX-C) Hox genes autonomously divert hh signaling from inducing kni, thereby allowing DTa branches to develop as salm-dependent thick and short tubes. Moreover, the differential expression of BX-C genes is partly responsible for the anterior-to-posterior gradual increase of the DT tube diameter through regulating the expression level of Salm, a transcriptional target of WNT/wg signaling. Thus, our results highlight how tube intrinsic differential competence can diversify tube morphology without changing availabilities of extrinsic factors. PMID:25615601

Analysis of enamel rod end patterns on tooth surface for personal identification--ameloglyphics.

PubMed

Manjunath, Krishnappa; Sivapathasundharam, Balasundharam; Saraswathi, Thillai R

2012-05-01

Ameloglyphics is the study of enamel rod end patterns on a tooth surface. Our aim was to study the in vivo analysis of enamel rod end patterns on tooth surfaces for personal identification. In this study, the maxillary left canine and 1st premolar of 30 men and 30 women were included. The cellulose acetate peel technique was used to record enamel rod endings on tooth surfaces. Photomicrographs of the acetate peel imprint were subjected to VeriFinger Standard SDK v5.0 software for obtaining enamel rod end patterns. All 120 enamel rod end patterns were subjected to visual analysis and biometric analysis. Biometric analysis revealed that the enamel rod end pattern is unique for each tooth in an individual. It shows both intra- and interindividual variation. Enamel rod end patterns were unique between the male and female subjects. Visual analysis showed that wavy branched subpattern was the predominant subpattern observed among examined teeth. Hence, ameloglyphics is a reliable technique for personal identification. © 2012 American Academy of Forensic Sciences.

Detecting Signals of Disproportionate Reporting from Singapore's Spontaneous Adverse Event Reporting System: An Application of the Sequential Probability Ratio Test.

PubMed

Chan, Cheng Leng; Rudrappa, Sowmya; Ang, Pei San; Li, Shu Chuen; Evans, Stephen J W

2017-08-01

The ability to detect safety concerns from spontaneous adverse drug reaction reports in a timely and efficient manner remains important in public health. This paper explores the behaviour of the Sequential Probability Ratio Test (SPRT) and ability to detect signals of disproportionate reporting (SDRs) in the Singapore context. We used SPRT with a combination of two hypothesised relative risks (hRRs) of 2 and 4.1 to detect signals of both common and rare adverse events in our small database. We compared SPRT with other methods in terms of number of signals detected and whether labelled adverse drug reactions were detected or the reaction terms were considered serious. The other methods used were reporting odds ratio (ROR), Bayesian Confidence Propagation Neural Network (BCPNN) and Gamma Poisson Shrinker (GPS). The SPRT produced 2187 signals in common with all methods, 268 unique signals, and 70 signals in common with at least one other method, and did not produce signals in 178 cases where two other methods detected them, and there were 403 signals unique to one of the other methods. In terms of sensitivity, ROR performed better than other methods, but the SPRT method found more new signals. The performances of the methods were similar for negative predictive value and specificity. Using a combination of hRRs for SPRT could be a useful screening tool for regulatory agencies, and more detailed investigation of the medical utility of the system is merited.

Retinoic acid and Wnt/beta-catenin have complementary roles in anterior/posterior patterning embryos of the basal chordate amphioxus.

PubMed

Onai, Takayuki; Lin, Hsiu-Chin; Schubert, Michael; Koop, Demian; Osborne, Peter W; Alvarez, Susana; Alvarez, Rosana; Holland, Nicholas D; Holland, Linda Z

2009-08-15

A role for Wnt/beta-catenin signaling in axial patterning has been demonstrated in animals as basal as cnidarians, while roles in axial patterning for retinoic acid (RA) probably evolved in the deuterostomes and may be chordate-specific. In vertebrates, these two pathways interact both directly and indirectly. To investigate the evolutionary origins of interactions between these two pathways, we manipulated Wnt/beta-catenin and RA signaling in the basal chordate amphioxus during the gastrula stage, which is the RA-sensitive period for anterior/posterior (A/P) patterning. The results show that Wnt/beta-catenin and RA signaling have distinctly different roles in patterning the A/P axis of the amphioxus gastrula. Wnt/beta-catenin specifies the identity of the ends of the embryo (high Wnt = posterior; low Wnt = anterior) but not intervening positions. Thus, upregulation of Wnt/beta-catenin signaling induces ectopic expression of posterior markers at the anterior tip of the embryo. In contrast, RA specifies position along the A/P axis, but not the identity of the ends of the embryo-increased RA signaling strongly affects the domains of Hox expression along the A/P axis but has little or no effect on the expression of either anterior or posterior markers. Although the two pathways may both influence such things as specification of neuronal identity, interactions between them in A/P patterning appear to be minimal.

A comparison of facial color pattern and gazing behavior in canid species suggests gaze communication in gray wolves (Canis lupus).

PubMed

Ueda, Sayoko; Kumagai, Gaku; Otaki, Yusuke; Yamaguchi, Shinya; Kohshima, Shiro

2014-01-01

As facial color pattern around the eyes has been suggested to serve various adaptive functions related to the gaze signal, we compared the patterns among 25 canid species, focusing on the gaze signal, to estimate the function of facial color pattern in these species. The facial color patterns of the studied species could be categorized into the following three types based on contrast indices relating to the gaze signal: A-type (both pupil position in the eye outline and eye position in the face are clear), B-type (only the eye position is clear), and C-type (both the pupil and eye position are unclear). A-type faces with light-colored irises were observed in most studied species of the wolf-like clade and some of the red fox-like clade. A-type faces tended to be observed in species living in family groups all year-round, whereas B-type faces tended to be seen in solo/pair-living species. The duration of gazing behavior during which the facial gaze-signal is displayed to the other individual was longest in gray wolves with typical A-type faces, of intermediate length in fennec foxes with typical B-type faces, and shortest in bush dogs with typical C-type faces. These results suggest that the facial color pattern of canid species is related to their gaze communication and that canids with A-type faces, especially gray wolves, use the gaze signal in conspecific communication.

Loss of functionally unique species may gradually undermine ecosystems

PubMed Central

O'Gorman, Eoin J.; Yearsley, Jon M.; Crowe, Tasman P.; Emmerson, Mark C.; Jacob, Ute; Petchey, Owen L.

2011-01-01

Functionally unique species contribute to the functional diversity of natural systems, often enhancing ecosystem functioning. An abundance of weakly interacting species increases stability in natural systems, suggesting that loss of weakly linked species may reduce stability. Any link between the functional uniqueness of a species and the strength of its interactions in a food web could therefore have simultaneous effects on ecosystem functioning and stability. Here, we analyse patterns in 213 real food webs and show that highly unique species consistently tend to have the weakest mean interaction strength per unit biomass in the system. This relationship is not a simple consequence of the interdependence of both measures on body size and appears to be driven by the empirical pattern of size structuring in aquatic systems and the trophic position of each species in the web. Food web resolution also has an important effect, with aggregation of species into higher taxonomic groups producing a much weaker relationship. Food webs with fewer unique and less weakly interacting species also show significantly greater variability in their levels of primary production. Thus, the loss of highly unique, weakly interacting species may eventually lead to dramatic state changes and unpredictable levels of ecosystem functioning. PMID:21106593

Sea Urchin Morphogenesis.

PubMed

McClay, David R

2016-01-01

In the sea urchin morphogenesis follows extensive molecular specification. The specification controls the many morphogenetic events and these, in turn, precede patterning steps that establish the larval body plan. To understand how the embryo is built it was necessary to understand those series of molecular steps. Here an example of the historical sequence of those discoveries is presented as it unfolded over the last 50 years, the years during which major progress in understanding development of many animals and plants was documented by CTDB. In sea urchin development a rich series of experimental studies first established many of the phenomenological components of skeletal morphogenesis and patterning without knowledge of the molecular components. The many discoveries of transcription factors, signals, and structural proteins that contribute to the shape of the endoskeleton of the sea urchin larva then followed as molecular tools became available. A number of transcription factors and signals were discovered that were necessary for specification, morphogenesis, and patterning. Perturbation of the transcription factors and signals provided the means for assembling models of the gene regulatory networks used for specification and controlled the subsequent morphogenetic events. The earlier experimental information informed perturbation experiments that asked how patterning worked. As a consequence it was learned that ectoderm provides a series of patterning signals to the skeletogenic cells and as a consequence the skeletogenic cells secrete a highly patterned skeleton based on their ability to genotypically decode the localized reception of several signals. We still do not understand the complexity of the signals received by the skeletogenic cells, nor do we understand in detail how the genotypic information shapes the secreted skeletal biomineral, but the current knowledge at least outlines the sequence of events and provides a useful template for future discoveries. © 2016 Elsevier Inc. All rights reserved.

Variations in motor unit recruitment patterns occur within and between muscles in the running rat (Rattus norvegicus).

PubMed

Hodson-Tole, E F; Wakeling, J M

2007-07-01

Motor units are generally considered to follow a set, orderly pattern of recruitment within each muscle with activation occurring in the slowest through to the fastest units. A growing body of evidence, however, suggests that recruitment patterns may not always follow such an orderly sequence. Here we investigate whether motor unit recruitment patterns vary within and between the ankle extensor muscles of the rat running at 40 cm s(-1) on a level treadmill. In the past it has been difficult to quantify motor unit recruitment patterns during locomotion; however, recent application of wavelet analysis techniques has made such detailed analysis of motor unit recruitment possible. Here we present methods for quantifying the interplay of fast and slow motor unit recruitment based on their myoelectric signals. Myoelectric data were collected from soleus, plantaris and medial gastrocnemius muscles representing populations of slow, mixed and fast fibres, respectively, and providing a good opportunity to relate myoelectric frequency content to motor unit recruitment patterns. Following wavelet transformation, principal component analysis quantified signal intensity and relative frequency content. Significant differences in signal frequency content occurred between different time points within a stride (P<0.001). We optimised high- and low-frequency wavelets to the major signals from the fast and slow motor units. The goodness-of-fit of the optimised wavelets to the signal intensity was high for all three muscles (r2>0.98). The low-frequency band had a significantly better fit to signals from the soleus muscle (P<0.001), while the high-frequency band had a significantly better fit to the medial gastrocnemius (P<0.001).

Three-Dimensional Gene Map of Cancer Cell Types: Structural Entropy Minimisation Principle for Defining Tumour Subtypes

PubMed Central

Li, Angsheng; Yin, Xianchen; Pan, Yicheng

2016-01-01

In this study, we propose a method for constructing cell sample networks from gene expression profiles, and a structural entropy minimisation principle for detecting natural structure of networks and for identifying cancer cell subtypes. Our method establishes a three-dimensional gene map of cancer cell types and subtypes. The identified subtypes are defined by a unique gene expression pattern, and a three-dimensional gene map is established by defining the unique gene expression pattern for each identified subtype for cancers, including acute leukaemia, lymphoma, multi-tissue, lung cancer and healthy tissue. Our three-dimensional gene map demonstrates that a true tumour type may be divided into subtypes, each defined by a unique gene expression pattern. Clinical data analyses demonstrate that most cell samples of an identified subtype share similar survival times, survival indicators and International Prognostic Index (IPI) scores and indicate that distinct subtypes identified by our algorithms exhibit different overall survival times, survival ratios and IPI scores. Our three-dimensional gene map establishes a high-definition, one-to-one map between the biologically and medically meaningful tumour subtypes and the gene expression patterns, and identifies remarkable cells that form singleton submodules. PMID:26842724

Accelerating Sequences in the Presence of Metal by Exploiting the Spatial Distribution of Off-Resonance

PubMed Central

Smith, Matthew R.; Artz, Nathan S.; Koch, Kevin M.; Samsonov, Alexey; Reeder, Scott B.

2014-01-01

Purpose To demonstrate feasibility of exploiting the spatial distribution of off-resonance surrounding metallic implants for accelerating multispectral imaging techniques. Theory Multispectral imaging (MSI) techniques perform time-consuming independent 3D acquisitions with varying RF frequency offsets to address the extreme off-resonance from metallic implants. Each off-resonance bin provides a unique spatial sensitivity that is analogous to the sensitivity of a receiver coil, and therefore provides a unique opportunity for acceleration. Methods Fully sampled MSI was performed to demonstrate retrospective acceleration. A uniform sampling pattern across off-resonance bins was compared to several adaptive sampling strategies using a total hip replacement phantom. Monte Carlo simulations were performed to compare noise propagation of two of these strategies. With a total knee replacement phantom, positive and negative off-resonance bins were strategically sampled with respect to the B0 field to minimize aliasing. Reconstructions were performed with a parallel imaging framework to demonstrate retrospective acceleration. Results An adaptive sampling scheme dramatically improved reconstruction quality, which was supported by the noise propagation analysis. Independent acceleration of negative and positive off-resonance bins demonstrated reduced overlapping of aliased signal to improve the reconstruction. Conclusion This work presents the feasibility of acceleration in the presence of metal by exploiting the spatial sensitivities of off-resonance bins. PMID:24431210

SOX1 links the function of neural patterning and Notch signalling in the ventral spinal cord during the neuron-glial fate switch

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

Genethliou, Nicholas; Panayiotou, Elena; Department of Biological Sciences, University of Cyprus, P.O. Box 20537, 1678 Nicosia

2009-12-25

During neural development the transition from neurogenesis to gliogenesis, known as the neuron-glial ({Nu}/G) fate switch, requires the coordinated function of patterning factors, pro-glial factors and Notch signalling. How this process is coordinated in the embryonic spinal cord is poorly understood. Here, we demonstrate that during the N/G fate switch in the ventral spinal cord (vSC) SOX1 links the function of neural patterning and Notch signalling. We show that, SOX1 expression in the vSC is regulated by PAX6, NKX2.2 and Notch signalling in a domain-specific manner. We further show that SOX1 regulates the expression of Hes1 and that loss ofmore » Sox1 leads to enhanced production of oligodendrocyte precursors from the pMN. Finally, we show that Notch signalling functions upstream of SOX1 during this fate switch and is independently required for the acquisition of the glial fate perse by regulating Nuclear Factor I A expression in a PAX6/SOX1/HES1/HES5-independent manner. These data integrate functional roles of neural patterning factors, Notch signalling and SOX1 during gliogenesis.« less

Porous silicon based micro-opto-electro-mechanical-systems (MOEMS) components for free space optical interconnects

NASA Astrophysics Data System (ADS)

Song, Da

2008-02-01

One of the major challenges confronting the current integrated circuits (IC) industry is the metal "interconnect bottleneck". To overcome this obstacle, free space optical interconnects (FSOIs) can be used to address the demand for high speed data transmission, multi-functionality and multi-dimensional integration for the next generation IC. One of the crucial elements in FSOIs system is to develop a high performance and flexible optical network to transform the incoming optical signal into a distributed set of optical signals whose direction, alignment and power can be independently controlled. Among all the optical materials for the realization of FSOI components, porous silicon (PSi) is one of the most promising candidates because of its unique optical properties, flexible fabrication methods and integration with conventional IC material sets. PSi-based Distributed Bragg Reflector (DBR) and Fabry-Perot (F-P) structures with unique optical properties are realized by electrochemical etching of silicon. By incorporating PSi optical structures with Micro-Opto-Electro-Mechanical-Systems (MOEMS), several components required for FSOI have been developed. The first type of component is the out-of-plane freestanding optical switch. Implementing a PSi DBR structure as an optically active region, the device can realize channel selection by changing the tilting angle of the micromirror supported by the thermal bimorph actuator. All the fabricated optical switches have reached kHz working frequency and life time of millions of cycles. The second type of component is the in-plane tunable optical filter. By introducing PSi F-P structure into the in-plane PSi film, a thermally tunable optical filter with a sensitivity of 7.9nm/V has been realized for add/drop optical signal selection. Also, for the first time, a new type of PSi based reconfigurable diffractive optical element (DOE) has been developed. By using patterned photoresist as a protective mask for electrochemical etching, the freestanding PSi-based MOEMS DOE has been created as a beam splitter to redistribute the incoming optical signal with onto desired detector arrays. All the developed devices are realized in array fashion and can be addressed and controlled individually. The combination of PSi and MOEMS opens the door for a new generation of silicon compatible optical interconnects.

Distance-dependent pattern blending can camouflage salient aposematic signals.

PubMed

Barnett, James B; Cuthill, Innes C; Scott-Samuel, Nicholas E

2017-07-12

The effect of viewing distance on the perception of visual texture is well known: spatial frequencies higher than the resolution limit of an observer's visual system will be summed and perceived as a single combined colour. In animal defensive colour patterns, distance-dependent pattern blending may allow aposematic patterns, salient at close range, to match the background to distant observers. Indeed, recent research has indicated that reducing the distance from which a salient signal can be detected can increase survival over camouflage or conspicuous aposematism alone. We investigated whether the spatial frequency of conspicuous and cryptically coloured stripes affects the rate of avian predation. Our results are consistent with pattern blending acting to camouflage salient aposematic signals effectively at a distance. Experiments into the relative rate of avian predation on edible model caterpillars found that increasing spatial frequency (thinner stripes) increased survival. Similarly, visual modelling of avian predators showed that pattern blending increased the similarity between caterpillar and background. These results show how a colour pattern can be tuned to reveal or conceal different information at different distances, and produce tangible survival benefits. © 2017 The Author(s).

New biometric modalities using internal physical characteristics

NASA Astrophysics Data System (ADS)

Mortenson, Juliana (Brooks)

2010-04-01

Biometrics is described as the science of identifying people based on physical characteristics such as their fingerprints, facial features, hand geometry, iris patterns, palm prints, or speech recognition. Notably, all of these physical characteristics are visible or detectable from the exterior of the body. These external characteristics can be lifted, photographed, copied or recorded for unauthorized access to a biometric system. Individual humans are unique internally, however, just as they are unique externally. New biometric modalities have been developed which identify people based on their unique internal characteristics. For example, "BoneprintsTM" use acoustic fields to scan the unique bone density pattern of a thumb pressed on a small acoustic sensor. Thanks to advances in piezoelectric materials the acoustic sensor can be placed in virtually any device such as a steering wheel, door handle, or keyboard. Similarly, "Imp-PrintsTM" measure the electrical impedance patterns of a hand to identify or verify a person's identity. Small impedance sensors can be easily embedded in devices such as smart cards, handles, or wall mounts. These internal biometric modalities rely on physical characteristics which are not visible or photographable, providing an added level of security. In addition, both the acoustic and impedance methods can be combined with physiologic measurements such as acoustic Doppler or impedance plethysmography, respectively. Added verification that the biometric pattern came from a living person can be obtained. These new biometric modalities have the potential to allay user concerns over protection of privacy, while providing a higher level of security.*

A novel approach for SEMG signal classification with adaptive local binary patterns.

PubMed

Ertuğrul, Ömer Faruk; Kaya, Yılmaz; Tekin, Ramazan

2016-07-01

Feature extraction plays a major role in the pattern recognition process, and this paper presents a novel feature extraction approach, adaptive local binary pattern (aLBP). aLBP is built on the local binary pattern (LBP), which is an image processing method, and one-dimensional local binary pattern (1D-LBP). In LBP, each pixel is compared with its neighbors. Similarly, in 1D-LBP, each data in the raw is judged against its neighbors. 1D-LBP extracts feature based on local changes in the signal. Therefore, it has high a potential to be employed in medical purposes. Since, each action or abnormality, which is recorded in SEMG signals, has its own pattern, and via the 1D-LBP these (hidden) patterns may be detected. But, the positions of the neighbors in 1D-LBP are constant depending on the position of the data in the raw. Also, both LBP and 1D-LBP are very sensitive to noise. Therefore, its capacity in detecting hidden patterns is limited. To overcome these drawbacks, aLBP was proposed. In aLBP, the positions of the neighbors and their values can be assigned adaptively via the down-sampling and the smoothing coefficients. Therefore, the potential to detect (hidden) patterns, which may express an illness or an action, is really increased. To validate the proposed feature extraction approach, two different datasets were employed. Achieved accuracies by the proposed approach were higher than obtained results by employed popular feature extraction approaches and the reported results in the literature. Obtained accuracy results were brought out that the proposed method can be employed to investigate SEMG signals. In summary, this work attempts to develop an adaptive feature extraction scheme that can be utilized for extracting features from local changes in different categories of time-varying signals.

Passive Transport Disrupts Grid Signals in the Parahippocampal Cortex.

PubMed

Winter, Shawn S; Mehlman, Max L; Clark, Benjamin J; Taube, Jeffrey S

2015-10-05

Navigation is usually thought of relative to landmarks, but neural signals representing space also use information generated by an animal's movements. These signals include grid cells, which fire at multiple locations, forming a repeating grid pattern. Grid cell generation depends upon theta rhythm, a 6-10 Hz electroencephalogram (EEG) oscillation that is modulated by the animals' movement velocity. We passively moved rats in a clear cart to eliminate motor related self-movement cues that drive moment-to-moment changes in theta rhythmicity. We found that passive movement maintained theta power and frequency at levels equivalent to low active movement velocity, spared overall head-direction (HD) cell characteristics, but abolished both velocity modulation of theta rhythmicity and grid cell firing patterns. These results indicate that self-movement motor cues are necessary for generating grid-specific firing patterns, possibly by driving velocity modulation of theta rhythmicity, which may be used as a speed signal to generate the repeating pattern of grid cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

Passive Transport Disrupts Grid Signals in the Parahippocampal Cortex

PubMed Central

Winter, Shawn S.; Mehlman, Max L.; Clark, Benjamin J.; Taube, Jeffrey S.

2015-01-01

Summary Navigation is usually thought of relative to landmarks, but neural signals representing space also use information generated by an animal’s movements. These signals include grid cells, which fire at multiple locations forming a repeating grid pattern. Grid cell generation depends upon theta rhythm, a 6-10 Hz EEG oscillation that is modulated by the animals’ movement velocity. We passively moved rats in a clear cart to eliminate motor related self-movement cues that drive moment-to-moment changes in theta rhythmicity. We found that passive movement maintained theta power and frequency at levels equivalent to low active movement velocity, spared overall HD cell characteristics, and abolished velocity modulation of theta rhythmicity and grid cell firing patterns. These results indicate that self-movement motor cues are necessary for generating grid-specific firing patterns, possibly by driving velocity modulation of theta rhythmicity. Velocity modulation of theta may be used as a speed signal to generate the repeating pattern of grid cells. PMID:26387719

Notch-mediated lateral inhibition regulates proneural wave propagation when combined with EGF-mediated reaction diffusion

PubMed Central

Sato, Makoto; Yasugi, Tetsuo; Minami, Yoshiaki; Miura, Takashi; Nagayama, Masaharu

2016-01-01

Notch-mediated lateral inhibition regulates binary cell fate choice, resulting in salt and pepper patterns during various developmental processes. However, how Notch signaling behaves in combination with other signaling systems remains elusive. The wave of differentiation in the Drosophila visual center or “proneural wave” accompanies Notch activity that is propagated without the formation of a salt and pepper pattern, implying that Notch does not form a feedback loop of lateral inhibition during this process. However, mathematical modeling and genetic analysis clearly showed that Notch-mediated lateral inhibition is implemented within the proneural wave. Because partial reduction in EGF signaling causes the formation of the salt and pepper pattern, it is most likely that EGF diffusion cancels salt and pepper pattern formation in silico and in vivo. Moreover, the combination of Notch-mediated lateral inhibition and EGF-mediated reaction diffusion enables a function of Notch signaling that regulates propagation of the wave of differentiation. PMID:27535937

Cdon acts as a Hedgehog decoy receptor during proximal-distal patterning of the optic vesicle

PubMed Central

Cardozo, Marcos Julián; Sánchez-Arrones, Luisa; Sandonis, África; Sánchez-Camacho, Cristina; Gestri, Gaia; Wilson, Stephen W.; Guerrero, Isabel; Bovolenta, Paola

2014-01-01

Patterning of the vertebrate optic vesicle into proximal/optic stalk and distal/neural retina involves midline-derived Hedgehog (Hh) signalling, which promotes stalk specification. In the absence of Hh signalling, the stalks are not specified, causing cyclopia. Recent studies showed that the cell adhesion molecule Cdon forms a heteromeric complex with the Hh receptor Patched 1 (Ptc1). This receptor complex binds Hh and enhances signalling activation, indicating that Cdon positively regulates the pathway. Here we show that in the developing zebrafish and chick optic vesicle, in which cdon and ptc1 are expressed with a complementary pattern, Cdon acts as a negative Hh signalling regulator. Cdon predominantly localizes to the basolateral side of neuroepithelial cells, promotes the enlargement of the neuroepithelial basal end-foot and traps Hh protein, thereby limiting its dispersion. This Ptc-independent function protects the retinal primordium from Hh activity, defines the stalk/retina boundary and thus the correct proximo-distal patterning of the eye. PMID:25001599

A multi-scale analysis of landscape statistics

Treesearch

Douglas H. Cain; Kurt H. Riitters; Kenneth Orvis

1997-01-01

It is now feasible to monitor some aspects of landscape ecological condition nationwide using remotely- sensed imagery and indicators of land cover pattern. Previous research showed redundancies among many reported pattern indicators and identified six unique dimensions of land cover pattern. This study tested the stability of those dimensions and representative...

Virtual Human Analogs to Rodent Spatial Pattern Separation and Completion Memory Tasks

ERIC Educational Resources Information Center

Paleja, Meera; Girard, Todd A.; Christensen, Bruce K.

2011-01-01

Spatial pattern separation (SPS) and spatial pattern completion (SPC) have played an increasingly important role in computational and rodent literatures as processes underlying associative memory. SPS and SPC are complementary processes, allowing the formation of unique representations and the reconstruction of complete spatial environments based…

A feedback mechanism controlling SCRAMBLED receptor accumulation and cell-type pattern in Arabidopsis.

PubMed

Kwak, Su-Hwan; Schiefelbein, John

2008-12-23

Cellular pattern formation in the root epidermis of Arabidopsis occurs in a position-dependent manner, generating root-hair (H) cells contacting two underlying cortical cells and nonhair (N) cells contacting one cortical cell. SCRAMBLED (SCM), a leucine-rich repeat receptor-like kinase (LRR-RLK), mediates this process through its effect on a downstream transcription factor regulatory network. After perception of a positional cue, the SCM signaling pathway is proposed to preferentially repress WEREWOLF (WER) transcription factor expression in H cells and thereby bias the outcome of mutual lateral inhibition acting between H and N cells. However, the molecular mechanism responsible for this preferential SCM signaling is unknown. Here, we analyze the distribution of the SCM receptor and the biological effect of altering its accumulation pattern. We find that SCM expression and accumulation in the epidermal cell layer is necessary and sufficient to direct the cell-type pattern. Further, SCM preferentially accumulates in H cells, and this accumulation pattern is dependent on the downstream transcription factors. Thus, SCM participates in an autoregulatory feedback loop, enabling cells engaged in SCM signaling to maintain high levels of SCM receptor, which provides a simple mechanism for reinforcing a bias in receptor-mediated signaling to ensure robust pattern formation.

EMG-based pattern recognition approach in post stroke robot-aided rehabilitation: a feasibility study

PubMed Central

2013-01-01

Background Several studies investigating the use of electromyographic (EMG) signals in robot-based stroke neuro-rehabilitation to enhance functional recovery. Here we explored whether a classical EMG-based patterns recognition approach could be employed to predict patients’ intentions while attempting to generate goal-directed movements in the horizontal plane. Methods Nine right-handed healthy subjects and seven right-handed stroke survivors performed reaching movements in the horizontal plane. EMG signals were recorded and used to identify the intended motion direction of the subjects. To this aim, a standard pattern recognition algorithm (i.e., Support Vector Machine, SVM) was used. Different tests were carried out to understand the role of the inter- and intra-subjects’ variability in affecting classifier accuracy. Abnormal muscular spatial patterns generating misclassification were evaluated by means of an assessment index calculated from the results achieved with the PCA, i.e., the so-called Coefficient of Expressiveness (CoE). Results Processing the EMG signals of the healthy subjects, in most of the cases we were able to build a static functional map of the EMG activation patterns for point-to-point reaching movements on the horizontal plane. On the contrary, when processing the EMG signals of the pathological subjects a good classification was not possible. In particular, patients’ aimed movement direction was not predictable with sufficient accuracy either when using the general map extracted from data of normal subjects and when tuning the classifier on the EMG signals recorded from each patient. Conclusions The experimental findings herein reported show that the use of EMG patterns recognition approach might not be practical to decode movement intention in subjects with neurological injury such as stroke. Rather than estimate motion from EMGs, future scenarios should encourage the utilization of these signals to detect and interpret the normal and abnormal muscle patterns and provide feedback on their correct recruitment. PMID:23855907

Parcellation of the human orbitofrontal cortex based on gray matter volume covariance.

PubMed

Liu, Huaigui; Qin, Wen; Qi, Haotian; Jiang, Tianzi; Yu, Chunshui

2015-02-01

The human orbitofrontal cortex (OFC) is an enigmatic brain region that cannot be parcellated reliably using diffusional and functional magnetic resonance imaging (fMRI) because there is signal dropout that results from an inherent defect in imaging techniques. We hypothesise that the OFC can be reliably parcellated into subregions based on gray matter volume (GMV) covariance patterns that are derived from artefact-free structural images. A total of 321 healthy young subjects were examined by high-resolution structural MRI. The OFC was parcellated into subregions-based GMV covariance patterns; and then sex and laterality differences in GMV covariance pattern of each OFC subregion were compared. The human OFC was parcellated into the anterior (OFCa), medial (OFCm), posterior (OFCp), intermediate (OFCi), and lateral (OFCl) subregions. This parcellation scheme was validated by the same analyses of the left OFC and the bilateral OFCs in male and female subjects. Both visual observation and quantitative comparisons indicated a unique GMV covariance pattern for each OFC subregion. These OFC subregions mainly covaried with the prefrontal and temporal cortices, cingulate cortex and amygdala. In addition, GMV correlations of most OFC subregions were similar across sex and laterality except for significant laterality difference in the OFCl. The right OFCl had stronger GMV correlation with the right inferior frontal cortex. Using high-resolution structural images, we established a reliable parcellation scheme for the human OFC, which may provide an in vivo guide for subregion-level studies of this region and improve our understanding of the human OFC at subregional levels. © 2014 Wiley Periodicals, Inc.

Genome-wide analysis of alternative splicing in medulloblastoma identifies splicing patterns characteristic of normal cerebellar development

PubMed Central

Menghi, Francesca; Jacques, Thomas S.; Barenco, Martino; Schwalbe, Ed C.; Clifford, Steven C.; Hubank, Mike; Ham, Jonathan

2011-01-01

Alternative splicing is an important mechanism for the generation of protein diversity at a post-transcriptional level. Modifications in the splicing patterns of several genes have been shown to contribute to the malignant transformation of different tissue types. In this study, we used the Affymetrix Exon arrays to investigate patterns of differential splicing between paediatric medulloblastomas and normal cerebellum on a genome-wide scale. Of the 1262 genes identified as potentially generating tumour-associated splice forms, we selected 14 examples of differential splicing of known cassette exons and successfully validated 11 of them by RT-PCR. The pattern of differential splicing of three validated events was characteristic for the molecular subset of Sonic Hedgehog (Shh)-driven medulloblastomas, suggesting that their unique gene signature includes the expression of distinctive transcript variants. Generally, we observed that tumour and normal fetal cerebellar samples shared significantly lower exon inclusion rates compared to normal adult cerebellum. We investigated whether tumour-associated splice forms were expressed in primary cultures of Shh-dependent mouse cerebellar granule cell precursors (GCPs) and found that Shh caused a decrease in the cassette exon inclusion rate of five out of the seven tested genes. Furthermore, we observed a significant increase in exon inclusion between post-natal days 7 and 14 of mouse cerebellar development, at the time when GCPs mature into post-mitotic neurons. We conclude that inappropriate splicing frequently occurs in human medulloblastomas and may be linked to the activation of developmental signalling pathways and a failure of cerebellar precursor cells to differentiate. PMID:21248070

Intricate but tight coupling of spiracular activity and abdominal ventilation during locust discontinuous gas exchange cycles.

PubMed

Talal, Stav; Gefen, Eran; Ayali, Amir

2018-03-15

Discontinuous gas exchange (DGE) is the best studied among insect gas exchange patterns. DGE cycles comprise three phases, which are defined by their spiracular state: closed, flutter and open. However, spiracle status has rarely been monitored directly; rather, it is often assumed based on CO 2 emission traces. In this study, we directly recorded electromyogram (EMG) signals from the closer muscle of the second thoracic spiracle and from abdominal ventilation muscles in a fully intact locust during DGE. Muscular activity was monitored simultaneously with CO 2 emission, under normoxia and under various experimental oxic conditions. Our findings indicate that locust DGE does not correspond well with the commonly described three-phase cycle. We describe unique DGE-related ventilation motor patterns, coupled to spiracular activity. During the open phase, when CO 2 emission rate is highest, the thoracic spiracles do not remain open; rather, they open and close rapidly. This fast spiracle activity coincides with in-phase abdominal ventilation, while alternating with the abdominal spiracle and thus facilitating a unidirectional air flow along the main trachea. A change in the frequency of rhythmic ventilation during the open phase suggests modulation by intra-tracheal CO 2 levels. A second, slow ventilatory movement pattern probably serves to facilitate gas diffusion during spiracle closure. Two flutter-like patterns are described in association with the different types of ventilatory activity. We offer a modified mechanistic model for DGE in actively ventilating insects, incorporating ventilatory behavior and changes in spiracle state. © 2018. Published by The Company of Biologists Ltd.

Transcriptional Regulation of Pattern-Triggered Immunity in Plants.

PubMed

Li, Bo; Meng, Xiangzong; Shan, Libo; He, Ping

2016-05-11

Perception of microbe-associated molecular patterns (MAMPs) by cell-surface-resident pattern recognition receptors (PRRs) induces rapid, robust, and selective transcriptional reprogramming, which is central for launching effective pattern-triggered immunity (PTI) in plants. Signal relay from PRR complexes to the nuclear transcriptional machinery via intracellular kinase cascades rapidly activates primary immune response genes. The coordinated action of gene-specific transcription factors and the general transcriptional machinery contribute to the selectivity of immune gene activation. In addition, PRR complexes and signaling components are often transcriptionally upregulated upon MAMP perception to ensure the robustness and sustainability of PTI outputs. In this review, we discuss recent advances in deciphering the signaling pathways and regulatory mechanisms that coordinately lead to timely and accurate MAMP-induced gene expression in plants. Copyright © 2016 Elsevier Inc. All rights reserved.

Complexity of cardiovascular rhythms during head-up tilt test by entropy of patterns.

PubMed

Wejer, Dorota; Graff, Beata; Makowiec, Danuta; Budrejko, Szymon; Struzik, Zbigniew R

2017-05-01

The head-up tilt (HUT) test, which provokes transient dynamical alterations in the regulation of cardiovascular system, provides insights into complex organization of this system. Based on signals with heart period intervals (RR-intervals) and/or systolic blood pressure (SBP), differences in the cardiovascular regulation between vasovagal patients (VVS) and the healthy people group (CG) are investigated. Short-term relations among signal data represented symbolically by three-beat patterns allow to qualify and quantify the complexity of the cardiovascular regulation by Shannon entropy. Four types of patterns: permutation, ordinal, deterministic and dynamical, are used, and different resolutions of signal values in the the symbolization are applied in order to verify how entropy of patterns depends on a way in which values of signals are preprocessed. At rest, in the physiologically important signal resolution ranges, independently of the type of patterns used in estimates, the complexity of SBP signals in VVS is different from the complexity found in CG. Entropy of VVS is higher than CG what could be interpreted as substantial presence of noisy ingredients in SBP of VVS. After tilting this relation switches. Entropy of CG occurs significantly higher than VVS for SBP signals. In the case of RR-intervals and large resolutions, the complexity after the tilt becomes reduced when compared to the complexity of RR-intervals at rest for both groups. However, in the case of VVS patients this reduction is significantly stronger than in CG. Our observations about opposite switches in entropy between CG and VVS might support a hypothesis that baroreflex in VVS affects stronger the heart rate because of the inefficient regulation (possibly impaired local vascular tone alternations) of the blood pressure.

Preparation of Iridescent 2D Photonic Crystals by Using a Mussel-Inspired Spatial Patterning of ZIF-8 with Potential Applications in Optical Switch and Chemical Sensor.

PubMed

Razmjou, Amir; Asadnia, Mohsen; Ghaebi, Omid; Yang, Hao-Cheng; Ebrahimi Warkiani, Majid; Hou, Jingwei; Chen, Vicki

2017-11-01

In this work, spatial patterning of a thin, dense, zeolitic imidazolate framework (ZIF-8) pattern was generated using photolithography and nanoscale (60 nm) dopamine coating. A bioinspired, unique, reversible, two-color iridescent pattern can be easily obtained for potential applications in sensing and photonics.

The evolution of nervous system patterning: insights from sea urchin development

PubMed Central

Angerer, Lynne M.; Yaguchi, Shunsuke; Angerer, Robert C.; Burke, Robert D.

2011-01-01

Recent studies of the sea urchin embryo have elucidated the mechanisms that localize and pattern its nervous system. These studies have revealed the presence of two overlapping regions of neurogenic potential at the beginning of embryogenesis, each of which becomes progressively restricted by separate, yet linked, signals, including Wnt and subsequently Nodal and BMP. These signals act to specify and localize the embryonic neural fields – the anterior neuroectoderm and the more posterior ciliary band neuroectoderm – during development. Here, we review these conserved nervous system patterning signals and consider how the relationships between them might have changed during deuterostome evolution. PMID:21828090

The efficacy of using human myoelectric signals to control the limbs of robots in space

NASA Technical Reports Server (NTRS)

Clark, Jane E.; Phillips, Sally J.

1988-01-01

This project was designed to investigate the usefulness of the myoelectric signal as a control in robotics applications. More specifically, the neural patterns associated with human arm and hand actions were studied to determine the efficacy of using these myoelectric signals to control the manipulator arm of a robot. The advantage of this approach to robotic control was the use of well-defined and well-practiced neural patterns already available to the system, as opposed to requiring the human operator to learn new tasks and establish new neural patterns in learning to control a joystick or mechanical coupling device.

Competitive aggregation dynamics using phase wave signals.

PubMed

Sakaguchi, Hidetsugu; Maeyama, Satomi

2014-10-21

Coupled equations of the phase equation and the equation of cell concentration n are proposed for competitive aggregation dynamics of slime mold in two dimensions. Phase waves are used as tactic signals of aggregation in this model. Several aggregation clusters are formed initially, and target patterns appear around the localized aggregation clusters. Owing to the competition among target patterns, the number of the localized aggregation clusters decreases, and finally one dominant localized pattern survives. If the phase equation is replaced with the complex Ginzburg-Landau equation, several spiral patterns appear, and n is localized near the center of the spiral patterns. After the competition among spiral patterns, one dominant spiral survives. Copyright © 2014 Elsevier Ltd. All rights reserved.

Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from Aquifex aeolicus.

PubMed

Pandelia, Maria-Eirini; Nitschke, Wolfgang; Infossi, Pascale; Giudici-Orticoni, Marie-Thérèse; Bill, Eckhard; Lubitz, Wolfgang

2011-04-12

Iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. In the oxygen-tolerant Hydrogenase I from Aquifex aeolicus such electron "wires" form a relay to a diheme cytb, an integral part of a respiration pathway for the reduction of O(2) to water. Amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. Electron paramagnetic resonance spectra exhibited complex signals that disclose interesting features and spin-coupling patterns; by redox titrations three iron-sulfur clusters were identified in their usual redox states, a [3Fe4S] and two [4Fe4S], but also a unique high-potential (HP) state was found. On the basis of (57)Fe Mössbauer spectroscopy we attribute this HP form to a superoxidized state of the [4Fe4S] center proximal to the [NiFe] site. The unique environment of this cluster, characterized by a surplus cysteine coordination, is able to tune the redox potentials and make it compliant with the [4Fe4S](3+) state. It is actually the first example of a biological [4Fe4S] center that physiologically switches between 3+, 2+, and 1+ oxidation states within a very small potential range. We suggest that the (1 + /2+) redox couple serves the classical electron transfer reaction, whereas the superoxidation step is associated with a redox switch against oxidative stress.

Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from Aquifex aeolicus

PubMed Central

Pandelia, Maria-Eirini; Nitschke, Wolfgang; Infossi, Pascale; Giudici-Orticoni, Marie-Thérèse; Bill, Eckhard; Lubitz, Wolfgang

2011-01-01

Iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. In the oxygen-tolerant Hydrogenase I from Aquifex aeolicus such electron “wires” form a relay to a diheme cytb, an integral part of a respiration pathway for the reduction of O2 to water. Amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. Electron paramagnetic resonance spectra exhibited complex signals that disclose interesting features and spin-coupling patterns; by redox titrations three iron-sulfur clusters were identified in their usual redox states, a [3Fe4S] and two [4Fe4S], but also a unique high-potential (HP) state was found. On the basis of 57Fe Mössbauer spectroscopy we attribute this HP form to a superoxidized state of the [4Fe4S] center proximal to the [NiFe] site. The unique environment of this cluster, characterized by a surplus cysteine coordination, is able to tune the redox potentials and make it compliant with the [4Fe4S]3+ state. It is actually the first example of a biological [4Fe4S] center that physiologically switches between 3+, 2+, and 1+ oxidation states within a very small potential range. We suggest that the (1 + /2+) redox couple serves the classical electron transfer reaction, whereas the superoxidation step is associated with a redox switch against oxidative stress. PMID:21444783

Research on the feature extraction and pattern recognition of the distributed optical fiber sensing signal

NASA Astrophysics Data System (ADS)

Wang, Bingjie; Sun, Qi; Pi, Shaohua; Wu, Hongyan

2014-09-01

In this paper, feature extraction and pattern recognition of the distributed optical fiber sensing signal have been studied. We adopt Mel-Frequency Cepstral Coefficient (MFCC) feature extraction, wavelet packet energy feature extraction and wavelet packet Shannon entropy feature extraction methods to obtain sensing signals (such as speak, wind, thunder and rain signals, etc.) characteristic vectors respectively, and then perform pattern recognition via RBF neural network. Performances of these three feature extraction methods are compared according to the results. We choose MFCC characteristic vector to be 12-dimensional. For wavelet packet feature extraction, signals are decomposed into six layers by Daubechies wavelet packet transform, in which 64 frequency constituents as characteristic vector are respectively extracted. In the process of pattern recognition, the value of diffusion coefficient is introduced to increase the recognition accuracy, while keeping the samples for testing algorithm the same. Recognition results show that wavelet packet Shannon entropy feature extraction method yields the best recognition accuracy which is up to 97%; the performance of 12-dimensional MFCC feature extraction method is less satisfactory; the performance of wavelet packet energy feature extraction method is the worst.

Calcium spikes, waves and oscillations in a large, patterned epithelial tissue

PubMed Central

Balaji, Ramya; Bielmeier, Christina; Harz, Hartmann; Bates, Jack; Stadler, Cornelia; Hildebrand, Alexander; Classen, Anne-Kathrin

2017-01-01

While calcium signaling in excitable cells, such as muscle or neurons, is extensively characterized, calcium signaling in epithelial tissues is little understood. Specifically, the range of intercellular calcium signaling patterns elicited by tightly coupled epithelial cells and their function in the regulation of epithelial characteristics are little explored. We found that in Drosophila imaginal discs, a widely studied epithelial model organ, complex spatiotemporal calcium dynamics occur. We describe patterns that include intercellular waves traversing large tissue domains in striking oscillatory patterns as well as spikes confined to local domains of neighboring cells. The spatiotemporal characteristics of intercellular waves and oscillations arise as emergent properties of calcium mobilization within a sheet of gap-junction coupled cells and are influenced by cell size and environmental history. While the in vivo function of spikes, waves and oscillations requires further characterization, our genetic experiments suggest that core calcium signaling components guide actomyosin organization. Our study thus suggests a possible role for calcium signaling in epithelia but importantly, introduces a model epithelium enabling the dissection of cellular mechanisms supporting the initiation, transmission and regeneration of long-range intercellular calcium waves and the emergence of oscillations in a highly coupled multicellular sheet. PMID:28218282

Individual Biometric Identification Using Multi-Cycle Electrocardiographic Waveform Patterns.

PubMed

Lee, Wonki; Kim, Seulgee; Kim, Daeeun

2018-03-28

The electrocardiogram (ECG) waveform conveys information regarding the electrical property of the heart. The patterns vary depending on the individual heart characteristics. ECG features can be potentially used for biometric recognition. This study presents a new method using the entire ECG waveform pattern for matching and demonstrates that the approach can potentially be employed for individual biometric identification. Multi-cycle ECG signals were assessed using an ECG measuring circuit, and three electrodes can be patched on the wrists or fingers for considering various measurements. For biometric identification, our-fold cross validation was used in the experiments for assessing how the results of a statistical analysis will generalize to an independent data set. Four different pattern matching algorithms, i.e., cosine similarity, cross correlation, city block distance, and Euclidean distances, were tested to compare the individual identification performances with a single channel of ECG signal (3-wire ECG). To evaluate the pattern matching for biometric identification, the ECG recordings for each subject were partitioned into training and test set. The suggested method obtained a maximum performance of 89.9% accuracy with two heartbeats of ECG signals measured on the wrist and 93.3% accuracy with three heartbeats for 55 subjects. The performance rate with ECG signals measured on the fingers improved up to 99.3% with two heartbeats and 100% with three heartbeats of signals for 20 subjects.

Improvement in recording and reading holograms

NASA Technical Reports Server (NTRS)

Hallock, J. N.

1968-01-01

Three-beam technique superimposes a number of patterns in the same plane of a hologram and then uniquely identifies each pattern by a suitable readout process. The developed readout process does not require any movement of parts.

Wnt/β-catenin signaling integrates patterning and metabolism of the insect growth zone.

PubMed

Oberhofer, Georg; Grossmann, Daniela; Siemanowski, Janna L; Beissbarth, Tim; Bucher, Gregor

2014-12-01

Wnt/β-catenin and hedgehog (Hh) signaling are essential for transmitting signals across cell membranes in animal embryos. Early patterning of the principal insect model, Drosophila melanogaster, occurs in the syncytial blastoderm, where diffusion of transcription factors obviates the need for signaling pathways. However, in the cellularized growth zone of typical short germ insect embryos, signaling pathways are predicted to play a more fundamental role. Indeed, the Wnt/β-catenin pathway is required for posterior elongation in most arthropods, although which target genes are activated in this context remains elusive. Here, we use the short germ beetle Tribolium castaneum to investigate two Wnt and Hh signaling centers located in the head anlagen and in the growth zone of early embryos. We find that Wnt/β-catenin signaling acts upstream of Hh in the growth zone, whereas the opposite interaction occurs in the head. We determine the target gene sets of the Wnt/β-catenin and Hh pathways and find that the growth zone signaling center activates a much greater number of genes and that the Wnt and Hh target gene sets are essentially non-overlapping. The Wnt pathway activates key genes of all three germ layers, including pair-rule genes, and Tc-caudal and Tc-twist. Furthermore, the Wnt pathway is required for hindgut development and we identify Tc-senseless as a novel hindgut patterning gene required in the early growth zone. At the same time, Wnt acts on growth zone metabolism and cell division, thereby integrating growth with patterning. Posterior Hh signaling activates several genes potentially involved in a proteinase cascade of unknown function. © 2014. Published by The Company of Biologists Ltd.

Wnt/β-catenin signaling integrates patterning and metabolism of the insect growth zone

PubMed Central

Oberhofer, Georg; Grossmann, Daniela; Siemanowski, Janna L.; Beissbarth, Tim; Bucher, Gregor

2014-01-01

Wnt/β-catenin and hedgehog (Hh) signaling are essential for transmitting signals across cell membranes in animal embryos. Early patterning of the principal insect model, Drosophila melanogaster, occurs in the syncytial blastoderm, where diffusion of transcription factors obviates the need for signaling pathways. However, in the cellularized growth zone of typical short germ insect embryos, signaling pathways are predicted to play a more fundamental role. Indeed, the Wnt/β-catenin pathway is required for posterior elongation in most arthropods, although which target genes are activated in this context remains elusive. Here, we use the short germ beetle Tribolium castaneum to investigate two Wnt and Hh signaling centers located in the head anlagen and in the growth zone of early embryos. We find that Wnt/β-catenin signaling acts upstream of Hh in the growth zone, whereas the opposite interaction occurs in the head. We determine the target gene sets of the Wnt/β-catenin and Hh pathways and find that the growth zone signaling center activates a much greater number of genes and that the Wnt and Hh target gene sets are essentially non-overlapping. The Wnt pathway activates key genes of all three germ layers, including pair-rule genes, and Tc-caudal and Tc-twist. Furthermore, the Wnt pathway is required for hindgut development and we identify Tc-senseless as a novel hindgut patterning gene required in the early growth zone. At the same time, Wnt acts on growth zone metabolism and cell division, thereby integrating growth with patterning. Posterior Hh signaling activates several genes potentially involved in a proteinase cascade of unknown function. PMID:25395458

Acoustic Signal Processing for Pipe Condition Assessment (WaterRF Report 4360)

EPA Science Inventory

Unique to prestressed concrete cylinder pipe (PCCP), individual wire breaks create an excitation in the pipe wall that may vary in response to the remaining compression of the pipe core. This project was designed to improve acoustic signal processing for pipe condition assessment...

Idiosyncratic Patterns of Representational Similarity in Prefrontal Cortex Predict Attentional Performance.

PubMed

Lee, Jeongmi; Geng, Joy J

2017-02-01

The efficiency of finding an object in a crowded environment depends largely on the similarity of nontargets to the search target. Models of attention theorize that the similarity is determined by representations stored within an "attentional template" held in working memory. However, the degree to which the contents of the attentional template are individually unique and where those idiosyncratic representations are encoded in the brain are unknown. We investigated this problem using representational similarity analysis of human fMRI data to measure the common and idiosyncratic representations of famous face morphs during an identity categorization task; data from the categorization task were then used to predict performance on a separate identity search task. We hypothesized that the idiosyncratic categorical representations of the continuous face morphs would predict their distractability when searching for each target identity. The results identified that patterns of activation in the lateral prefrontal cortex (LPFC) as well as in face-selective areas in the ventral temporal cortex were highly correlated with the patterns of behavioral categorization of face morphs and search performance that were common across subjects. However, the individually unique components of the categorization behavior were reliably decoded only in right LPFC. Moreover, the neural pattern in right LPFC successfully predicted idiosyncratic variability in search performance, such that reaction times were longer when distractors had a higher probability of being categorized as the target identity. These results suggest that the prefrontal cortex encodes individually unique components of categorical representations that are also present in attentional templates for target search. Everyone's perception of the world is uniquely shaped by personal experiences and preferences. Using functional MRI, we show that individual differences in the categorization of face morphs between two identities could be decoded from the prefrontal cortex and the ventral temporal cortex. Moreover, the individually unique representations in prefrontal cortex predicted idiosyncratic variability in attentional performance when looking for each identity in the "crowd" of another morphed face in a separate search task. Our results reveal that the representation of task-related information in prefrontal cortex is individually unique and preserved across categorization and search performance. This demonstrates the possibility of predicting individual behaviors across tasks with patterns of brain activity. Copyright © 2017 the authors 0270-6474/17/371257-12$15.00/0.

A Flexible High-Performance Photoimaging Device Based on Bioinspired Hierarchical Multiple-Patterned Plasmonic Nanostructures.

PubMed

Lee, Yoon Ho; Lee, Tae Kyung; Kim, Hongki; Song, Inho; Lee, Jiwon; Kang, Saewon; Ko, Hyunhyub; Kwak, Sang Kyu; Oh, Joon Hak

2018-03-01

In insect eyes, ommatidia with hierarchical structured cornea play a critical role in amplifying and transferring visual signals to the brain through optic nerves, enabling the perception of various visual signals. Here, inspired by the structure and functions of insect ommatidia, a flexible photoimaging device is reported that can simultaneously detect and record incoming photonic signals by vertically stacking an organic photodiode and resistive memory device. A single-layered, hierarchical multiple-patterned back reflector that can exhibit various plasmonic effects is incorporated into the organic photodiode. The multiple-patterned flexible organic photodiodes exhibit greatly enhanced photoresponsivity due to the increased light absorption in comparison with the flat systems. Moreover, the flexible photoimaging device shows a well-resolved spatiotemporal mapping of optical signals with excellent operational and mechanical stabilities at low driving voltages below half of the flat systems. Theoretical calculation and scanning near-field optical microscopy analyses clearly reveal that multiple-patterned electrodes have much stronger surface plasmon coupling than flat and single-patterned systems. The developed methodology provides a versatile and effective route for realizing high-performance optoelectronic and photonic systems. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Micro-Electronic Nose System

NASA Astrophysics Data System (ADS)

Zee, Frank C.

2011-12-01

The ability to "smell" various gas vapors and complex odors is important for many applications such as environmental monitoring for detecting toxic gases as well as quality control in the processing of food, cosmetics, and other chemical products for commercial industries. Mimicking the architecture of the biological nose, a miniature electronic nose system was designed and developed consisting of an array of sensor devices, signal-processing circuits, and software pattern-recognition algorithms. The array of sensors used polymer/carbon-black composite thin-films, which would swell or expand reversibly and reproducibly and cause a resistance change upon exposure to a wide variety of gases. Two types of sensor devices were fabricated using silicon micromachining techniques to form "wells" that confined the polymer/carbon-black to a small and specific area. The first type of sensor device formed the "well" by etching into the silicon substrate using bulk micromachining. The second type built a high-aspect-ratio "well" on the surface of a silicon wafer using SU-8 photoresist. Two sizes of "wells" were fabricated: 500 x 600 mum² and 250 x 250 mum². Custom signal-processing circuits were implemented on a printed circuit board and as an application-specific integrated-circuit (ASIC) chip. The circuits were not only able to measure and amplify the small resistance changes, which corresponded to small ppm (parts-per-million) changes in gas concentrations, but were also adaptable to accommodate the various characteristics of the different thin-films. Since the thin-films were not specific to any one particular gas vapor, an array of sensors each containing a different thin-film was used to produce a distributed response pattern when exposed to a gas vapor. Pattern recognition, including a clustering algorithm and two artificial neural network algorithms, was used to classify the response pattern and identify the gas vapor or odor. Two gas experiments were performed, one at low gas concentrations between 100 and 600 ppm for two gas vapors and the other at high gas concentrations between 2000 ppm and the saturated vapor pressure of three gas vapors. The array of sensors and circuits were able to uniquely detect and measure these gas vapors and showed a linear response to their concentration levels for both experiments. The results also demonstrated that a reduction in the sensor area by two orders of magnitude (from 4.32 mm² to 0.0625 mm²) did not affect the sensor response. By applying pattern-recognition algorithms, the electronic nose system was able to correctly identify the different gas vapors from the pattern responses of the sensor array.

Joint learning of ultrasonic backscattering statistical physics and signal confidence primal for characterizing atherosclerotic plaques using intravascular ultrasound.

PubMed

Sheet, Debdoot; Karamalis, Athanasios; Eslami, Abouzar; Noël, Peter; Chatterjee, Jyotirmoy; Ray, Ajoy K; Laine, Andrew F; Carlier, Stephane G; Navab, Nassir; Katouzian, Amin

2014-01-01

Intravascular Ultrasound (IVUS) is a predominant imaging modality in interventional cardiology. It provides real-time cross-sectional images of arteries and assists clinicians to infer about atherosclerotic plaques composition. These plaques are heterogeneous in nature and constitute fibrous tissue, lipid deposits and calcifications. Each of these tissues backscatter ultrasonic pulses and are associated with a characteristic intensity in B-mode IVUS image. However, clinicians are challenged when colocated heterogeneous tissue backscatter mixed signals appearing as non-unique intensity patterns in B-mode IVUS image. Tissue characterization algorithms have been developed to assist clinicians to identify such heterogeneous tissues and assess plaque vulnerability. In this paper, we propose a novel technique coined as Stochastic Driven Histology (SDH) that is able to provide information about co-located heterogeneous tissues. It employs learning of tissue specific ultrasonic backscattering statistical physics and signal confidence primal from labeled data for predicting heterogeneous tissue composition in plaques. We employ a random forest for the purpose of learning such a primal using sparsely labeled and noisy samples. In clinical deployment, the posterior prediction of different lesions constituting the plaque is estimated. Folded cross-validation experiments have been performed with 53 plaques indicating high concurrence with traditional tissue histology. On the wider horizon, this framework enables learning of tissue-energy interaction statistical physics and can be leveraged for promising clinical applications requiring tissue characterization beyond the application demonstrated in this paper. Copyright © 2013 Elsevier B.V. All rights reserved.

Discontinuity of cortical gradients reflects sensory impairment

PubMed Central

Saadon-Grosman, Noam; Tal, Zohar; Itshayek, Eyal; Amedi, Amir; Arzy, Shahar

2015-01-01

Topographic maps and their continuity constitute a fundamental principle of brain organization. In the somatosensory system, whole-body sensory impairment may be reflected either in cortical signal reduction or disorganization of the somatotopic map, such as disturbed continuity. Here we investigated the role of continuity in pathological states. We studied whole-body cortical representations in response to continuous sensory stimulation under functional MRI (fMRI) in two unique patient populations—patients with cervical sensory Brown-Séquard syndrome (injury to one side of the spinal cord) and patients before and after surgical repair of cervical disk protrusion—enabling us to compare whole-body representations in the same study subjects. We quantified the spatial gradient of cortical activation and evaluated the divergence from a continuous pattern. Gradient continuity was found to be disturbed at the primary somatosensory cortex (S1) and the supplementary motor area (SMA), in both patient populations: contralateral to the disturbed body side in the Brown-Séquard group and before repair in the surgical group, which was further improved after intervention. Results corresponding to the nondisturbed body side and after surgical repair were comparable with control subjects. No difference was found in the fMRI signal power between the different conditions in the two groups, as well as with respect to control subjects. These results suggest that decreased sensation in our patients is related to gradient discontinuity rather than signal reduction. Gradient continuity may be crucial for somatotopic and other topographical organization, and its disruption may characterize pathological processing. PMID:26655739

Hypothalamic Response to the Chemo-Signal Androstadienone in Gender Dysphoric Children and Adolescents

PubMed Central

Burke, Sarah M.; Cohen-Kettenis, Peggy T.; Veltman, Dick J.; Klink, Daniel T.; Bakker, Julie

2014-01-01

The odorous steroid androstadienone, a putative male chemo-signal, was previously reported to evoke sex differences in hypothalamic activation in adult heterosexual men and women. In order to investigate whether puberty modulated this sex difference in response to androstadienone, we measured the hypothalamic responsiveness to this chemo-signal in 39 pre-pubertal and 41 adolescent boys and girls by means of functional magnetic resonance imaging. We then investigated whether 36 pre-pubertal children and 38 adolescents diagnosed with gender dysphoria (GD; DSM-5) exhibited sex-atypical (in accordance with their experienced gender), rather than sex-typical (in accordance with their natal sex) hypothalamic activations during olfactory stimulation with androstadienone. We found that the sex difference in responsiveness to androstadienone was already present in pre-pubertal control children and thus likely developed during early perinatal development instead of during sexual maturation. Adolescent girls and boys with GD both responded remarkably like their experienced gender, thus sex-atypical. In contrast, pre-pubertal girls with GD showed neither a typically male nor female hypothalamic activation pattern and pre-pubertal boys with GD had hypothalamic activations in response to androstadienone that were similar to control boys, thus sex-typical. We present here a unique data set of boys and girls diagnosed with GD at two different developmental stages, showing that these children possess certain sex-atypical functional brain characteristics and may have undergone atypical sexual differentiation of the brain. PMID:24904525

Detectors for the Atacama B-mode Search experiment

NASA Astrophysics Data System (ADS)

Appel, John William

Inflation is the leading theory for explaining the initial conditions that brought about our homogeneous and isotropic Universe. It predicts the presence of gravitational waves in the early Universe, which implant a characteristic B-mode polarization pattern on the Cosmic Microwave Background (CMB). The Atacama B-mode Search (ABS) experiment is a polarimeter observing from Cerro Toco (located in the Atacama desert of Chile at an altitude of 5190 m), searching for the yet undetected B-mode signal. ABS carries 480 superconducting Transition Edge Sensor (TES) Bolometers that couple 150 GHz radiation via planar Ortho-Mode Transducers (OMTs) mounted at the output of corrugated feedhorns. The feedhorn beam is projected onto the sky through crossed Dragonian reflectors, a set of reflective and absorptive filters, and a rotating Half Wave Plate (HWP) that modulates any polarized sky signal at 10.2 Hz. The bolometers are cooled to 300 mK by a He3-He4 adsorption fridge system backed by pulse tubes. The reflectors are located within the 4 K cavity of the cryostat, while the HWP is mounted on frictionless air bearings above the cryostat window. This thesis discusses the development and construction of the ABS detector focal plane, and presents results of its performance in the field through August 2012. The ABS detector array sensitivity of 31 μKs 1/2, together with the experiment's unique set of systematic controls, and expected multi-year integration time, could detect a B-mode signal with tensor to scalar ratio r ˜ 0.1.

The Drosophila T-box transcription factor Midline functions within the Notch–Delta signaling pathway to specify sensory organ precursor cell fates and regulates cell survival within the eye imaginal disc

PubMed Central

Das, Sudeshna; Chen, Q. Brent; Saucier, Joseph D.; Drescher, Brandon; Zong, Yan; Morgan, Sarah; Forstall, John; Meriwether, Andrew; Toranzo, Randy; Leal, Sandra M.

2014-01-01

We report that the T-box transcription factor Midline (Mid), an evolutionary conserved homolog of the vertebrate Tbx20 protein, functions within the Notch–Delta signaling pathway essential for specifying the fates of sensory organ precursor cells. This complements an established history of research showing that Mid regulates the cell-fate specification of diverse cell types within the developing heart, epidermis and central nervous system. Tbx20 has been detected in diverse neuronal and epithelial cells of embryonic eye tissues in both mice and humans. However, the mechanisms by which either Mid or Tbx20 function to regulate cell-fate specification or other critical aspects of eye development including cell survival have not yet been elucidated. We have also gathered preliminary evidence suggesting that Mid may play an indirect, but vital role in selecting SOP cells within the third-instar larval eye disc by regulating the expression of the proneural gene atonal. During subsequent pupal stages, Mid specifies SOP cell fates as a member of the Notch–Delta signaling hierarchy and is essential for maintaining cell viability within by inhibiting apoptotic pathways. We present several new hypotheses that seek to understand the role of Mid in regulating developmental processes downstream of the Notch receptor that are critical for specifying unique cell fates, patterning the adult eye and maintaining cellular homeostasis during eye disc morphogenesis. PMID:23962751

Magnetic Resonance Fingerprinting - a promising new approach to obtain standardized imaging biomarkers from MRI.

PubMed

2015-04-01

Current routine MRI examinations rely on the acquisition of qualitative images that have a contrast "weighted" for a mixture of (magnetic) tissue properties. Recently, a novel approach was introduced, namely MR Fingerprinting (MRF) with a completely different approach to data acquisition, post-processing and visualization. Instead of using a repeated, serial acquisition of data for the characterization of individual parameters of interest, MRF uses a pseudo randomized acquisition that causes the signals from different tissues to have a unique signal evolution or 'fingerprint' that is simultaneously a function of the multiple material properties under investigation. The processing after acquisition involves a pattern recognition algorithm to match the fingerprints to a predefined dictionary of predicted signal evolutions. These can then be translated into quantitative maps of the magnetic parameters of interest. MR Fingerprinting (MRF) is a technique that could theoretically be applied to most traditional qualitative MRI methods and replaces them with acquisition of truly quantitative tissue measures. MRF is, thereby, expected to be much more accurate and reproducible than traditional MRI and should improve multi-center studies and significantly reduce reader bias when diagnostic imaging is performed. Key Points • MR fingerprinting (MRF) is a new approach to data acquisition, post-processing and visualization.• MRF provides highly accurate quantitative maps of T1, T2, proton density, diffusion.• MRF may offer multiparametric imaging with high reproducibility, and high potential for multicenter/ multivendor studies.

A decade of decoding reward-related fMRI signals and where we go from here.

PubMed

Kahnt, Thorsten

2017-06-04

Information about potential rewards in the environment is essential for guiding adaptive behavior, and understanding neural reward processes may provide insights into neuropsychiatric dysfunctions. Over the past 10 years, multivoxel pattern analysis (MVPA) techniques have been used to study brain areas encoding information about expected and experienced outcomes. These studies have identified reward signals throughout the brain, including the striatum, medial prefrontal cortex, orbitofrontal cortex, dorsolateral prefrontal cortex, and parietal cortex. This review article discusses some of the assumptions and models that are used to interpret results from these studies, and how they relate to findings from animal electrophysiology. The article reviews and summarizes some of the key findings from MVPA studies on reward. In particular, it first focuses on studies that, in addition to mapping out the brain areas that process rewards, have provided novel insights into the coding mechanisms of value and reward. Then, it discusses examples of how multivariate imaging approaches are being used more recently to decode features of expected rewards that go beyond value, such as the identity of an expected outcome or the action required to obtain it. The study of such complex and multifaceted reward representations highlights the key advantage of using representational methods, which are uniquely able to reveal these signals and may narrow the gap between animal and human research. Applied in a clinical context, MVPA may advance our understanding of neuropsychiatric disorders and the development of novel treatment strategies. Copyright © 2017 Elsevier Inc. All rights reserved.

A coded tracking telemetry system

USGS Publications Warehouse

Howey, P.W.; Seegar, W.S.; Fuller, M.R.; Titus, K.; Amlaner, Charles J.

1989-01-01

We describe the general characteristics of an automated radio telemetry system designed to operate for prolonged periods on a single frequency. Each transmitter sends a unique coded signal to a receiving system that encodes and records only the appropriater, pre-programmed codes. A record of the time of each reception is stored on diskettes in a micro-computer. This system enables continuous monitoring of infrequent signals (e.g. one per minute or one per hour), thus extending operation life or allowing size reduction of the transmitter, compared to conventional wildlife telemetry. Furthermore, when using unique codes transmitted on a single frequency, biologists can monitor many individuals without exceeding the radio frequency allocations for wildlife.

The Chemical Biology of HNO Signaling

PubMed Central

Bianco, Christopher L.; Toscano, John P.; Bartberger, Michael D.; Fukuto, Jon M.

2016-01-01

Nitroxyl (HNO) is a simple molecule with significant potential as a pharmacological agent. For example, its use in the possible treatment of heart failure has received recent attention due to its unique therapeutic properties. Recent progress has been made on the elucidation of the mechanisms associated with its biological signaling. Importantly, the biochemical mechanisms described for HNO bioactivity are consistent with its unique and novel chemical properties/reactivity. To date, much of the biology of HNO can be associated with interactions and modification of important regulatory thiol proteins. Herein will be provided a description of HNO chemistry and how this chemistry translates to some of its reported biological effects. PMID:27555493

Multi-functional optical signal processing using optical spectrum control circuit

NASA Astrophysics Data System (ADS)

Hayashi, Shuhei; Ikeda, Tatsuhiko; Mizuno, Takayuki; Takahashi, Hiroshi; Tsuda, Hiroyuki

2015-02-01

Processing ultra-fast optical signals without optical/electronic conversion is in demand and time-to-space conversion has been proposed as an effective solution. We have designed and fabricated an arrayed-waveguide grating (AWG) based optical spectrum control circuit (OSCC) using silica planar lightwave circuit (PLC) technology. This device is composed of an AWG, tunable phase shifters and a mirror. The principle of signal processing is to spatially decompose the signal's frequency components by using the AWG. Then, the phase of each frequency component is controlled by the tunable phase shifters. Finally, the light is reflected back to the AWG by the mirror and synthesized. Amplitude of each frequency component can be controlled by distributing the power to high diffraction order light. The spectral controlling range of the OSCC is 100 GHz and its resolution is 1.67 GHz. This paper describes equipping the OSCC with optical coded division multiplex (OCDM) encoder/decoder functionality. The encoding principle is to apply certain phase patterns to the signal's frequency components and intentionally disperse the signal. The decoding principle is also to apply certain phase patterns to the frequency components at the receiving side. If the applied phase pattern compensates the intentional dispersion, the waveform is regenerated, but if the pattern is not appropriate, the waveform remains dispersed. We also propose an arbitrary filter function by exploiting the OSCC's amplitude and phase control attributes. For example, a filtered optical signal transmitted through multiple optical nodes that use the wavelength multiplexer/demultiplexer can be equalized.

Evolution of Novel Signal Traits in the Absence of Female Preferences in Neoconocephalus Katydids (Orthoptera, Tettigoniidae)

PubMed Central

Bush, Sarah L.; Schul, Johannes

2010-01-01

Background Significance Communication signals that function to bring together the sexes are important for maintaining reproductive isolation in many taxa. Changes in male calls are often attributed to sexual selection, in which female preferences initiate signal divergence. Natural selection can also influence signal traits if calls attract predators or parasitoids, or if calling is energetically costly. Neutral evolution is often neglected in the context of acoustic communication. Methodology/Principal Findings We describe a signal trait that appears to have evolved in the absence of either sexual or natural selection. In the katydid genus Neoconocephalus, calls with a derived pattern in which pulses are grouped into pairs have evolved five times independently. We have previously shown that in three of these species, females require the double pulse pattern for call recognition, and hence the recognition system of the females is also in a derived state. Here we describe the remaining two species and find that although males produce the derived call pattern, females use the ancestral recognition mechanism in which no pulse pattern is required. Females respond equally well to the single and double pulse calls, indicating that the derived trait is selectively neutral in the context of mate recognition. Conclusions/Significance These results suggest that 1) neutral changes in signal traits could be important in the diversification of communication systems, and 2) males rather than females may be responsible for initiating signal divergence. PMID:20805980

Signaling by Bone Morphogenetic Proteins directs formation of an ectodermal signaling center that regulates craniofacial development

PubMed Central

Foppiano, Silvia; Hu, Diane; Marcucio, Ralph S.

2008-01-01

We previously described a signaling center, the Frontonasal Ectodermal Zone (FEZ) that regulates growth and patterning of the frontonasal process (FNP). The FEZ is comprised of FNP ectoderm flanking a boundary between Sonic hedgehog (Shh) and Fibroblast growth factor 8 (Fgf8) expression domains. Our objective was to examine BMP signaling during formation of the FEZ. We blocked BMP signaling throughout the FNP prior to FEZ formation by infecting chick embryos at stage 10 (HH10) with a replication competent avian retrovirus encoding the BMP antagonist Noggin. We assessed gene expression patterns in the FNP 72 hours after infection (~HH22) and observed that Shh expression was reduced or absent. In the mesenchyme we observed that Bmp2 transcripts were absent while the Bmp4 expression domain was expanded proximally. In addition to the molecular changes, infected embryos also exhibited facial malformations at 72 and 96 hours after infection suggesting that the FEZ did not form. Our data indicate that reduced cell proliferation, but not apoptosis, in the mesenchyme contributed to the phenotype that we observed. Additionally, adding exogenous SHH into the mesenchyme of RCAS-Noggin infected embryos did not restore Bmp2 and Bmp4 to a normal pattern of expression. These data indicate that BMP signaling mediates interactions between tissues in the FNP that regulate FEZ formation; and that the correct pattern of Bmp2 and Bmp4, but not Bmp7, expression in the FNP mesenchyme requires signaling by the BMP pathway. PMID:18028903

An intelligent signal processing and pattern recognition technique for defect identification using an active sensor network

NASA Astrophysics Data System (ADS)

Su, Zhongqing; Ye, Lin

2004-08-01

The practical utilization of elastic waves, e.g. Rayleigh-Lamb waves, in high-performance structural health monitoring techniques is somewhat impeded due to the complicated wave dispersion phenomena, the existence of multiple wave modes, the high susceptibility to diverse interferences, the bulky sampled data and the difficulty in signal interpretation. An intelligent signal processing and pattern recognition (ISPPR) approach using the wavelet transform and artificial neural network algorithms was developed; this was actualized in a signal processing package (SPP). The ISPPR technique comprehensively functions as signal filtration, data compression, characteristic extraction, information mapping and pattern recognition, capable of extracting essential yet concise features from acquired raw wave signals and further assisting in structural health evaluation. For validation, the SPP was applied to the prediction of crack growth in an alloy structural beam and construction of a damage parameter database for defect identification in CF/EP composite structures. It was clearly apparent that the elastic wave propagation-based damage assessment could be dramatically streamlined by introduction of the ISPPR technique.

Involvement of Hedgehog and FGF signalling in the lamprey telencephalon: evolution of regionalization and dorsoventral patterning of the vertebrate forebrain.

PubMed

Sugahara, Fumiaki; Aota, Shin-ichi; Kuraku, Shigehiro; Murakami, Yasunori; Takio-Ogawa, Yoko; Hirano, Shigeki; Kuratani, Shigeru

2011-03-01

Dorsoventral (DV) specification is a crucial step for the development of the vertebrate telencephalon. Clarifying the origin of this mechanism will lead to a better understanding of vertebrate central nervous system (CNS) evolution. Based on the lamprey, a sister group of the gnathostomes (jawed vertebrates), we identified three lamprey Hedgehog (Hh) homologues, which are thought to play central signalling roles in telencephalon patterning. However, unlike in gnathostomes, none of these genes, nor Lhx6/7/8, a marker for the migrating interneuron subtype, was expressed in the ventral telencephalon, consistent with the reported absence of the medial ganglionic eminence (MGE) in this animal. Homologues of Gsh2, Isl1/2 and Sp8, which are involved in the patterning of the lateral ganglionic eminence (LGE) of gnathostomes, were expressed in the lamprey subpallium, as in gnathostomes. Hh signalling is necessary for induction of the subpallium identity in the gnathostome telencephalon. When Hh signalling was inhibited, the ventral identity was disrupted in the lamprey, suggesting that prechordal mesoderm-derived Hh signalling might be involved in the DV patterning of the telencephalon. By blocking fibroblast growth factor (FGF) signalling, the ventral telencephalon was suppressed in the lamprey, as in gnathostomes. We conclude that Hh- and FGF-dependent DV patterning, together with the resultant LGE identity, are likely to have been established in a common ancestor before the divergence of cyclostomes and gnathostomes. Later, gnathostomes would have acquired a novel Hh expression domain corresponding to the MGE, leading to the obtainment of cortical interneurons.

Aggregation Dynamics Using Phase Wave Signals and Branching Patterns

NASA Astrophysics Data System (ADS)

Sakaguchi, Hidetsugu; Kusagaki, Takuma

2016-09-01

The aggregation dynamics of slime mold is studied using coupled equations of phase ϕ and cell concentration n. Phase waves work as tactic signals for aggregation. Branching structures appear during the aggregation. A stationary branching pattern appears like a river network, if cells are uniformly supplied into the system.

Maximum a posteriori decoder for digital communications

NASA Technical Reports Server (NTRS)

Altes, Richard A. (Inventor)

1997-01-01

A system and method for decoding by identification of the most likely phase coded signal corresponding to received data. The present invention has particular application to communication with signals that experience spurious random phase perturbations. The generalized estimator-correlator uses a maximum a posteriori (MAP) estimator to generate phase estimates for correlation with incoming data samples and for correlation with mean phases indicative of unique hypothesized signals. The result is a MAP likelihood statistic for each hypothesized transmission, wherein the highest value statistic identifies the transmitted signal.

Adhesive micro-line periodicity determines guidance of axonal outgrowth†

PubMed Central

Huang, Yu; Fothergill, Thomas; Lumbard, Derek C.; Dent, Erik W.; Williams, Justin C.

2014-01-01

Adhesive micro-lines of various sub-cellular geometries were created using a non-traditional micro stamping technique. This technique employed the use of commercially available diffraction gratings as the molds for the micro stamps, a method which is quick and inexpensive, and which could easily be adopted as a patterning tool in a variety of research efforts. The atypical saw-tooth profile of the micro stamps enabled a unique degree of control and flexibility over patterned line and gap widths. Cortical neurons cultured on patterned poly-lysine micro-lines on PDMS exhibit a startling transition in axonal guidance: From the expected parallel guidance to an unexpected perpendicular guidance that becomes dominant as patterned lines and gaps become sufficiently narrow. This transition is most obvious when the lines are narrow relative to gaps, while the periodicity of the pattern is reduced. Axons growing perpendicular to micro-lines exhibited ‘vinculated’ growth, a unique morphological phenotype consisting of periodic orthogonal extensions along the axon. PMID:23250489

Effects of Age, Gender and Hemispheric Location on T2 Hypointensity in the Pulvinar at 3T.

PubMed

White, Matthew L; Zhang, Yan; Helvey, Jason T; Yu, Fang; Omojola, Matthew F

2014-12-01

Pulvinar signal intensity decrease on T2-weighted images has been reported in some neurological abnormalities. We aimed to define the normal T2 signal hypointensity pattern present in the pulvinar to avoid erroneous radiological interpretation. One hundred and forty-two subjects (54 men and 88 women; age range 9-91 years) with unremarkable brain 3T MR findings were enrolled. MR images were analyzed with regard to signal intensity of the pulvinar relative to the thalamus on fluid attenuated inversion recovery images. Effects of age, gender and hemispheric location on the degree of T2 hypointensity were statistically analyzed. The statistical association was measured between the pattern of signal changes in the pulvinar region and that in the putamen and the globus pallidus. We detected a linear signal decrease in the pulvinar region with age. The male subjects had a more rapid decrease of signal with age than female subjects. The right pulvinar region had a higher chance of hypointensity compared to the left. A positive linear association was found when signal change from the pulvinar region was compared with signal in the putamen and globus pallidus. We detected a linear signal decrease with age in the pulvinar. The physiological signal features of the pulvinar also depend on gender and hemispheric lateralization. The pattern of signal change in the pulvinar is similar to but not the same as that in the putamen and globus pallidus.

A new approach to pattern metrology

NASA Astrophysics Data System (ADS)

Ausschnitt, Christopher P.

2004-05-01

We describe an approach to pattern metrology that enables the simultaneous determination of critical dimensions, overlay and film thickness. A single optical system captures nonzero- and zero-order diffracted signals from illuminated grating targets, as well as unpatterned regions of the surrounding substrate. Differential targets provide in situ dimensional calibration. CD target signals are analyzed to determine average dimension, profile attributes, and effective dose and defocus. In turn, effective dose and defocus determines all CDs pre-correlated to the dose and focus settings of the exposure tool. Overlay target signals are analyzed to determine the relative reflectivity of the layer pair and the overlay error between them. Compared to commercially available pattern metrology (SEM, optical microscopy, AFM, scatterometry and schnitzlometry), our approach promises improved signal-to-noise, higher throughput and smaller targets. We have dubbed this optical chimera MOXIE (Metrology Of eXtremely Irrational Exuberance).

Faster embryonic segmentation through elevated Delta-Notch signalling

PubMed Central

Liao, Bo-Kai; Jörg, David J.; Oates, Andrew C.

2016-01-01

An important step in understanding biological rhythms is the control of period. A multicellular, rhythmic patterning system termed the segmentation clock is thought to govern the sequential production of the vertebrate embryo's body segments, the somites. Several genetic loss-of-function conditions, including the Delta-Notch intercellular signalling mutants, result in slower segmentation. Here, we generate DeltaD transgenic zebrafish lines with a range of copy numbers and correspondingly increased signalling levels, and observe faster segmentation. The highest-expressing line shows an altered oscillating gene expression wave pattern and shortened segmentation period, producing embryos with more, shorter body segments. Our results reveal surprising differences in how Notch signalling strength is quantitatively interpreted in different organ systems, and suggest a role for intercellular communication in regulating the output period of the segmentation clock by altering its spatial pattern. PMID:27302627

A Comparison of Facial Color Pattern and Gazing Behavior in Canid Species Suggests Gaze Communication in Gray Wolves (Canis lupus)

PubMed Central

Ueda, Sayoko; Kumagai, Gaku; Otaki, Yusuke; Yamaguchi, Shinya; Kohshima, Shiro

2014-01-01

As facial color pattern around the eyes has been suggested to serve various adaptive functions related to the gaze signal, we compared the patterns among 25 canid species, focusing on the gaze signal, to estimate the function of facial color pattern in these species. The facial color patterns of the studied species could be categorized into the following three types based on contrast indices relating to the gaze signal: A-type (both pupil position in the eye outline and eye position in the face are clear), B-type (only the eye position is clear), and C-type (both the pupil and eye position are unclear). A-type faces with light-colored irises were observed in most studied species of the wolf-like clade and some of the red fox-like clade. A-type faces tended to be observed in species living in family groups all year-round, whereas B-type faces tended to be seen in solo/pair-living species. The duration of gazing behavior during which the facial gaze-signal is displayed to the other individual was longest in gray wolves with typical A-type faces, of intermediate length in fennec foxes with typical B-type faces, and shortest in bush dogs with typical C-type faces. These results suggest that the facial color pattern of canid species is related to their gaze communication and that canids with A-type faces, especially gray wolves, use the gaze signal in conspecific communication. PMID:24918751

Aging in the natural world: comparative data reveal similar mortality patterns across primates.

PubMed

Bronikowski, Anne M; Altmann, Jeanne; Brockman, Diane K; Cords, Marina; Fedigan, Linda M; Pusey, Anne; Stoinski, Tara; Morris, William F; Strier, Karen B; Alberts, Susan C

2011-03-11

Human senescence patterns-late onset of mortality increase, slow mortality acceleration, and exceptional longevity-are often described as unique in the animal world. Using an individual-based data set from longitudinal studies of wild populations of seven primate species, we show that contrary to assumptions of human uniqueness, human senescence falls within the primate continuum of aging; the tendency for males to have shorter life spans and higher age-specific mortality than females throughout much of adulthood is a common feature in many, but not all, primates; and the aging profiles of primate species do not reflect phylogenetic position. These findings suggest that mortality patterns in primates are shaped by local selective forces rather than phylogenetic history.

Inhibition of Wnt signaling by Wise (Sostdc1) and negative feedback from Shh controls tooth number and patterning.

PubMed

Ahn, Youngwook; Sanderson, Brian W; Klein, Ophir D; Krumlauf, Robb

2010-10-01

Mice carrying mutations in Wise (Sostdc1) display defects in many aspects of tooth development, including tooth number, size and cusp pattern. To understand the basis of these defects, we have investigated the pathways modulated by Wise in tooth development. We present evidence that, in tooth development, Wise suppresses survival of the diastema or incisor vestigial buds by serving as an inhibitor of Lrp5- and Lrp6-dependent Wnt signaling. Reducing the dosage of the Wnt co-receptor genes Lrp5 and Lrp6 rescues the Wise-null tooth phenotypes. Inactivation of Wise leads to elevated Wnt signaling and, as a consequence, vestigial tooth buds in the normally toothless diastema region display increased proliferation and continuous development to form supernumerary teeth. Conversely, gain-of-function studies show that ectopic Wise reduces Wnt signaling and tooth number. Our analyses demonstrate that the Fgf and Shh pathways are major downstream targets of Wise-regulated Wnt signaling. Furthermore, our experiments revealed that Shh acts as a negative-feedback regulator of Wnt signaling and thus determines the fate of the vestigial buds and later tooth patterning. These data provide insight into the mechanisms that control Wnt signaling in tooth development and into how crosstalk among signaling pathways controls tooth number and morphogenesis.

Encoding of temporal signals by the TGF-β pathway and implications for embryonic patterning

PubMed Central

Sorre, Benoit; Warmflash, Aryeh; Brivanlou, Ali H.; Siggia, Eric D.

2014-01-01

Summary Genetics and biochemistry have defined the components and wiring of the signaling pathways that pattern the embryo. Among them, the TGF-β pathway has the potential to behave as a morphogen: invitro experiments have clearly established that it can dictate cell fate in a concentration dependent manner. How morphogens convey positional information in a developing embryo, where signal levels are changing with time, is less understood. Using integrated microfluidic cell culture and time-lapse microscopy, we demonstrate here that the speed of ligand presentation has a key and previously unexpected influence on TGF-β signaling outcomes. The response to a TGF-β concentration step is transient and adaptive, slowly increasing the ligand concentration diminishes the response and well-spaced pulses of ligand combine additively resulting in greater pathway output than with constant stimulation. Our results suggest that in an embryonic context, the speed of change of ligand concentration is an instructive signal for patterning. PMID:25065773

Integrating patterning signals: Wnt/GSK3 regulates the duration of the BMP/Smad1 signal.

PubMed

Fuentealba, Luis C; Eivers, Edward; Ikeda, Atsushi; Hurtado, Cecilia; Kuroda, Hiroki; Pera, Edgar M; De Robertis, Edward M

2007-11-30

BMP receptors determine the intensity of BMP signals via Smad1 C-terminal phosphorylations. Here we show that a finely controlled cell biological pathway terminates this activity. The duration of the activated pSmad1(Cter) signal was regulated by sequential Smad1 linker region phosphorylations at conserved MAPK and GSK3 sites required for its polyubiquitinylation and transport to the centrosome. Proteasomal degradation of activated Smad1 and total polyubiquitinated proteins took place in the centrosome. Inhibitors of the Erk, p38, and JNK MAPKs, as well as GSK3 inhibitors, prolonged the duration of a pulse of BMP7. Wnt signaling decreased pSmad1(GSK3) antigen levels and redistributed it from the centrosome to cytoplasmic LRP6 signalosomes. In Xenopus embryos, it was found that Wnts induce epidermis and that this required an active BMP-Smad pathway. Epistatic experiments suggested that the dorsoventral (BMP) and anteroposterior (Wnt/GSK3) patterning gradients are integrated at the level of Smad1 phosphorylations during embryonic pattern formation.

Synchronization transmission of laser pattern signal within uncertain switched network

NASA Astrophysics Data System (ADS)

Lü, Ling; Li, Chengren; Li, Gang; Sun, Ao; Yan, Zhe; Rong, Tingting; Gao, Yan

2017-06-01

We propose a new technology for synchronization transmission of laser pattern signal within uncertain network with controllable topology. In synchronization process, the connection of dynamic network can vary at all time according to different demands. Especially, we construct the Lyapunov function of network through designing a special semi-positive definite function, and the synchronization transmission of laser pattern signal within uncertain network with controllable topology can be realized perfectly, which effectively avoids the complicated calculation for solving the second largest eignvalue of the coupling matrix of the dynamic network in order to obtain the network synchronization condition. At the same time, the uncertain parameters in dynamic equations belonging to network nodes can also be identified accurately via designing the identification laws of uncertain parameters. In addition, there are not any limitations for the synchronization target of network in the new technology, in other words, the target can either be a state variable signal of an arbitrary node within the network or an exterior signal.

Antibody protection reveals extended epitopes on the human TSH receptor.

PubMed

Latif, Rauf; Teixeira, Avelino; Michalek, Krzysztof; Ali, M Rejwan; Schlesinger, Max; Baliram, Ramkumarie; Morshed, Syed A; Davies, Terry F

2012-01-01

Stimulating, and some blocking, antibodies to the TSH receptor (TSHR) have conformation-dependent epitopes reported to involve primarily the leucine rich repeat region of the ectodomain (LRD). However, successful crystallization of TSHR residues 22-260 has omitted important extracellular non-LRD residues including the hinge region which connects the TSHR ectodomain to the transmembrane domain and which is involved in ligand induced signal transduction. The aim of the present study, therefore, was to determine if TSHR antibodies (TSHR-Abs) have non-LRD binding sites outside the LRD. To obtain this information we employed the method of epitope protection in which we first protected TSHR residues 1-412 with intact TSHR antibodies and then enzymatically digested the unprotected residues. Those peptides remaining were subsequently delineated by mass spectrometry. Fourteen out of 23 of the reported stimulating monoclonal TSHR-Ab crystal contact residues were protected by this technique which may reflect the higher binding energies of certain residues detected in this approach. Comparing the protected epitopes of two stimulating TSHR-Abs we found both similarities and differences but both antibodies also contacted the hinge region and the amino terminus of the TSHR following the signal peptide and encompassing cysteine box 1 which has previously been shown to be important for TSH binding and activation. A monoclonal blocking TSHR antibody revealed a similar pattern of binding regions but the residues that it contacted on the LRD were again distinct. These data demonstrated that conformationally dependent TSHR-Abs had epitopes not confined to the LRDs but also incorporated epitopes not revealed in the available crystal structure. Furthermore, the data also indicated that in addition to overlapping contact regions within the LRD, there are unique epitope patterns for each of the antibodies which may contribute to their functional heterogeneity.

Antibody Protection Reveals Extended Epitopes on the Human TSH Receptor

PubMed Central

Latif, Rauf; Teixeira, Avelino; Michalek, Krzysztof; Ali, M. Rejwan; Schlesinger, Max; Baliram, Ramkumarie; Morshed, Syed A.; Davies, Terry F.

2012-01-01

Stimulating, and some blocking, antibodies to the TSH receptor (TSHR) have conformation-dependent epitopes reported to involve primarily the leucine rich repeat region of the ectodomain (LRD). However, successful crystallization of TSHR residues 22–260 has omitted important extracellular non-LRD residues including the hinge region which connects the TSHR ectodomain to the transmembrane domain and which is involved in ligand induced signal transduction. The aim of the present study, therefore, was to determine if TSHR antibodies (TSHR-Abs) have non-LRD binding sites outside the LRD. To obtain this information we employed the method of epitope protection in which we first protected TSHR residues 1–412 with intact TSHR antibodies and then enzymatically digested the unprotected residues. Those peptides remaining were subsequently delineated by mass spectrometry. Fourteen out of 23 of the reported stimulating monoclonal TSHR-Ab crystal contact residues were protected by this technique which may reflect the higher binding energies of certain residues detected in this approach. Comparing the protected epitopes of two stimulating TSHR-Abs we found both similarities and differences but both antibodies also contacted the hinge region and the amino terminus of the TSHR following the signal peptide and encompassing cysteine box 1 which has previously been shown to be important for TSH binding and activation. A monoclonal blocking TSHR antibody revealed a similar pattern of binding regions but the residues that it contacted on the LRD were again distinct. These data demonstrated that conformationally dependent TSHR-Abs had epitopes not confined to the LRDs but also incorporated epitopes not revealed in the available crystal structure. Furthermore, the data also indicated that in addition to overlapping contact regions within the LRD, there are unique epitope patterns for each of the antibodies which may contribute to their functional heterogeneity. PMID:22957097

Trends in funding for research on pain: a report on the National Institutes Of Health grant awards over the years 2003 to 2007.

PubMed

Bradshaw, David H; Empy, Court; Davis, Phillip; Lipschitz, David; Dalton, Peter; Nakamura, Yoshio; Chapman, C Richard

2008-12-01

In recent years, the National Institutes of Health (NIH) has experienced unprecedented reductions in its customary annual budget increases. Consequently, researchers, health care policy planners and others have a pressing need for accurate information on NIH funding patterns. We created a unique and objective system for compiling, classifying, and analyzing data on NIH grant awards and funding for research on pain, nausea, and dyspnea using naïve observers, cross-validation by multiple raters, and face validation by experts. We present results of our method and analyses for the period from 2003 to 2007. Following a 12% increase from 2003 to 2004, funding for pain research fell by 9.4% per year on average over the next 3 years. The percent of the total NIH budget going to support pain research increased to 0.78% in 2004 but fell to 0.61% in 2007. A piecewise regression model confirmed the declining trend represented a significant fit to the data (R(2)=0.98, p=0.024). Separate breakdowns by Institutes showed similar patterns. Analyses of nausea and dyspnea research support revealed small but steady increases over the same period. Declining support for pain research disproportionate to decreases in the NIH budget signals a need for measures to promote funding for meritorious applications. Results of 5 year trends in numbers of grants and funding for research in pain, nausea, and dyspnea by the NIH show overall declines for pain but slight increases for nausea and dyspnea. Declining support for pain research that exceeds the reductions in the total NIH budget signals a need for measures to increase pain research funding.

Bacteria in the vaginal microbiome alter the innate immune response and barrier properties of the human vaginal epithelia in a species-specific manner.

PubMed

Doerflinger, Sylvie Y; Throop, Andrea L; Herbst-Kralovetz, Melissa M

2014-06-15

Bacterial vaginosis increases the susceptibility to sexually transmitted infections and negatively affects women's reproductive health. To investigate host-vaginal microbiota interactions and the impact on immune barrier function, we colonized 3-dimensional (3-D) human vaginal epithelial cells with 2 predominant species of vaginal microbiota (Lactobacillus iners and Lactobacillus crispatus) or 2 prevalent bacteria associated with bacterial vaginosis (Atopobium vaginae and Prevotella bivia). Colonization of 3-D vaginal epithelial cell aggregates with vaginal microbiota was observed with direct attachment to host cell surface with no cytotoxicity. A. vaginae infection yielded increased expression membrane-associated mucins and evoked a robust proinflammatory, immune response in 3-D vaginal epithelial cells (ie, expression of CCL20, hBD-2, interleukin 1β, interleukin 6, interleukin 8, and tumor necrosis factor α) that can negatively affect barrier function. However, P. bivia and L. crispatus did not significantly upregulate pattern-recognition receptor-signaling, mucin expression, antimicrobial peptides/defensins, or proinflammatory cytokines in 3-D vaginal epithelial cell aggregates. Notably, L. iners induced pattern-recognition receptor-signaling activity, but no change was observed in mucin expression or secretion of interleukin 6 and interleukin 8. We identified unique species-specific immune signatures from vaginal epithelial cells elicited by colonization with commensal and bacterial vaginosis-associated bacteria. A. vaginae elicited a signature that is consistent with significant disruption of immune barrier properties, potentially resulting in enhanced susceptibility to sexually transmitted infections during bacterial vaginosis. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Temporal and Embryonic Lineage-Dependent Regulation of Human Vascular SMC Development by NOTCH3

PubMed Central

Granata, Alessandra; Bernard, William G.; Zhao, Ning; Mccafferty, John; Lilly, Brenda

2015-01-01

Vascular smooth muscle cells (SMCs), which arise from multiple embryonic progenitors, have unique lineage-specific properties and this diversity may contribute to spatial patterns of vascular diseases. We developed in vitro methods to generate distinct vascular SMC subtypes from human pluripotent stem cells, allowing us to explore their intrinsic differences and the mechanisms involved in SMC development. Since Notch signaling is thought to be one of the several key regulators of SMC differentiation and function, we profiled the expression of Notch receptors, ligands, and downstream elements during the development of origin-specific SMC subtypes. NOTCH3 expression in our in vitro model varied in a lineage- and developmental stage-specific manner so that the highest expression in mature SMCs was in those derived from paraxial mesoderm (PM). This pattern was consistent with the high expression level of NOTCH3 observed in the 8–9 week human fetal descending aorta, which is populated by SMCs of PM origin. Silencing NOTCH3 in mature SMCs in vitro reduced SMC markers in cells of PM origin preferentially. Conversely, during early development, NOTCH3 was highly expressed in vitro in SMCs of neuroectoderm (NE) origin. Inhibition of NOTCH3 in early development resulted in a significant downregulation of specific SMC markers exclusively in the NE lineage. Corresponding to this prediction, the Notch3-null mouse showed reduced expression of Acta2 in the neural crest-derived SMCs of the aortic arch. Thus, Notch3 signaling emerges as one of the key regulators of vascular SMC differentiation and maturation in vitro and in vivo in a lineage- and temporal-dependent manner. PMID:25539150

Genetics Home Reference: Naegeli-Franceschetti-Jadassohn syndrome/dermatopathia pigmentosa reticularis

MedlinePlus

... that are the basis for each person's unique fingerprints. Additional features of NFJS/DPR can include a ... Mutations and Health Inheritance Pattern This condition is inherited in an autosomal dominant pattern , which means one ...

Cellular targeting and host-specific recognition of cyst nematode CLE proteins

USDA-ARS?s Scientific Manuscript database

Cyst nematodes produce secreted peptide mimics of plant CLAVATA3/ESR (CLE) peptides likely involved in redirecting CLE signaling pathways active in roots to form unique and essential feeding cells. The hallmark structure of plant CLEs, which includes an N-terminal signal peptide, a highly variable d...

In situ hybridization protocol for enhanced detection of gene expression in the planarian Schmidtea mediterranea

PubMed Central

2013-01-01

Background The freshwater planarian Schmidtea mediterranea has emerged as a powerful model for studies of regenerative, stem cell, and germ cell biology. Whole-mount in situ hybridization (WISH) and whole-mount fluorescent in situ hybridization (FISH) are critical methods for determining gene expression patterns in planarians. While expression patterns for a number of genes have been elucidated using established protocols, determining the expression patterns for particularly low-abundance transcripts remains a challenge. Results We show here that a short bleaching step in formamide dramatically enhances signal intensity of WISH and FISH. To further improve signal sensitivity we optimized blocking conditions for multiple anti-hapten antibodies, developed a copper sulfate quenching step that virtually eliminates autofluorescence, and enhanced signal intensity through iterative rounds of tyramide signal amplification. For FISH on regenerating planarians, we employed a heat-induced antigen retrieval step that provides a better balance between permeabilization of mature tissues and preservation of regenerating tissues. We also show that azide most effectively quenches peroxidase activity between rounds of development for multicolor FISH experiments. Finally, we apply these modifications to elucidate the expression patterns of a few low-abundance transcripts. Conclusion The modifications we present here provide significant improvements in signal intensity and signal sensitivity for WISH and FISH in planarians. Additionally, these modifications might be of widespread utility for whole-mount FISH in other model organisms. PMID:23497040

Genomic status of MET potentiates sensitivity to MET and MEK inhibition in NF1-related malignant peripheral nerve sheath tumors.

PubMed

Peacock, Jacqueline D; Pridgeon, Matthew G; Tovar, Elizabeth A; Essenburg, Curt J; Bowman, Megan J; Madaj, Zachary B; Koeman, Julie; Boguslawski, Elissa A; Grit, Jamie; Dodd, Rebecca D; Khachaturov, Vadim; Cardona, Diana M; Chen, Mark; Kirsch, David G; Maina, Flavio; Dono, Rosanna; Winn, Mary E; Graveel, Carrie R; Steensma, Matthew R

2018-05-02

Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are highly resistant sarcomas that occur in up to 13% of individuals with Neurofibromatosis Type 1 (NF1). Genomic analysis of longitudinally collected tumor samples in a case of MPNST disease progression revealed early hemizygous microdeletions in NF1 and TP53, with progressive amplifications of MET, HGF, and EGFR. To examine the role of MET in MPNST progression, we developed mice with enhanced MET expression and Nf1 ablation (Nf1fl/KO;lox-stop-loxMETtg/+;Plp-creERTtg/+; referred to as NF1 MET). NF1-MET mice express a robust MPNST phenotype in the absence of additional mutations. A comparison of NF1-MET MPNSTs with MPNSTs derived from Nf1KO/+;p53R172H;Plp-creERTtg/+ (NF1-P53) and Nf1KO/+;Plp-creERTtg/+ (NF1) mice revealed unique Met, Ras, and PI3K signaling patterns. NF1-MET MPNSTs were uniformly sensitive to the highly selective MET inhibitor, capmatinib, whereas a heterogeneous response to MET inhibition was observed in NF1-P53 and NF1 MPNSTs. Combination therapy of capmatinib and the MEK inhibitor trametinib resulted in reduced response variability, enhanced suppression of tumor growth, and suppressed RAS/ERK and PI3K/AKT signaling. These results highlight the influence of concurrent genomic alterations on RAS effector signaling and therapy response to tyrosine kinase inhibitors. Moreover, these findings expand our current understanding of the role of MET signaling in MPNST progression and identify a potential therapeutic niche for NF1-related MPNSTs. Copyright ©2018, American Association for Cancer Research.

Directed midbrain and spinal cord neurogenesis from pluripotent stem cells to model development and disease in a dish

PubMed Central

Allodi, Ilary; Hedlund, Eva

2014-01-01

Induction of specific neuronal fates is restricted in time and space in the developing CNS through integration of extrinsic morphogen signals and intrinsic determinants. Morphogens impose regional characteristics on neural progenitors and establish distinct progenitor domains. Such domains are defined by unique expression patterns of fate determining transcription factors. These processes of neuronal fate specification can be recapitulated in vitro using pluripotent stem cells. In this review, we focus on the generation of dopamine neurons and motor neurons, which are induced at ventral positions of the neural tube through Sonic hedgehog (Shh) signaling, and defined at anteroposterior positions by fibroblast growth factor (Fgf) 8, Wnt1, and retinoic acid (RA). In vitro utilization of these morphogenic signals typically results in the generation of multiple neuronal cell types, which are defined at the intersection of these signals. If the purpose of in vitro neurogenesis is to generate one cell type only, further lineage restriction can be accomplished by forced expression of specific transcription factors in a permissive environment. Alternatively, cell-sorting strategies allow for selection of neuronal progenitors or mature neurons. However, modeling development, disease and prospective therapies in a dish could benefit from structured heterogeneity, where desired neurons are appropriately synaptically connected and thus better reflect the three-dimensional structure of that region. By modulating the extrinsic environment to direct sequential generation of neural progenitors within a domain, followed by self-organization and synaptic establishment, a reductionist model of that brain region could be created. Here we review recent advances in neuronal fate induction in vitro, with a focus on the interplay between cell intrinsic and extrinsic factors, and discuss the implications for studying development and disease in a dish. PMID:24904255

Integrated three-dimensional optical MEMS for chip-based fluorescence detection

NASA Astrophysics Data System (ADS)

Hung, Kuo-Yung; Tseng, Fan-Gang; Khoo, Hwa-Seng

2009-04-01

This paper presents a novel fluorescence sensing chip for parallel protein microarray detection in the context of a 3-in-1 protein chip system. This portable microchip consists of a monolithic integration of CMOS-based avalanche photo diodes (APDs) combined with a polymer micro-lens, a set of three-dimensional (3D) inclined mirrors for separating adjacent light signals and a low-noise transformer-free dc-dc boost mini-circuit to power the APDs (ripple below 1.28 mV, 0-5 V input, 142 V and 12 mA output). We fabricated our APDs using the planar CMOS process so as to facilitate the post-CMOS integration of optical MEMS components such as the lenses. The APD arrays were arranged in unique circular patterns appropriate for detecting the specific fluorescently labelled protein spots in our study. The array-type APDs were designed so as to compensate for any alignment error as detected by a positional error signal algorithm. The condenser lens was used as a structure for light collection to enhance the fluorescent signals by about 25%. This element also helped to reduce the light loss due to surface absorption. We fabricated an inclined mirror to separate two adjacent fluorescent signals from different specimens. Excitation using evanescent waves helped reduce the interference of the excitation light source. This approach also reduced the number of required optical lenses and minimized the complexity of the structural design. We achieved detection floors for anti-rabbit IgG and Cy5 fluorescent dye as low as 0.5 ng/µl (~3.268 nM). We argue that the intrinsic nature of point-to-point and batch-detection methods as showcased in our chip offers advantages over the serial-scanning approach used in traditional scanner systems. In addition, our system is low cost and lightweight.

Directed midbrain and spinal cord neurogenesis from pluripotent stem cells to model development and disease in a dish.

PubMed

Allodi, Ilary; Hedlund, Eva

2014-01-01

Induction of specific neuronal fates is restricted in time and space in the developing CNS through integration of extrinsic morphogen signals and intrinsic determinants. Morphogens impose regional characteristics on neural progenitors and establish distinct progenitor domains. Such domains are defined by unique expression patterns of fate determining transcription factors. These processes of neuronal fate specification can be recapitulated in vitro using pluripotent stem cells. In this review, we focus on the generation of dopamine neurons and motor neurons, which are induced at ventral positions of the neural tube through Sonic hedgehog (Shh) signaling, and defined at anteroposterior positions by fibroblast growth factor (Fgf) 8, Wnt1, and retinoic acid (RA). In vitro utilization of these morphogenic signals typically results in the generation of multiple neuronal cell types, which are defined at the intersection of these signals. If the purpose of in vitro neurogenesis is to generate one cell type only, further lineage restriction can be accomplished by forced expression of specific transcription factors in a permissive environment. Alternatively, cell-sorting strategies allow for selection of neuronal progenitors or mature neurons. However, modeling development, disease and prospective therapies in a dish could benefit from structured heterogeneity, where desired neurons are appropriately synaptically connected and thus better reflect the three-dimensional structure of that region. By modulating the extrinsic environment to direct sequential generation of neural progenitors within a domain, followed by self-organization and synaptic establishment, a reductionist model of that brain region could be created. Here we review recent advances in neuronal fate induction in vitro, with a focus on the interplay between cell intrinsic and extrinsic factors, and discuss the implications for studying development and disease in a dish.

Costimulatory receptors in a teleost fish: Typical CD28, elusive CTLA4

USGS Publications Warehouse

Bernard, D.; Riteau, B.; Hansen, J.D.; Phillips, R.B.; Michel, F.; Boudinot, P.; Benmansour, A.

2006-01-01

T cell activation requires both specific recognition of the peptide-MHC complex by the TCR and additional signals delivered by costimulatory receptors. We have identified rainbow trout sequences similar to CD28 (rbtCD28) and CTLA4 (rbtCTLA4). rbtCD28 and rbtCTLA4 are composed of an extracellular Ig-superfamily V domain, a transmembrane region, and a cytoplasmic tail. The presence of a conserved ligand binding site within the V domain of both molecules suggests that these receptors likely recognize the fish homologues of the B7 family. The mRNA expression pattern of rbtCD28 and rbtCTLA4 in naive trout is reminiscent to that reported in humans and mice, because rbtCTLA4 expression within trout leukocytes was quickly up-regulated following PHA stimulation and virus infection. The cytoplasmic tail of rbtCD28 possesses a typical motif that is conserved in mammalian costimulatory receptors for signaling purposes. A chimeric receptor made of the extracellular domain of human CD28 fused to the cytoplasmic tail of rbtCD28 promoted TCR-induced IL-2 production in a human T cell line, indicating that rbtCD28 is indeed a positive costimulator. The cytoplasmic tail of rtrtCTLA4 lacked obvious signaling motifs and accordingly failed to signal when fused to the huCD28 extracellular domain. Interestingly, rbtCTLA4 and rbtCD28 are not positioned on the same chromosome and thus do not belong to a unique costimulatory cluster as in mammals. Finally, oar results raise questions about the origin and evolution of positive and negative costimulation in vertebrate immune systems. Copyright ?? 2006 by The American Association of Immunologists, Inc.

Notch-Induced Expression of FZD7 Requires Noncanonical NOTCH3 Signaling in Human Breast Epithelial Cells.

PubMed

Bhat, Vasudeva; Sun, Yu Jia; Weger, Steve; Raouf, Afshin

2016-04-01

The evolutionarily conserved Notch and Wnt signaling pathways have demonstrated roles in normal mammary gland development and in breast carcinogenesis. We previously reported that in human mammary gland, signaling through NOTCH3 alone regulates the commitment of the undifferentiated bipotential progenitors to the luminal cell fate, indicating that NOTCH3 may regulate the expression of unique genes apart from the other Notch receptors. In this study, we used gain of function and loss of function experiments and found that a Wnt signaling receptor, Frizzled7 (FZD7), is a unique and nonredundant target of NOTCH3 in human breast epithelial cells. Interestingly, neither the constitutively active forms of NOTCH1-2, 4 nor loss of expression of these receptors were able to alter expression of FZD7 in human breast epithelial cells. We further show that FZD7-expressing cells are found more frequently in the luminal progenitor-enriched subpopulation of cells obtained from breast reduction samples compared with the undifferentiated bipotent progenitors. Also, we show that NOTCH3-induced expression of FZD7 occurs in the absence of CSL (CBF1-Suppressor of Hairless-Lag-1). Our data suggest that noncanonical Notch signaling through NOTCH3 could modulate Wnt signaling via FZD7 and in this way, might be involved in luminal cell differentiation.

Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics

PubMed Central

Haake, Scott M.; Li, Jiannong; Bai, Yun; Kinose, Fumi; Fang, Bin; Welsh, Eric; Zent, Roy; Dhillon, Jasreman; Pow-Sang, Julio; Chen, Yian Ann; Koomen, John; Rathmell, W. Kimryn; Fishman, Mayer; Haura, Eric B.

2016-01-01

Purpose Targeted therapies in renal cell carcinoma (RCC) are limited by acquired resistance. Novel therapeutic targets are needed to combat resistance and, ideally, target the unique biology of RCC subtypes. Experimental Design Tyrosine kinases provide critical oncogenic signaling and their inhibition has significantly impacted cancer care. In order to describe a landscape of tyrosine kinase activity in RCC that could inform novel therapeutic strategies, we performed a mass spectrometry-based system-wide survey of tyrosine phosphorylation in 10 RCC cell lines as well as 15 clear cell and 15 papillary RCC human tumors. To prioritize identified tyrosine kinases for further analysis, a 63 tyrosine kinase inhibitor (TKI) drug screen was performed. Results Among the cell lines, 28 unique tyrosine phosphosites were identified across 19 kinases and phosphatases including EGFR, MET, JAK2, and FAK in nearly all samples. Multiple FAK TKIs decreased cell viability by at least 50% and inhibited RCC cell line adhesion, invasion, and proliferation. Among the tumors, 49 unique tyrosine phosphosites were identified across 44 kinases and phosphatases. FAK pY576/7 was found in all tumors and many cell lines, while DDR1 pY792/6 was preferentially enriched in the papillary RCC tumors. Both tyrosine kinases are capable of transmitting signals from the extracellular matrix and emerged as novel RCC therapeutic targets. Conclusions Tyrosine kinase profiling informs novel therapeutic strategies in RCC and highlights the unique biology amongst kidney cancer subtypes. PMID:27220961