Mechanical roles of apical constriction, cell elongation, and cell migration during neural tube formation in Xenopus.

PubMed

Inoue, Yasuhiro; Suzuki, Makoto; Watanabe, Tadashi; Yasue, Naoko; Tateo, Itsuki; Adachi, Taiji; Ueno, Naoto

2016-12-01

Neural tube closure is an important and necessary process during the development of the central nervous system. The formation of the neural tube structure from a flat sheet of neural epithelium requires several cell morphogenetic events and tissue dynamics to account for the mechanics of tissue deformation. Cell elongation changes cuboidal cells into columnar cells, and apical constriction then causes them to adopt apically narrow, wedge-like shapes. In addition, the neural plate in Xenopus is stratified, and the non-neural cells in the deep layer (deep cells) pull the overlying superficial cells, eventually bringing the two layers of cells to the midline. Thus, neural tube closure appears to be a complex event in which these three physical events are considered to play key mechanical roles. To test whether these three physical events are mechanically sufficient to drive neural tube formation, we employed a three-dimensional vertex model and used it to simulate the process of neural tube closure. The results suggest that apical constriction cued the bending of the neural plate by pursing the circumference of the apical surface of the neural cells. Neural cell elongation in concert with apical constriction further narrowed the apical surface of the cells and drove the rapid folding of the neural plate, but was insufficient for complete neural tube closure. Migration of the deep cells provided the additional tissue deformation necessary for closure. To validate the model, apical constriction and cell elongation were inhibited in Xenopus laevis embryos. The resulting cell and tissue shapes resembled the corresponding simulation results.

Neocortical layers I and II of the hedgehog (Erinaceus europaeus). I. Intrinsic organization.

PubMed

Valverde, F; Facal-Valverde, M V

1986-01-01

The intrinsic organization and interlaminar connections in neocortical layers I and II have been studied in adult hedgehogs (Erinaceus europaeus) using the Golgi method. Layer I contains a dense plexus of horizontal fibers, the terminal dendritic bouquets of pyramidal cells of layer II and of underlying layers, and varieties of intrinsic neurons. Four main types of cells were found in layer I. Small horizontal cells represent most probably persisting foetal horizontal cells described for other mammals. Large horizontal cells, tufted cells, and spinous horizontal cells were also found in this layer. Layer II contains primitive pyramidal cells representing the most outstanding feature of the neocortex of the hedgehog. Most pyramidal cells in layer II have two, three or more apical dendrites, richly covered by spines predominating over the basal dendrites. These cells resemble pyramidal cells found in the piriform cortex, hippocampus and other olfactory areas. It is suggested that the presence of these neurons reflects the retention of a primitive character in neocortical evolution. Cells with intrinsic axons were found among pyramidal cells in layer II. These have smooth dendrites penetrating layer I and local axons forming extremely complex terminal arborizations around the bodies and proximal dendritic portions of pyramidal cells. They most probably effect numerous axo-somatic contacts resembling basket cells. The similarity of some axonal terminals with the chandelier type of axonal arborization is discussed. Other varieties of cells located in deep cortical layers and having ascending axons for layers I and II were also studied. It is concluded that the two first neocortical layers represent a level of important integration in this primitive mammal.

Processing of chromatic information in a deep convolutional neural network.

PubMed

Flachot, Alban; Gegenfurtner, Karl R

2018-04-01

Deep convolutional neural networks are a class of machine-learning algorithms capable of solving non-trivial tasks, such as object recognition, with human-like performance. Little is known about the exact computations that deep neural networks learn, and to what extent these computations are similar to the ones performed by the primate brain. Here, we investigate how color information is processed in the different layers of the AlexNet deep neural network, originally trained on object classification of over 1.2M images of objects in their natural contexts. We found that the color-responsive units in the first layer of AlexNet learned linear features and were broadly tuned to two directions in color space, analogously to what is known of color responsive cells in the primate thalamus. Moreover, these directions are decorrelated and lead to statistically efficient representations, similar to the cardinal directions of the second-stage color mechanisms in primates. We also found, in analogy to the early stages of the primate visual system, that chromatic and achromatic information were segregated in the early layers of the network. Units in the higher layers of AlexNet exhibit on average a lower responsivity for color than units at earlier stages.

Vertical distribution of the prokaryotic cell size in the Mediterranean Sea

NASA Astrophysics Data System (ADS)

La Ferla, R.; Maimone, G.; Azzaro, M.; Conversano, F.; Brunet, C.; Cabral, A. S.; Paranhos, R.

2012-12-01

Distributions of prokaryotic cell size and morphology were studied in different areas of the Mediterranean Sea by using image analysis on samples collected from surface down to bathypelagic layers (max depth 4,900 m) in the Southern Tyrrhenian, Southern Adriatic and Eastern Mediterranean Seas. Distribution of cell size of prokaryotes in marine ecosystem is very often not considered, which makes our study first in the context of prokaryotic ecology. In the deep Mediterranean layers, an usually-not-considered form of carbon sequestration through prokaryotic cells has been highlighted, which is consistent with an increase in cell size with the depth of the water column. A wide range in prokaryotic cell volumes was observed (between 0.045 and 0.566 μm3). Increase in cell size with depth was opposed to cell abundance distribution. Our results from microscopic observations were confirmed by the increasing HNA/LNA ratio (HNA, cells with high nucleic acid content; LNA, cells with low nucleic acid content) along the water column. Implications of our results on the increasing cell size with depth are in the fact that the quantitative estimation of prokaryotic biomass changes along the water column and the amount of carbon sequestered in the deep biota is enhanced.

Blubber morphology in wild bottlenose dolphins (Tursiops truncatus) from the Southeastern United States: influence of geographic location, age class, and reproductive state.

PubMed

Montie, Eric W; Garvin, Scott R; Fair, Patricia A; Bossart, Gregory D; Mitchum, Greg B; McFee, Wayne E; Speakman, Todd; Starczak, Victoria R; Hahn, Mark E

2008-04-01

This study investigated blubber morphology and correlations of histological measurements with ontogeny, geography, and reproductive state in live, wild bottlenose dolphins (Tursiops truncatus) from the southeastern United States. Surgical skin-blubber biopsies (N=74) were collected from dolphins during capture-release studies conducted in two geographic locations: Charleston, SC (N=38) and Indian River Lagoon, FL (N=36). Histological analysis of blubber revealed stratification into superficial, middle, and deep layers. Adipocytes of the middle blubber were 1.6x larger in Charleston subadults than in Indian River Lagoon subadults (4,590+/-340 compared to 2,833+/-335 microm2 per cell). Charleston subadult dolphins contained higher levels of total blubber lipids than Charleston adult animals (49.3%+/-1.9% compared to 34.2%+/-1.7%), and this difference was manifested in more adipocytes in the middle blubber layer (19.2+/-0.9 compared to 14.9+/-0.5 cells per field). However, dolphins from Indian River Lagoon did not exhibit this pattern, and the adipocyte cell counts of subadults were approximately equal to those of the adults (16.0+/-1.4 compared to 13.4+/-0.8 cells per field). The colder year-round water temperatures in Charleston compared to Indian River Lagoon may explain these differences. Adipocytes in the deep blubber layer were significantly smaller in lactating and simultaneously pregnant and lactating animals compared to pregnant dolphins (840+/-179, 627+/-333, and 2,776+/-586 microm2 per cell, respectively). Total blubber lipid content and adipocyte size in the deep blubber of mothers with calves decreased linearly with calf length. Lactating females may utilize lipids from the deep blubber during periods of increased energetic demands associated with offspring care. This study demonstrates that ontogeny, geography, and reproductive state may influence morphological parameters such as structural fiber densities and adipocyte numbers and sizes, measured in bottlenose dolphin blubber. Copyright (c) 2007 Wiley-Liss, Inc.

[Soil organic carbon mineralization of Black Locust forest in the deep soil layer of the hilly region of the Loess Plateau, China].

PubMed

Ma, Xin-Xin; Xu, Ming-Xiang; Yang, Kai

2012-11-01

The deep soil layer (below 100 cm) stores considerable soil organic carbon (SOC). We can reveal its stability and provide the basis for certification of the deep soil carbon sinks by studying the SOC mineralization in the deep soil layer. With the shallow soil layer (0-100 cm) as control, the SOC mineralization under the condition (temperature 15 degrees C, the soil water content 8%) of Black Locust forest in the deep soil layer (100-400 cm) of the hilly region of the Loess Plateau was studied. The results showed that: (1) There was a downward trend in the total SOC mineralization with the increase of soil depth. The total SOC mineralization in the sub-deep soil (100-200 cm) and deep soil (200-400 cm) were equivalent to approximately 88.1% and 67.8% of that in the shallow layer (0-100 cm). (2) Throughout the carbon mineralization process, the same as the shallow soil, the sub-deep and deep soil can be divided into 3 stages. In the rapid decomposition phase, the ratio of the mineralization or organic carbon to the total mineralization in the sub-deep and deep layer (0-10 d) was approximately 50% of that in the shallow layer (0-17 d). In the slow decomposition phase, the ratio of organic carbon mineralization to total mineralization in the sub-deep, deep layer (11-45 d) was 150% of that in the shallow layer (18-45 d). There was no significant difference in this ratio among these three layers (46-62 d) in the relatively stable stage. (3) There was no significant difference (P > 0.05) in the mineralization rate of SOC among the shallow, sub-deep, deep layers. The stability of SOC in the deep soil layer (100-400 cm) was similar to that in the shallow soil layer and the SOC in the deep soil layer was also involved in the global carbon cycle. The change of SOC in the deep soil layer should be taken into account when estimating the effects of soil carbon sequestration in the Hilly Region of the Loess Plateau, China.

Layer-specific input to distinct cell types in layer 6 of monkey primary visual cortex.

PubMed

Briggs, F; Callaway, E M

2001-05-15

Layer 6 of monkey V1 contains a physiologically and anatomically diverse population of excitatory pyramidal neurons. Distinctive arborization patterns of axons and dendrites within the functionally specialized cortical layers define eight types of layer 6 pyramidal neurons and suggest unique information processing roles for each cell type. To address how input sources contribute to cellular function, we examined the laminar sources of functional excitatory input onto individual layer 6 pyramidal neurons using scanning laser photostimulation. We find that excitatory input sources correlate with cell type. Class I neurons with axonal arbors selectively targeting magnocellular (M) recipient layer 4Calpha receive input from M-dominated layer 4B, whereas class I neurons whose axonal arbors target parvocellular (P) recipient layer 4Cbeta receive input from P-dominated layer 2/3. Surprisingly, these neuronal types do not differ significantly in the inputs they receive directly from layers 4Calpha or 4Cbeta. Class II cells, which lack dense axonal arbors within layer 4C, receive excitatory input from layers targeted by their local axons. Specifically, type IIA cells project axons to and receive input from the deep but not superficial layers. Type IIB neurons project to and receive input from the deepest and most superficial, but not middle layers. Type IIC neurons arborize throughout the cortical layers and tend to receive inputs from all cortical layers. These observations have implications for the functional roles of different layer 6 cell types in visual information processing.

The suborbicularis oculi fat (SOOF) and the fascial planes: has everything already been explained?

PubMed

Andretto Amodeo, Chiara; Casasco, Andrea; Icaro Cornaglia, Antonia; Kang, Robert; Keller, Gregory S

2014-01-01

During anatomic and surgical dissections, a connection was seen between the superficial layer of the deep temporal fascia and the prezygomatic area. These findings were in contrast to previous evaluations. This study defines this connection, which is important to understand from both surgical and anatomic standpoints. To define the connection between the superficial layer of the deep temporal fascia and the prezygomatic area and demonstrate the presence of a deep fascial layer in the midface. Anatomical study performed at the Laboratoire d'Anatomie de la Faculté de Médecine de Nice, Sophia Antipolis, France; at the Centre du Don des Corps de l'Université Paris Descartes, Paris, France; and at the Department of Experimental Medicine, Histology, and Embryology Unit of the University of Pavia, Pavia, Italy. Twenty-four hemifaces of 14 white cadavers were dissected to define the relationship between deep temporal fascia and the midface. Four biopsy samples were harvested for histologic analysis. Dissection of 24 hemifaces from the fresh cadavers revealed the following findings. There is a connection of the deep fascia of the temple (superficial layer of deep temporal fascia) to the midface that divides the fat deep to the orbicularis muscle into 2 layers. One layer of fat is the so-called suborbicularis oculi fat (SOOF), which is superficial to the deep fascia, and the other layer of fat (preperiosteal) is deep to the deep fascia and adherent to malar bone. These findings are in contrast to previous anatomical findings. RESULTS In 12 hemifaces, the superficial layer of the deep temporal fascia directly reached the prezygomatic area as a continuous fascial layer. In 16 hemifaces, the superficial sheet of the deep temporal fascia inserted at the level of the zygomatic and lateral orbital rim and continued as a deep fascial layer over the prezygomatic area. In all specimens, a deep fascial layer was present in the prezygomatic-infraorbital area. This deep fascial layer is adherent to the muscles of the infraorbital area, and it divided the fat located deep to the orbicularis oculi muscle into 2 layers: the SOOF and a deeper layer. Histologic examination of the biopsy samples confirmed these findings. This study demonstrates the existence of a deep fascial layer in the midface. This fascia is connected to the superficial layer of the deep temporal fascia, and it divides the fat deep to the orbicularis oculi muscle into 2 layers. This new finding carries interesting implications related to the classic concept of the superficial musculoaponeurotic system. NA.

The Neuronal Organization of a Unique Cerebellar Specialization: The Valvula Cerebelli of a Mormyrid Fish

PubMed Central

Shi, Zhigang; Zhang, Yueping; Meek, Johannes; Qiao, Jiantian; Han, Victor Z.

2018-01-01

The distal valvula cerebelli is the most prominent part of the mormyrid cerebellum. It is organized in ridges of ganglionic and molecular layers, oriented perpendicular to the granular layer. We have combined intracellular recording and labelling techniques to reveal the cellular morphology of the valvula ridges in slice preparations. We have also locally ejected tracer in slices and in intact animals to examine its input fibers. The palisade dendrites and fine axon arbors of Purkinje cells are oriented in the horizontal plane of the ridge. The dendrites of basal efferent cells and large central cells are confined to the molecular layer, but are not planer. Basal efferent cell axons are thick, and join the basal bundle leaving the cerebellum. Large central cell axons are also thick, and traverse long distances in the transverse plane, with local collaterals in the ganglionic layer. Vertical cells and small central cells also have thick axons with local collaterals. The dendrites of Golgi cells are confined to the molecular layer, but their axon arbors are either confined to the granular layer or proliferate in both the granular and ganglionic layers. Dendrites of deep stellate cells are distributed in the molecular layer, with fine axon arbors in the ganglionic layer. Granule cell axons enter the molecular layer as parallel fibers without bifurcating. Climbing fibers run in the horizontal plane and terminate exclusively in the ganglionic layer. Our results confirm and extend previous studies and suggest a new concept of the circuitry of the mormyrid valvula cerebelli. PMID:18537139

Electronic properties of deep-level defects in proton irradiated AlGaAs-GaAs solar cells

NASA Technical Reports Server (NTRS)

Li, S. S.

1981-01-01

Deep level transient spectroscopy and capacitance voltage techniques as well as analysis of the forward current voltage (I-V) characteristics and SEM-EIC data were carried out for proton irradiated GaAs solar cells over a wide range of proton energies and proton fluences. Defect and recombination parameters such as defect energy levels and density, carrier capture cross sections and lifetimes as well as diffusion lengths in the undoped n-GaAs LPE layers were determined. Good correlation between these defect parameters and solar cell performance parameters was obtained for GaAs solar cells irradiated by 200 and 290 KeV protons. It was found that 200 to 290 KeV protons will produce the most defects and damages to the GaAs solar cell structure used. The influence of the low temperature (200 to 400 C) periodic thermal annealing on the deep level defects and the performance of the 200 KeV proton irradiated cells is discussed.

The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology

PubMed Central

Kadurin, Artur; Aliper, Alexander; Kazennov, Andrey; Mamoshina, Polina; Vanhaelen, Quentin; Khrabrov, Kuzma; Zhavoronkov, Alex

2017-01-01

Recent advances in deep learning and specifically in generative adversarial networks have demonstrated surprising results in generating new images and videos upon request even using natural language as input. In this paper we present the first application of generative adversarial autoencoders (AAE) for generating novel molecular fingerprints with a defined set of parameters. We developed a 7-layer AAE architecture with the latent middle layer serving as a discriminator. As an input and output the AAE uses a vector of binary fingerprints and concentration of the molecule. In the latent layer we also introduced a neuron responsible for growth inhibition percentage, which when negative indicates the reduction in the number of tumor cells after the treatment. To train the AAE we used the NCI-60 cell line assay data for 6252 compounds profiled on MCF-7 cell line. The output of the AAE was used to screen 72 million compounds in PubChem and select candidate molecules with potential anti-cancer properties. This approach is a proof of concept of an artificially-intelligent drug discovery engine, where AAEs are used to generate new molecular fingerprints with the desired molecular properties. PMID:28029644

Bidirectional synaptic plasticity in the cerebellum-like mammalian dorsal cochlear nucleus

NASA Astrophysics Data System (ADS)

Fujino, Kiyohiro; Oertel, Donata

2003-01-01

The dorsal cochlear nucleus integrates acoustic with multimodal sensory inputs from widespread areas of the brain. Multimodal inputs are brought to spiny dendrites of fusiform and cartwheel cells in the molecular layer by parallel fibers through synapses that are subject to long-term potentiation and long-term depression. Acoustic cues are brought to smooth dendrites of fusiform cells in the deep layer by auditory nerve fibers through synapses that do not show plasticity. Plasticity requires Ca2+-induced Ca2+ release; its sensitivity to antagonists of N-methyl-D-aspartate and metabotropic glutamate receptors differs in fusiform and cartwheel cells.

Does the Deep Layer of the Deep Temporalis Fascia Really Exist?

PubMed

Li, Hui; Li, Kaide; Jia, Wenhao; Han, Chaoying; Chen, Jinlong; Liu, Lei

2018-04-14

It has been widely accepted that a split of the deep temporal fascia occurs approximately 2 to 3 cm above the zygomatic arch and extends into the superficial and deep layers. The deep layer of the deep temporal fascia is between the superficial temporal fat pad and the temporal muscle. However, during procedures, the authors noted the absence of the deep layer of the deep temporal fascia between the superficial temporal fat pad and the temporal muscle. This prospective study was conducted to clarify the presence or absence of a deep layer of the deep temporal fascia. Anatomic layers of the soft tissues of the temporal region, with reference to the deep temporal fascia, were investigated in 130 cases operated on for zygomaticofacial fractures using the supratemporal approach from June 2013 to June 2017. Of 130 surgeries, the authors found the absence of a thick, obviously identifiable, fascial layer between the superficial temporal fat pad and the temporal muscle. In fact, the authors found nothing above the temporal muscle in most cases. In a few cases, the authors observed only a small amount of scattered loose connective tissue between the superficial temporal fat pad and the temporal muscle. This clinical study showed the absence of a thick, obviously identifiable, fascial layer between the superficial temporal fat pad and the temporal muscle, which suggests that a "deep layer of the deep temporal fascia" might not exist. Copyright © 2018. Published by Elsevier Inc.

EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm.

PubMed

Kim, Seong Gon; Harwani, Mrudul; Grama, Ananth; Chaterji, Somali

2016-12-08

We present EP-DNN, a protocol for predicting enhancers based on chromatin features, in different cell types. Specifically, we use a deep neural network (DNN)-based architecture to extract enhancer signatures in a representative human embryonic stem cell type (H1) and a differentiated lung cell type (IMR90). We train EP-DNN using p300 binding sites, as enhancers, and TSS and random non-DHS sites, as non-enhancers. We perform same-cell and cross-cell predictions to quantify the validation rate and compare against two state-of-the-art methods, DEEP-ENCODE and RFECS. We find that EP-DNN has superior accuracy with a validation rate of 91.6%, relative to 85.3% for DEEP-ENCODE and 85.5% for RFECS, for a given number of enhancer predictions and also scales better for a larger number of enhancer predictions. Moreover, our H1 → IMR90 predictions turn out to be more accurate than IMR90 → IMR90, potentially because H1 exhibits a richer signature set and our EP-DNN model is expressive enough to extract these subtleties. Our work shows how to leverage the full expressivity of deep learning models, using multiple hidden layers, while avoiding overfitting on the training data. We also lay the foundation for exploration of cross-cell enhancer predictions, potentially reducing the need for expensive experimentation.

EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm

NASA Astrophysics Data System (ADS)

Kim, Seong Gon; Harwani, Mrudul; Grama, Ananth; Chaterji, Somali

2016-12-01

We present EP-DNN, a protocol for predicting enhancers based on chromatin features, in different cell types. Specifically, we use a deep neural network (DNN)-based architecture to extract enhancer signatures in a representative human embryonic stem cell type (H1) and a differentiated lung cell type (IMR90). We train EP-DNN using p300 binding sites, as enhancers, and TSS and random non-DHS sites, as non-enhancers. We perform same-cell and cross-cell predictions to quantify the validation rate and compare against two state-of-the-art methods, DEEP-ENCODE and RFECS. We find that EP-DNN has superior accuracy with a validation rate of 91.6%, relative to 85.3% for DEEP-ENCODE and 85.5% for RFECS, for a given number of enhancer predictions and also scales better for a larger number of enhancer predictions. Moreover, our H1 → IMR90 predictions turn out to be more accurate than IMR90 → IMR90, potentially because H1 exhibits a richer signature set and our EP-DNN model is expressive enough to extract these subtleties. Our work shows how to leverage the full expressivity of deep learning models, using multiple hidden layers, while avoiding overfitting on the training data. We also lay the foundation for exploration of cross-cell enhancer predictions, potentially reducing the need for expensive experimentation.

Atomic force microscopy stiffness tomography on living Arabidopsis thaliana cells reveals the mechanical properties of surface and deep cell-wall layers during growth.

PubMed

Radotić, Ksenija; Roduit, Charles; Simonović, Jasna; Hornitschek, Patricia; Fankhauser, Christian; Mutavdžić, Dragosav; Steinbach, Gabor; Dietler, Giovanni; Kasas, Sandor

2012-08-08

Cell-wall mechanical properties play a key role in the growth and the protection of plants. However, little is known about genuine wall mechanical properties and their growth-related dynamics at subcellular resolution and in living cells. Here, we used atomic force microscopy (AFM) stiffness tomography to explore stiffness distribution in the cell wall of suspension-cultured Arabidopsis thaliana as a model of primary, growing cell wall. For the first time that we know of, this new imaging technique was performed on living single cells of a higher plant, permitting monitoring of the stiffness distribution in cell-wall layers as a function of the depth and its evolution during the different growth phases. The mechanical measurements were correlated with changes in the composition of the cell wall, which were revealed by Fourier-transform infrared (FTIR) spectroscopy. In the beginning and end of cell growth, the average stiffness of the cell wall was low and the wall was mechanically homogenous, whereas in the exponential growth phase, the average wall stiffness increased, with increasing heterogeneity. In this phase, the difference between the superficial and deep wall stiffness was highest. FTIR spectra revealed a relative increase in the polysaccharide/lignin content. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Monsoon dependent ecosystems: Implications of the vertical distribution of soil moisture on land surface-atmosphere interactions

NASA Astrophysics Data System (ADS)

Sanchez-Mejia, Zulia M.

Uncertainty of predicted change in precipitation frequency and intensity motivates the scientific community to better understand, quantify, and model the possible outcome of dryland ecosystems. In pulse dependent ecosystems (i.e. monsoon driven) soil moisture is tightly linked to atmospheric processes. Here, I analyze three overarching questions; Q1) How does soil moisture presence or absence in a shallow or deep layer influence the surface energy budget and planetary boundary layer characteristics?, Q2) What is the role of vegetation on ecosystem albedo in the presence or absence of deep soil moisture?, Q3) Can we develop empirical relationships between soil moisture and the planetary boundary layer height to help evaluate the role of future precipitation changes in land surface atmosphere interactions? . To address these questions I use a conceptual framework based on the presence or absence of soil moisture in a shallow or deep layer. I define these layers by using root profiles and establish soil moisture thresholds for each layer using four years of observations from the Santa Rita Creosote Ameriflux site. Soil moisture drydown curves were used to establish the shallow layer threshold in the shallow layer, while NEE (Net Ecosystem Exchange of carbon dioxide) was used to define the deep soil moisture threshold. Four cases were generated using these thresholds: Case 1, dry shallow layer and dry deep layer; Case 2, wet shallow layer and dry deep layer; Case 3, wet shallow layer and wet deep layer, and Case 4 dry shallow and wet deep layer. Using this framework, I related data from the Ameriflux site SRC (Santa Rita Creosote) from 2008 to 2012 and from atmospheric soundings from the nearby Tucson Airport; conducted field campaigns during 2011 and 2012 to measure albedo from individual bare and canopy patches that were then evaluated in a grid to estimate the influence of deep moisture on albedo via vegetation cover change; and evaluated the potential of using a two-layer bucket model and empirical relationships to evaluate the link between deep soil moisture and the planetary boundary layer height under changing precipitation regime. My results indicate that (1) the presence or absence of water in two layers plays a role in surface energy dynamics, (2) soil moisture presence in the deep layer is linked with decreased ecosystem albedo and planetary boundary layer height, (3) deep moisture sustains vegetation greenness and decreases albedo, and (4) empirical relationships are useful in modeling planetary boundary layer height from dryland ecosystems. Based on these results we argue that deep soil moisture plays an important role in land surface-atmosphere interactions.

Flotillins control zebrafish epiboly through their role in cadherin-mediated cell-cell adhesion.

PubMed

Morris, Eduardo A Rios; Bodin, Stéphane; Delaval, Bénédicte; Comunale, Franck; Georget, Virginie; Costa, Manoel L; Lutfalla, Georges; Gauthier-Rouvière, Cécile

2017-05-01

Zebrafish gastrulation and particularly epiboly that involves coordinated movements of several cell layers is a dynamic process for which regulators remain to be identified. We show here that Flotillin 1 and 2, ubiquitous and highly conserved proteins, are required for epiboly. Flotillins knockdown compromised embryo survival, strongly delayed epiboly and impaired deep cell radial intercalation and directed collective migration without affecting enveloping layer cell movement. At the molecular level, we identified that Flotillins are required for the formation of E-cadherin-mediated cell-cell junctions. These results provide the first in vivo evidence that Flotillins regulate E-cadherin-mediated cell-cell junctions to allow epiboly progression. © 2017 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

Introduction to Phase-Resolving Wave Modeling with FUNWAVE

DTIC Science & Technology

2015-07-01

Boussinesq wave models have become a useful tool for modeling surface wave transformation from deep water to the swash zone, as well as wave-induced...overlapping area of ghost cells, three rows deep , as required by the fourth-order MUSCL-TVD scheme. The MPI with nonblocking communication was used to...implemented ERDC/CHL CHETN-I-87 July 2015 12 SPONGE LAYER SPONGE_ON Sponge_west_width Sponge_east_width Sponge_south_width

Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics

PubMed Central

Handel, Adam E.; Chintawar, Satyan; Lalic, Tatjana; Whiteley, Emma; Vowles, Jane; Giustacchini, Alice; Argoud, Karene; Sopp, Paul; Nakanishi, Mahito; Bowden, Rory; Cowley, Sally; Newey, Sarah; Akerman, Colin; Ponting, Chris P.; Cader, M. Zameel

2016-01-01

Induced pluripotent stem cell (iPSC)-derived cortical neurons potentially present a powerful new model to understand corticogenesis and neurological disease. Previous work has established that differentiation protocols can produce cortical neurons, but little has been done to characterize these at cellular resolution. In particular, it is unclear to what extent in vitro two-dimensional, relatively disordered culture conditions recapitulate the development of in vivo cortical layer identity. Single-cell multiplex reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) was used to interrogate the expression of genes previously implicated in cortical layer or phenotypic identity in individual cells. Totally, 93.6% of single cells derived from iPSCs expressed genes indicative of neuronal identity. High proportions of single neurons derived from iPSCs expressed glutamatergic receptors and synaptic genes. And, 68.4% of iPSC-derived neurons expressing at least one layer marker could be assigned to a laminar identity using canonical cortical layer marker genes. We compared single-cell RNA-seq of our iPSC-derived neurons to available single-cell RNA-seq data from human fetal and adult brain and found that iPSC-derived cortical neurons closely resembled primary fetal brain cells. Unexpectedly, a subpopulation of iPSC-derived neurons co-expressed canonical fetal deep and upper cortical layer markers. However, this appeared to be concordant with data from primary cells. Our results therefore provide reassurance that iPSC-derived cortical neurons are highly similar to primary cortical neurons at the level of single cells but suggest that current layer markers, although effective, may not be able to disambiguate cortical layer identity in all cells. PMID:26740550

Morphological characterization of rat entorhinal neurons in vivo: soma-dendritic structure and axonal domains.

PubMed

Lingenhöhl, K; Finch, D M

1991-01-01

We used in vivo intracellular labeling with horseradish peroxidase in order to study the soma-dendritic morphology and axonal projections of rat entorhinal neurons. The cells responded to hippocampal stimulation with inhibitory postsynaptic potentials, and thus likely received direct or indirect hippocampal input. All cells (n = 24) showed extensive dendritic domains that extended in some cases for more than 1 mm. The dendrites of layer II neurons were largely restricted to layers I and II or layers I-III, while the dendrites of deeper cells could extend through all cortical layers. Computed 3D rotations showed that the basilar dendrites of deep pyramids extended roughly parallel to the cortical layering, and that they were mostly confined to the layer containing the soma and layers immediately adjacent. Total dendritic lengths averaged 9.8 mm +/- 3.8 (SD), and ranged from 5 mm to more than 18 mm. Axonal processes could be visualized in 21 cells. Most of these showed axonal branching within the entorhinal cortex, sometimes extensive. Efferent axonal domains were reconstructed in detail in 3 layer II stellate cells. All 3 projected axons across the subicular complex to the dentate gyrus. One of these cells showed an extensive net-like axonal domain that also projected to several other structures, including the hippocampus proper, subicular complex, and the amygdalo-piriform transition area. The axons of layer III and IV cells projected to the angular bundle, where they continued in a rostral direction. In contrast to the layer II, III and IV cells, no efferent axonal branches leaving the entorhinal cortex could be visualized in 5 layer V neurons. The data indicate that entorhinal neurons can integrate input from a considerable volume of entorhinal cortex by virtue of their extensive dendritic domains, and provide a further basis for specifying the layers in which cells receive synaptic input. The extensive axonal branching pattern seen in most of the cells would support divergent propagation of their activity.

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments.

PubMed

Engelhardt, Tim; Kallmeyer, Jens; Cypionka, Heribert; Engelen, Bert

2014-07-01

Marine sediments cover two-thirds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. To better understand controlling factors of microbial life, we have analyzed viral abundance within a comprehensive set of globally distributed subsurface sediments. Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (∼14 Ma old) and the most oligotrophic subsurface sediments of the world's oceans (South Pacific Gyre (SPG)). The numbers of viruses (10(4)-10(9) cm(-3), counted by epifluorescence microscopy) generally decreased with sediment depth, but always exceeded the total cell counts. The enormous numbers of viruses indicate their impact as a controlling factor for prokaryotic mortality in the marine deep biosphere. The virus-to-cell ratios increased in deeper and more oligotrophic layers, exhibiting values of up to 225 in the deep subsurface of the SPG. High numbers of phages might be due to absorption onto the sediment matrix and a diminished degradation by exoenzymes. However, even in the oldest sediments, microbial communities are capable of maintaining viral populations, indicating an ongoing viral production and thus, viruses provide an independent indicator for microbial life in the marine deep biosphere.

Experience-Dependent Rewiring of Specific Inhibitory Connections in Adult Neocortex

PubMed Central

Kätzel, Dennis; Miesenböck, Gero

2014-01-01

Although neocortical connectivity is remarkably stereotyped, the abundance of some wiring motifs varies greatly between cortical areas. To examine if regional wiring differences represent functional adaptations, we have used optogenetic raster stimulation to map the laminar distribution of GABAergic interneurons providing inhibition to pyramidal cells in layer 2/3 (L2/3) of adult mouse barrel cortex during sensory deprivation and recovery. Whisker trimming caused large, motif-specific changes in inhibitory synaptic connectivity: ascending inhibition from deep layers 4 and 5 was attenuated to 20%–45% of baseline, whereas inhibition from superficial layers remained stable (L2/3) or increased moderately (L1). The principal mechanism of deprivation-induced plasticity was motif-specific changes in inhibitory-to-excitatory connection probabilities; the strengths of extant connections were left unaltered. Whisker regrowth restored the original balance of inhibition from deep and superficial layers. Targeted, reversible modifications of specific inhibitory wiring motifs thus contribute to the adaptive remodeling of cortical circuits. PMID:24586113

Laminar Organization of Attentional Modulation in Macaque Visual Area V4.

PubMed

Nandy, Anirvan S; Nassi, Jonathan J; Reynolds, John H

2017-01-04

Attention is critical to perception, serving to select behaviorally relevant information for privileged processing. To understand the neural mechanisms of attention, we must discern how attentional modulation varies by cell type and across cortical layers. Here, we test whether attention acts non-selectively across cortical layers or whether it engages the laminar circuit in specific and selective ways. We find layer- and cell-class-specific differences in several different forms of attentional modulation in area V4. Broad-spiking neurons in the superficial layers exhibit attention-mediated increases in firing rate and decreases in variability. Spike count correlations are highest in the input layer and attention serves to reduce these correlations. Superficial and input layer neurons exhibit attention-dependent decreases in low-frequency (<10 Hz) coherence, but deep layer neurons exhibit increases in coherence in the beta and gamma frequency ranges. Our study provides a template for attention-mediated laminar information processing that might be applicable across sensory modalities. Copyright © 2017 Elsevier Inc. All rights reserved.

Meteorological variables to aid forecasting deep slab avalanches on persistent weak layers

USGS Publications Warehouse

Marienthal, Alex; Hendrikx, Jordy; Birkeland, Karl; Irvine, Kathryn M.

2015-01-01

Deep slab avalanches are particularly challenging to forecast. These avalanches are difficult to trigger, yet when they release they tend to propagate far and can result in large and destructive avalanches. We utilized a 44-year record of avalanche control and meteorological data from Bridger Bowl ski area in southwest Montana to test the usefulness of meteorological variables for predicting seasons and days with deep slab avalanches. We defined deep slab avalanches as those that failed on persistent weak layers deeper than 0.9 m, and that occurred after February 1st. Previous studies often used meteorological variables from days prior to avalanches, but we also considered meteorological variables over the early months of the season. We used classification trees and random forests for our analyses. Our results showed seasons with either dry or wet deep slabs on persistent weak layers typically had less precipitation from November through January than seasons without deep slabs on persistent weak layers. Days with deep slab avalanches on persistent weak layers often had warmer minimum 24-hour air temperatures, and more precipitation over the prior seven days, than days without deep slabs on persistent weak layers. Days with deep wet slab avalanches on persistent weak layers were typically preceded by three days of above freezing air temperatures. Seasonal and daily meteorological variables were found useful to aid forecasting dry and wet deep slab avalanches on persistent weak layers, and should be used in combination with continuous observation of the snowpack and avalanche activity.

[Expression of vimentin and GFAP and development of the retina in the trout].

PubMed

De Guevara, R; Pairault, C; Pinganaud, G

1994-08-01

The glial cell development was studied during the edification of the retina and the optic tract, in a teleost, the rainbow trout. The intermediate filament proteins, vimentin and glial fibrillary acidic protein (GFAP) were visualized by an indirect immunohistochemical method. Results show that both vimentin and GFAP are early expressed in the developing retina and, particularly in the Müller cells, a coexpression of vimentin and GFAP is observed from embryonic to adult stages. The ganglion cell layer and the optic fiber layer both exhibit GFAP-positive structures. The deep staining for GFAP is also seen in the optic nerve and induces us to credit astrocyte-like cells with a leading role in the pattern formation of this tract.

Electrophysiological mapping of the accessory olfactory bulb of the rabbit (Oryctolagus cuniculus).

PubMed

van Groen, T; Ruardy, L; da Silva, F H

1986-07-01

Field potentials elicited by electrical stimulation of the vomeronasal nerve were measured in the accessory olfactory bulb of the rabbit. Maps were made of the distribution of surface field potentials and of the corresponding depth profiles. The surface maps followed closely the contours of the accessory olfactory bulb: at the frontal border the field potential tended to zero and at the center of the structure the field potential attained a maximum. Depth profiles of the field potentials through the accessory olfactory bulb presented a surface-negative wave and, in depth, a positive wave. The polarity reversal occurred at the deep part of the granule cell layer. The zero equipotential line followed closely the curvature of the granule cell layer. Current source density analysis of the depth profiles revealed a main sink at the external plexiform and granule cell layers. This indicates that the main activity in the accessory olfactory bulb is generated by the synapses between the mitral cells and the granule cells as is found in the main olfactory bulb.

Quantitative evaluation of deep and shallow tissue layers' contribution to fNIRS signal using multi-distance optodes and independent component analysis.

PubMed

Funane, Tsukasa; Atsumori, Hirokazu; Katura, Takusige; Obata, Akiko N; Sato, Hiroki; Tanikawa, Yukari; Okada, Eiji; Kiguchi, Masashi

2014-01-15

To quantify the effect of absorption changes in the deep tissue (cerebral) and shallow tissue (scalp, skin) layers on functional near-infrared spectroscopy (fNIRS) signals, a method using multi-distance (MD) optodes and independent component analysis (ICA), referred to as the MD-ICA method, is proposed. In previous studies, when the signal from the shallow tissue layer (shallow signal) needs to be eliminated, it was often assumed that the shallow signal had no correlation with the signal from the deep tissue layer (deep signal). In this study, no relationship between the waveforms of deep and shallow signals is assumed, and instead, it is assumed that both signals are linear combinations of multiple signal sources, which allows the inclusion of a "shared component" (such as systemic signals) that is contained in both layers. The method also assumes that the partial optical path length of the shallow layer does not change, whereas that of the deep layer linearly increases along with the increase of the source-detector (S-D) distance. Deep- and shallow-layer contribution ratios of each independent component (IC) are calculated using the dependence of the weight of each IC on the S-D distance. Reconstruction of deep- and shallow-layer signals are performed by the sum of ICs weighted by the deep and shallow contribution ratio. Experimental validation of the principle of this technique was conducted using a dynamic phantom with two absorbing layers. Results showed that our method is effective for evaluating deep-layer contributions even if there are high correlations between deep and shallow signals. Next, we applied the method to fNIRS signals obtained on a human head with 5-, 15-, and 30-mm S-D distances during a verbal fluency task, a verbal working memory task (prefrontal area), a finger tapping task (motor area), and a tetrametric visual checker-board task (occipital area) and then estimated the deep-layer contribution ratio. To evaluate the signal separation performance of our method, we used the correlation coefficients of a laser-Doppler flowmetry (LDF) signal and a nearest 5-mm S-D distance channel signal with the shallow signal. We demonstrated that the shallow signals have a higher temporal correlation with the LDF signals and with the 5-mm S-D distance channel than the deep signals. These results show the MD-ICA method can discriminate between deep and shallow signals. Copyright © 2013 Elsevier Inc. All rights reserved.

Understanding the dimensional and mechanical properties of coastal Langmuir Circulations

NASA Astrophysics Data System (ADS)

Shrestha, Kalyan; Kuehl, Joseph; Anderson, William

2017-11-01

Non-linear interaction of surface waves and wind-driven shear instability in the upper ocean mixed layer form counter-rotating vortical structures called Langmuir Circulations. This oceanic microscale turbulence is one of the key contributors of mixing and vertical transport in the upper ocean mixed layer. Langmuir turbulence in the open (deep) ocean has already been the topic of a large research effort. However, coastal Langmuir cells are distinctly different from Langmuir cells in open-ocean regions, where additional bottom-boundary layer shear alters the kinematic properties of Langmuir cells. For this study, we have conducted a wide-ranging numerical study (solving the grid-filtered Craik-Leibovich equations) of coastal Langmuir turbulence, assessing which parameters affect Langmuir cells and defining the parametric hierarchy. The Stokes profile (aggregate velocity due to orbital wave motion) is functionally dependent on Stokes drift velocity and wavenumber of the surface waves. We explain that these parameters, which correspond to the environmental forcing variables, control the horizontal and vertical length scales of Langmuir cell respectively. This result is important in understanding the transport and dispersion of materials in the upper mixed layer of coastal ocean. We argue that wind stress is a parameter governing the strength of Langmuir cells.

Spatial extent and dissipation of the deep chlorophyll layer in Lake Ontario during the Lake Ontario lower foodweb assessment, 2003 and 2008

USGS Publications Warehouse

Watkins, J. M.; Weidel, Brian M.; Rudstam, L. G.; Holek, K. T.

2014-01-01

Increasing water clarity in Lake Ontario has led to a vertical redistribution of phytoplankton and an increased importance of the deep chlorophyll layer in overall primary productivity. We used in situ fluorometer profiles collected in lakewide surveys of Lake Ontario in 2008 to assess the spatial extent and intensity of the deep chlorophyll layer. In situ fluorometer data were corrected with extracted chlorophyll data using paired samples from Lake Ontario collected in August 2008. The deep chlorophyll layer was present offshore during the stratified conditions of late July 2008 with maximum values from 4-13 μg l-1 corrected chlorophyll a at 10 to 17 m depth within the metalimnion. Deep chlorophyll layer was closely associated with the base of the thermocline and a subsurface maximum of dissolved oxygen, indicating the feature's importance as a growth and productivity maximum. Crucial to the deep chlorophyll layer formation, the photic zone extended deeper than the surface mixed layer in mid-summer. The layer extended through most of the offshore in July 2008, but was not present in the easternmost transect that had a deeper surface mixed layer. By early September 2008, the lakewide deep chlorophyll layer had dissipated. A similar formation and dissipation was observed in the lakewide survey of Lake Ontario in 2003.

The Epithelial Cell Adhesion Molecule EpCAM Is Required for Epithelial Morphogenesis and Integrity during Zebrafish Epiboly and Skin Development

PubMed Central

Slanchev, Krasimir; Carney, Thomas J.; Stemmler, Marc P.; Koschorz, Birgit; Amsterdam, Adam; Schwarz, Heinz; Hammerschmidt, Matthias

2009-01-01

The aberrant expression of the transmembrane protein EpCAM is associated with tumor progression, affecting different cellular processes such as cell–cell adhesion, migration, proliferation, differentiation, signaling, and invasion. However, the in vivo function of EpCAM still remains elusive due to the lack of genetic loss-of-function studies. Here, we describe epcam (tacstd) null mutants in zebrafish. Maternal-zygotic mutants display compromised basal protrusive activity and epithelial morphogenesis in cells of the enveloping layer (EVL) during epiboly. In partial redundancy with E-cadherin (Ecad), EpCAM made by EVL cells is further required for cell–cell adhesion within the EVL and, possibly, for proper attachment of underlying deep cells to the inner surface of the EVL, thereby also affecting deep cell epiboly movements. During later development, EpCAM per se becomes indispensable for epithelial integrity within the periderm of the skin, secondarily leading to disrupted morphology of the underlying basal epidermis and moderate hyper-proliferation of skin cells. On the molecular level, EVL cells of epcam mutant embryos display reduced levels of membranous Ecad, accompanied by an enrichment of tight junction proteins and a basal extension of apical junction complexes (AJCs). Our data suggest that EpCAM acts as a partner of E-cadherin to control adhesiveness and integrity as well as plasticity and morphogenesis within simple epithelia. In addition, EpCAM is required for the interaction of the epithelia with underlying cell layers. PMID:19609345

Current source density correlates of cerebellar Golgi and Purkinje cell responses to tactile input

PubMed Central

Tahon, Koen; Wijnants, Mike; De Schutter, Erik

2011-01-01

The overall circuitry of the cerebellar cortex has been known for over a century, but the function of many synaptic connections remains poorly characterized in vivo. We used a one-dimensional multielectrode probe to estimate the current source density (CSD) of Crus IIa in response to perioral tactile stimuli in anesthetized rats and to correlate current sinks and sources to changes in the spike rate of corecorded Golgi and Purkinje cells. The punctate stimuli evoked two distinct early waves of excitation (at <10 and ∼20 ms) associated with current sinks in the granular layer. The second wave was putatively of corticopontine origin, and its associated sink was located higher in the granular layer than the first trigeminal sink. The distinctive patterns of granular-layer sinks correlated with the spike responses of corecorded Golgi cells. In general, Golgi cell spike responses could be linearly reconstructed from the CSD profile. A dip in simple-spike activity of coregistered Purkinje cells correlated with a current source deep in the molecular layer, probably generated by basket cell synapses, interspersed between sparse early sinks presumably generated by synapses from granule cells. The late (>30 ms) enhancement of simple-spike activity in Purkinje cells was characterized by the absence of simultaneous sinks in the granular layer and by the suppression of corecorded Golgi cell activity, pointing at inhibition of Golgi cells by Purkinje axon collaterals as a likely mechanism of late Purkinje cell excitation. PMID:21228303

Deficiency of interstitial cells of Cajal in the small intestine of patients with Crohn's disease.

PubMed

Porcher, Christophe; Baldo, Marjolaine; Henry, Monique; Orsoni, Pierre; Julé, Yvon; Ward, Sean M

2002-01-01

Interstitial cells of Cajal are critical for the generation of electrical slow waves that regulate the phasic contractile activity of the tunica muscularis of the GI tract. Under certain pathophysiological conditions loss of interstitial cells of Cajal may play a role in the generation of certain motility disorders. The aim of the present study was to determine if there is an abnormality in the density or distribution of interstitial cells of Cajal from patients with Crohn's disease. Small intestines from control subjects and patients with Crohn's disease were examined using immunohistochemistry and antibodies against the Kit receptor, which is expressed in interstitial cells of Cajal within the tunica muscularis of the GI tract. The density and distribution of interstitial cells of Cajal were assessed in the longitudinal and circular muscle layers and in the myenteric and deep muscular plexus regions of Crohn's and control tissues. Tissues from Crohn's disease patients showed an almost complete abolition of interstitial cells of Cajal within the longitudinal and circular muscle layers and a significant reduction in numbers at the level of the myenteric and deep muscular plexuses. In tissues from Crohn's disease patients, the density of interstitial cells of Cajal was reduced throughout the tunica muscularis in comparison to control small intestines. The disturbance of intestinal motility that occurs in patients with Crohn's disease may be a consequence of the loss of or defects in specific populations of interstitial cells of Cajal within the tunica muscularis.

Arctic Ocean Model Intercomparison Using Sound Speed

NASA Astrophysics Data System (ADS)

Dukhovskoy, D. S.; Johnson, M. A.

2002-05-01

The monthly and annual means from three Arctic ocean - sea ice climate model simulations are compared for the period 1979-1997. Sound speed is used to integrate model outputs of temperature and salinity along a section between Barrow and Franz Josef Land. A statistical approach is used to test for differences among the three models for two basic data subsets. We integrated and then analyzed an upper layer between 2 m - 50 m, and also a deep layer from 500 m to the bottom. The deep layer is characterized by low time-variability. No high-frequency signals appear in the deep layer having been filtered out in the upper layer. There is no seasonal signal in the deep layer and the monthly means insignificantly oscillate about the long-period mean. For the deep ocean the long-period mean can be considered quasi-constant, at least within the 19 year period of our analysis. Thus we assumed that the deep ocean would be the best choice for comparing the means of the model outputs. The upper (mixed) layer was chosen to contrast the deep layer dynamics. There are distinct seasonal and interannual signals in the sound speed time series in this layer. The mixed layer is a major link in the ocean - air interaction mechanism. Thus, different mean states of the upper layer in the models might cause different responses in other components of the Arctic climate system. The upper layer also strongly reflects any differences in atmosphere forcing. To compare data from the three models we have used a one-way t-test for the population mean, the Wilcoxon one-sample signed-rank test (when the requirement of normality of tested data is violated), and one-way ANOVA method and F-test to verify our hypothesis that the model outputs have the same mean sound speed. The different statistical approaches have shown that all models have different mean characteristics of the deep and upper layers of the Arctic Ocean.

Applying deep learning technology to automatically identify metaphase chromosomes using scanning microscopic images: an initial investigation

NASA Astrophysics Data System (ADS)

Qiu, Yuchen; Lu, Xianglan; Yan, Shiju; Tan, Maxine; Cheng, Samuel; Li, Shibo; Liu, Hong; Zheng, Bin

2016-03-01

Automated high throughput scanning microscopy is a fast developing screening technology used in cytogenetic laboratories for the diagnosis of leukemia or other genetic diseases. However, one of the major challenges of using this new technology is how to efficiently detect the analyzable metaphase chromosomes during the scanning process. The purpose of this investigation is to develop a computer aided detection (CAD) scheme based on deep learning technology, which can identify the metaphase chromosomes with high accuracy. The CAD scheme includes an eight layer neural network. The first six layers compose of an automatic feature extraction module, which has an architecture of three convolution-max-pooling layer pairs. The 1st, 2nd and 3rd pair contains 30, 20, 20 feature maps, respectively. The seventh and eighth layers compose of a multiple layer perception (MLP) based classifier, which is used to identify the analyzable metaphase chromosomes. The performance of new CAD scheme was assessed by receiver operation characteristic (ROC) method. A number of 150 regions of interest (ROIs) were selected to test the performance of our new CAD scheme. Each ROI contains either interphase cell or metaphase chromosomes. The results indicate that new scheme is able to achieve an area under the ROC curve (AUC) of 0.886+/-0.043. This investigation demonstrates that applying a deep learning technique may enable to significantly improve the accuracy of the metaphase chromosome detection using a scanning microscopic imaging technology in the future.

The stimulus selectivity and connectivity of layer six principal cells reveals cortical microcircuits underlying visual processing.

PubMed

Vélez-Fort, Mateo; Rousseau, Charly V; Niedworok, Christian J; Wickersham, Ian R; Rancz, Ede A; Brown, Alexander P Y; Strom, Molly; Margrie, Troy W

2014-09-17

Sensory computations performed in the neocortex involve layer six (L6) cortico-cortical (CC) and cortico-thalamic (CT) signaling pathways. Developing an understanding of the physiological role of these circuits requires dissection of the functional specificity and connectivity of the underlying individual projection neurons. By combining whole-cell recording from identified L6 principal cells in the mouse primary visual cortex (V1) with modified rabies virus-based input mapping, we have determined the sensory response properties and upstream monosynaptic connectivity of cells mediating the CC or CT pathway. We show that CC-projecting cells encompass a broad spectrum of selectivity to stimulus orientation and are predominantly innervated by deep layer V1 neurons. In contrast, CT-projecting cells are ultrasparse firing, exquisitely tuned to orientation and direction information, and receive long-range input from higher cortical areas. This segregation in function and connectivity indicates that L6 microcircuits route specific contextual and stimulus-related information within and outside the cortical network. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Laminar recordings in frontal cortex suggest distinct layers for maintenance and control of working memory

PubMed Central

Bastos, André M.; Loonis, Roman; Kornblith, Simon; Lundqvist, Mikael; Miller, Earl K.

2018-01-01

All of the cerebral cortex has some degree of laminar organization. These different layers are composed of neurons with distinct connectivity patterns, embryonic origins, and molecular profiles. There are little data on the laminar specificity of cognitive functions in the frontal cortex, however. We recorded neuronal spiking/local field potentials (LFPs) using laminar probes in the frontal cortex (PMd, 8A, 8B, SMA/ACC, DLPFC, and VLPFC) of monkeys performing working memory (WM) tasks. LFP power in the gamma band (50–250 Hz) was strongest in superficial layers, and LFP power in the alpha/beta band (4–22 Hz) was strongest in deep layers. Memory delay activity, including spiking and stimulus-specific gamma bursting, was predominately in superficial layers. LFPs from superficial and deep layers were synchronized in the alpha/beta bands. This was primarily unidirectional, with alpha/beta bands in deep layers driving superficial layer activity. The phase of deep layer alpha/beta modulated superficial gamma bursting associated with WM encoding. Thus, alpha/beta rhythms in deep layers may regulate the superficial layer gamma bands and hence maintenance of the contents of WM. PMID:29339471

Laminar recordings in frontal cortex suggest distinct layers for maintenance and control of working memory.

PubMed

Bastos, André M; Loonis, Roman; Kornblith, Simon; Lundqvist, Mikael; Miller, Earl K

2018-01-30

All of the cerebral cortex has some degree of laminar organization. These different layers are composed of neurons with distinct connectivity patterns, embryonic origins, and molecular profiles. There are little data on the laminar specificity of cognitive functions in the frontal cortex, however. We recorded neuronal spiking/local field potentials (LFPs) using laminar probes in the frontal cortex (PMd, 8A, 8B, SMA/ACC, DLPFC, and VLPFC) of monkeys performing working memory (WM) tasks. LFP power in the gamma band (50-250 Hz) was strongest in superficial layers, and LFP power in the alpha/beta band (4-22 Hz) was strongest in deep layers. Memory delay activity, including spiking and stimulus-specific gamma bursting, was predominately in superficial layers. LFPs from superficial and deep layers were synchronized in the alpha/beta bands. This was primarily unidirectional, with alpha/beta bands in deep layers driving superficial layer activity. The phase of deep layer alpha/beta modulated superficial gamma bursting associated with WM encoding. Thus, alpha/beta rhythms in deep layers may regulate the superficial layer gamma bands and hence maintenance of the contents of WM. Copyright © 2018 the Author(s). Published by PNAS.

Aponeurosis of the levator palpebrae superioris in Chinese subjects

PubMed Central

Pan, Er; Nie, Yun-Fei; Wang, Zhen-Jun; Peng, Li-Xia; Wu, Yan-Hong; Li, Qin

2016-01-01

Abstract An accurate understanding of the anatomy of the levator palpebrae superioris aponeurosis (LPSA) is critical for successful blepharoplasty of aponeurotic ptosis. We investigated the macroscopic and microscopic anatomy of the LPSA. This prospective live gross anatomy study enrolled 200 adult Chinese patients with bilateral mild ptosis undergoing elective blepharoplasty. Full-thick eyelid tissues and sagittal sections from the eyelid skin to the conjunctiva were examined with Masson trichrome staining or antismooth muscle actin (SMA) immunohistochemistry. Gross anatomy showed that the space between the superficial and deep layers of the LPSA could be accessed after incising the overlying superficial fascia, by retracting the white line. Adipose layers were clearly observed in 195 out of 200 patients with bilateral mild ptosis, among which 180 cases had the superficial layer connected to the uncoated adipose. Fifteen cases had the superficial layer connected to the smoothly coated layer, and 5 cases had the superficial layer directly connected to the deep loose fiber, almost without adipose. In previously untreated patients, the LPSA space was located beneath the intact orbital septum. In those with previous surgeries, it was beneath the superficial layer of the LPSA, underlying the destructed orbital septum. Cadaveric histology showed that the deep layer of the LPSA extended into the anterior layer of the tarsal plate and the superficial layer reflexed upward in continuity with the vertical orbital septum. An occult space existed between the 2 layers of the LPSA, with a smooth lining on the deep layer. The superficial layer of the LPSA was SMA-immunonegative but the deep layer was slightly immunopositive for SMA. An occult anatomic space exists between the superficial and deep layers of the LPSA, in proximity to the superior tarsal plate margin. Recognition of the more anatomically significant LPSA deep layer may help improve the aesthetic outcome of blepharoplasty. PMID:27495084

Subset of Cortical Layer 6b Neurons Selectively Innervates Higher Order Thalamic Nuclei in Mice.

PubMed

Hoerder-Suabedissen, Anna; Hayashi, Shuichi; Upton, Louise; Nolan, Zachary; Casas-Torremocha, Diana; Grant, Eleanor; Viswanathan, Sarada; Kanold, Patrick O; Clasca, Francisco; Kim, Yongsoo; Molnár, Zoltán

2018-05-01

The thalamus receives input from 3 distinct cortical layers, but input from only 2 of these has been well characterized. We therefore investigated whether the third input, derived from layer 6b, is more similar to the projections from layer 6a or layer 5. We studied the projections of a restricted population of deep layer 6 cells ("layer 6b cells") taking advantage of the transgenic mouse Tg(Drd1a-cre)FK164Gsat/Mmucd (Drd1a-Cre), that selectively expresses Cre-recombinase in a subpopulation of layer 6b neurons across the entire cortical mantle. At P8, 18% of layer 6b neurons are labeled with Drd1a-Cre::tdTomato in somatosensory cortex (SS), and some co-express known layer 6b markers. Using Cre-dependent viral tracing, we identified topographical projections to higher order thalamic nuclei. VGluT1+ synapses formed by labeled layer 6b projections were found in posterior thalamic nucleus (Po) but not in the (pre)thalamic reticular nucleus (TRN). The lack of TRN collaterals was confirmed with single-cell tracing from SS. Transmission electron microscopy comparison of terminal varicosities from layer 5 and layer 6b axons in Po showed that L6b varicosities are markedly smaller and simpler than the majority from L5. Our results suggest that L6b projections to the thalamus are distinct from both L5 and L6a projections.

Tropical-Cyclone Flow Asymmetries Induced by a Uniform Flow Revisited

DTIC Science & Technology

2011-11-01

environment and they are deep, extending into the upper troposphere (not shown here). By 24 hours, convective cells are distributed over all four...GA. 2000 Evaluation of numerical predictions of boundary layer structure during the lake Michigan ozone study. J. Appl. Met., 39, 337-351. Shapiro LJ

Behavior of Photocarriers in the Light-Induced Metastable State in the p-n Heterojunction of a Cu(In,Ga)Se2 Solar Cell with CBD-ZnS Buffer Layer.

PubMed

Lee, Woo-Jung; Yu, Hye-Jung; Wi, Jae-Hyung; Cho, Dae-Hyung; Han, Won Seok; Yoo, Jisu; Yi, Yeonjin; Song, Jung-Hoon; Chung, Yong-Duck

2016-08-31

We fabricated Cu(In,Ga)Se2 (CIGS) solar cells with a chemical bath deposition (CBD)-ZnS buffer layer grown with varying ammonia concentrations in aqueous solution. The solar cell performance was degraded with increasing ammonia concentration, due to actively dissolved Zn atoms during CBD-ZnS precipitation. These formed interfacial defect states, such as hydroxide species in the CBD-ZnS film, and interstitial and antisite Zn defects at the p-n heterojunction. After light/UV soaking, the CIGS solar cell performance drastically improved, with a rise in fill factor. With the Zn-based buffer layer, the light soaking treatment containing blue photons induced a metastable state and enhanced the CIGS solar cell performance. To interpret this effect, we suggest a band structure model of the p-n heterojunction to explain the flow of photocarriers under white light at the initial state, and then after light/UV soaking. The determining factor is a p+ defect layer, containing an amount of deep acceptor traps, located near the CIGS surface. The p+ defect layer easily captures photoexcited electrons, and then when it becomes quasi-neutral, attracts photoexcited holes. This alters the barrier height and controls the photocurrent at the p-n junction, and fill factor values, determining the solar cell performance.

Deep Learning and Developmental Learning: Emergence of Fine-to-Coarse Conceptual Categories at Layers of Deep Belief Network.

PubMed

Sadeghi, Zahra

2016-09-01

In this paper, I investigate conceptual categories derived from developmental processing in a deep neural network. The similarity matrices of deep representation at each layer of neural network are computed and compared with their raw representation. While the clusters generated by raw representation stand at the basic level of abstraction, conceptual categories obtained from deep representation shows a bottom-up transition procedure. Results demonstrate a developmental course of learning from specific to general level of abstraction through learned layers of representations in a deep belief network. © The Author(s) 2016.

Meteorological variables associated with deep slab avalanches on persistent weak layers

USGS Publications Warehouse

Marienthal, Alex; Hendrikx, Jordy; Birkeland, Karl; Irvine, Kathryn M.

2014-01-01

Deep slab avalanches are a particularly challenging avalanche forecasting problem. These avalanches are typically difficult to trigger, yet when they are triggered they tend to propagate far and result in large and destructive avalanches. For this work we define deep slab avalanches as those that fail on persistent weak layers deeper than 0.9m (3 feet), and that occur after February 1st. We utilized a 44-year record of avalanche control and meteorological data from Bridger Bowl Ski Area to test the usefulness of meteorological variables for predicting deep slab avalanches. As in previous studies, we used data from the days preceding deep slab cycles, but we also considered meteorological metrics over the early months of the season. We utilized classification trees for our analyses. Our results showed warmer temperatures in the prior twenty-four hours and more loading over the seven days before days with deep slab avalanches on persistent weak layers. In line with previous research, extended periods of above freezing temperatures led to days with deep wet slab avalanches on persistent weak layers. Seasons with either dry or wet avalanches on deep persistent weak layers typically had drier early months, and often had some significant snow depth prior to those dry months. This paper provides insights for ski patrollers, guides, and avalanche forecasters who struggle to forecast deep slab avalanches on persistent weak layers late in the season.

Defective TiO 2 with high photoconductive gain for efficient and stable planar heterojunction perovskite solar cells

DOE PAGES

Li, Yanbo; Cooper, Jason K.; Liu, Wenjun; ...

2016-08-18

Formation of planar heterojunction perovskite solar cells exhibiting both high efficiency and stability under continuous operation remains a challenge. Here, we show this can be achieved by using a defective TiO 2 thin film as the electron transport layer. TiO 2 layers with native defects are deposited by electron beam evaporation in an oxygen-deficient environment. Deep-level hole traps are introduced in the TiO 2 layers and contribute to a high photoconductive gain and reduced photocatalytic activity. The high photoconductivity of the TiO 2 electron transport layer leads to improved efficiency for the fabricated planar devices. A maximum power conversion efficiencymore » of 19.0% and an average PCE of 17.5% are achieved. In addition, the reduced photocatalytic activity of the TiO 2 layer leads to enhanced long-Term stability for the planar devices. Under continuous operation near the maximum power point, an efficiency of over 15.4% is demonstrated for 100 h.« less

A Case of Bilateral Descemet's Membrane and Subepithelial Opacity: In vivo Laser Confocal Microscopic Study.

PubMed

Hatta, Yukiko; Yokogawa, Hideaki; Kobayashi, Akira; Torisaki, Makoto; Sugiyama, Kazuhisa

2013-01-01

To report the in vivo laser confocal microscopy findings from a patient with Descemet's membrane and subepithelial opacity OU. A healthy 41-year-old male with Descemet's membrane and subepithelial opacity OU was studied. Routine ophthalmic examination, standard slit-lamp biomicroscopy, and in vivo laser confocal microscopic analysis of the entire corneal layer were performed. Slit-lamp biomicroscopy revealed subepithelial opacity in the mid-peripheral to peripheral cornea and numerous opacities located at the level of Descemet's membrane. It was difficult to distinguish the precise histological location of the opacity. In vivo laser confocal microscopy showed numerous hyperreflective particles in the subepithelium to superficial stroma and hyperreflectivity of Descemet's membrane. No abnormalities could be detected in the epithelial cell layer, midstromal layer, deep stromal layer, or endothelial cell layer. Although the origin of the corneal opacities was unclear, in vivo laser confocal microscopy was useful for observing microstructural abnormalities in a case of Descemet's membrane and subepithelial opacity.

A Case of Bilateral Descemet's Membrane and Subepithelial Opacity: In vivo Laser Confocal Microscopic Study

PubMed Central

Hatta, Yukiko; Yokogawa, Hideaki; Kobayashi, Akira; Torisaki, Makoto; Sugiyama, Kazuhisa

2013-01-01

Purpose To report the in vivo laser confocal microscopy findings from a patient with Descemet's membrane and subepithelial opacity OU. Case Report A healthy 41-year-old male with Descemet's membrane and subepithelial opacity OU was studied. Routine ophthalmic examination, standard slit-lamp biomicroscopy, and in vivo laser confocal microscopic analysis of the entire corneal layer were performed. Slit-lamp biomicroscopy revealed subepithelial opacity in the mid-peripheral to peripheral cornea and numerous opacities located at the level of Descemet's membrane. It was difficult to distinguish the precise histological location of the opacity. In vivo laser confocal microscopy showed numerous hyperreflective particles in the subepithelium to superficial stroma and hyperreflectivity of Descemet's membrane. No abnormalities could be detected in the epithelial cell layer, midstromal layer, deep stromal layer, or endothelial cell layer. Conclusion Although the origin of the corneal opacities was unclear, in vivo laser confocal microscopy was useful for observing microstructural abnormalities in a case of Descemet's membrane and subepithelial opacity. PMID:23626574

A direct translaminar inhibitory circuit tunes cortical output

PubMed Central

Pluta, Scott; Naka, Alexander; Veit, Julia; Telian, Gregory; Yao, Lucille; Hakim, Richard; Taylor, David; Adesnik, Hillel

2015-01-01

Summary Anatomical and physiological experiments have outlined a blueprint for the feed-forward flow of activity in cortical circuits: signals are thought to propagate primarily from the middle cortical layer, L4, up to L2/3, and down to the major cortical output layer, L5. Pharmacological manipulations, however, have contested this model and suggested that L4 may not be critical for sensory responses of neurons in either superficial or deep layers. To address these conflicting models we reversibly manipulated L4 activity in awake, behaving mice using cell-type specific optogenetics. In contrast to both prevailing models, we show that activity in L4 directly suppresses L5, in part by activating deep, fast spiking inhibitory neurons. Our data suggest that the net impact of L4 activity is to sharpen the spatial representations of L5 neurons. Thus we establish a novel translaminar inhibitory circuit in the sensory cortex that acts to enhance the feature selectivity of cortical output. PMID:26414615

Deep SOMs for automated feature extraction and classification from big data streaming

NASA Astrophysics Data System (ADS)

Sakkari, Mohamed; Ejbali, Ridha; Zaied, Mourad

2017-03-01

In this paper, we proposed a deep self-organizing map model (Deep-SOMs) for automated features extracting and learning from big data streaming which we benefit from the framework Spark for real time streams and highly parallel data processing. The SOMs deep architecture is based on the notion of abstraction (patterns automatically extract from the raw data, from the less to more abstract). The proposed model consists of three hidden self-organizing layers, an input and an output layer. Each layer is made up of a multitude of SOMs, each map only focusing at local headmistress sub-region from the input image. Then, each layer trains the local information to generate more overall information in the higher layer. The proposed Deep-SOMs model is unique in terms of the layers architecture, the SOMs sampling method and learning. During the learning stage we use a set of unsupervised SOMs for feature extraction. We validate the effectiveness of our approach on large data sets such as Leukemia dataset and SRBCT. Results of comparison have shown that the Deep-SOMs model performs better than many existing algorithms for images classification.

Enhancement of free tropospheric ozone production by deep convection

NASA Technical Reports Server (NTRS)

Pickering, Kenneth E.; Thompson, Anne M.; Scala, John R.; Tao, Wei-Kuo; Simpson, Joanne

1994-01-01

It is found from model simulations of trace gas and meteorological data from aircraft campaigns that deep convection may enhance the potential for photochemical ozone production in the middle and upper troposphere by up to a factor of 60. Examination of half a dozen individual convective episodes show that the degree of enhancement is highly variable. Factors affecting enhancement include boundary layer NO(x) mixing ratios, differences in the strength and structure of convective cells, as well as variation in the amount of background pollution already in the free troposphere.

A deep-level transient spectroscopy study of gamma-ray irradiation on the passivation properties of silicon nitride layer on silicon

NASA Astrophysics Data System (ADS)

Dong, Peng; Yu, Xuegong; Ma, Yao; Xie, Meng; Li, Yun; Huang, Chunlai; Li, Mo; Dai, Gang; Zhang, Jian

2017-08-01

Plasma-enhanced chemical vapor deposited silicon nitride (SiNx) films are extensively used as passivation material in the solar cell industry. Such SiNx passivation layers are the most sensitive part to gamma-ray irradiation in solar cells. In this work, deep-level transient spectroscopy has been applied to analyse the influence of gamma-ray irradiation on the passivation properties of SiNx layer on silicon. It is shown that the effective carrier lifetime decreases with the irradiation dose. At the same time, the interface state density is significantly increased after irradiation, and its energy distribution is broadened and shifts deeper with respect to the conduction band edge, which makes the interface states becoming more efficient recombination centers for carriers. Besides, C-V characteristics show a progressive negative shift with increasing dose, indicating the generation of effective positive charges in SiNx films. Such positive charges are beneficial for shielding holes from the n-type silicon substrates, i. e. the field-effect passivation. However, based on the reduced carrier lifetime after irradiation, it can be inferred that the irradiation induced interface defects play a dominant role over the trapped positive charges, and therefore lead to the degradation of passivation properties of SiNx on silicon.

Ge nanopillar solar cells epitaxially grown by metalorganic chemical vapor deposition

PubMed Central

Kim, Youngjo; Lam, Nguyen Dinh; Kim, Kangho; Park, Won-Kyu; Lee, Jaejin

2017-01-01

Radial junction solar cells with vertically aligned wire arrays have been widely studied to improve the power conversion efficiency. In this work, we report the first Ge nanopillar solar cell. Nanopillar arrays are selectively patterned on p-type Ge (100) substrates using nanosphere lithography and deep reactive ion etching processes. Nanoscale radial and planar junctions are realized by an n-type Ge emitter layer which is epitaxially grown by MOCVD using isobutylgermane. In situ epitaxial surface passivation is employed using an InGaP layer to avoid high surface recombination rates and Fermi level pinning. High quality n-ohmic contact is realized by protecting the top contact area during the nanopillar patterning. The short circuit current density and the power conversion efficiency of the Ge nanopillar solar cell are demonstrated to be improved up to 18 and 30%, respectively, compared to those of the Ge solar cell with a planar surface. PMID:28209964

Comparison and Interpretation of Admittance Spectroscopy and Deep Level Transient Spectroscopy from Co-Evaporated and Solution-Deposited Cu2ZnSn(Sx, Se1-x)4 Solar Cells

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

Caruso, A. E.; Lund, E. A.; Kosyak, V.

2016-11-21

Cu2ZnSn(S, Se)4 (CZTSe) is an earth-abundant semiconductor with potential for economical thin-film photovoltaic devices. Short minority carrier lifetimes contribute to low open circuit voltage and efficiency. Deep level defects that may contribute to lower minority carrier lifetimes in kesterites have been theoretically predicted, however very little experimental characterization of these deep defects exists. In this work we use admittance spectroscopy (AS) and deep level transient spectroscopy (DLTS) to characterize devices built using CZTSSe absorber layers deposited via both coevaporation and solution processing. AS reveals a band of widely-distributed activation energies for traps or energy barriers for transport, especially in themore » solution deposited case. DLTS reveals signatures of deep majority and minority traps within both types of samples.« less

Parallel odor processing by mitral and middle tufted cells in the olfactory bulb.

PubMed

Cavarretta, Francesco; Burton, Shawn D; Igarashi, Kei M; Shepherd, Gordon M; Hines, Michael L; Migliore, Michele

2018-05-16

The olfactory bulb (OB) transforms sensory input into spatially and temporally organized patterns of activity in principal mitral (MC) and middle tufted (mTC) cells. Thus far, the mechanisms underlying odor representations in the OB have been mainly investigated in MCs. However, experimental findings suggest that MC and mTC may encode parallel and complementary odor representations. We have analyzed the functional roles of these pathways by using a morphologically and physiologically realistic three-dimensional model to explore the MC and mTC microcircuits in the glomerular layer and deeper plexiform layer. The model makes several predictions. MCs and mTCs are controlled by similar computations in the glomerular layer but are differentially modulated in deeper layers. The intrinsic properties of mTCs promote their synchronization through a common granule cell input. Finally, the MC and mTC pathways can be coordinated through the deep short-axon cells in providing input to the olfactory cortex. The results suggest how these mechanisms can dynamically select the functional network connectivity to create the overall output of the OB and promote the dynamic synchronization of glomerular units for any given odor stimulus.

Layer-specific morphological and molecular differences in neocortical astrocytes and their dependence on neuronal layers.

PubMed

Lanjakornsiripan, Darin; Pior, Baek-Jun; Kawaguchi, Daichi; Furutachi, Shohei; Tahara, Tomoaki; Katsuyama, Yu; Suzuki, Yutaka; Fukazawa, Yugo; Gotoh, Yukiko

2018-04-24

Non-pial neocortical astrocytes have historically been thought to comprise largely a nondiverse population of protoplasmic astrocytes. Here we show that astrocytes of the mouse somatosensory cortex manifest layer-specific morphological and molecular differences. Two- and three-dimensional observations revealed that astrocytes in the different layers possess distinct morphologies as reflected by differences in cell orientation, territorial volume, and arborization. The extent of ensheathment of synaptic clefts by astrocytes in layer II/III was greater than that by those in layer VI. Moreover, differences in gene expression were observed between upper-layer and deep-layer astrocytes. Importantly, layer-specific differences in astrocyte properties were abrogated in reeler and Dab1 conditional knockout mice, in which neuronal layers are disturbed, suggesting that neuronal layers are a prerequisite for the observed morphological and molecular differences of neocortical astrocytes. This study thus demonstrates the existence of layer-specific interactions between neurons and astrocytes, which may underlie their layer-specific functions.

Deep Subsurface Microbial Communities Shaped by the Chicxulub Impactor

NASA Astrophysics Data System (ADS)

Cockell, C. S.; Coolen, M.; Schaefer, B.; Grice, K.; Gulick, S. P. S.; Morgan, J. V.; Kring, D. A.; Osinski, G.

2017-12-01

Fresh core material was obtained by drilling of the Chicxulub impact crater during IODP-ICDP Expedition 364 to assess the present-day biosphere in the crater structure. Cell enumerations through the core show that beneath the post-impact sedimentary rock there is a region of enhanced cell abundance that corresponds to the upper impact suevite layer (Units 1G/2A). We also observed a peak in cell numbers in samples at the bottom of suevite Unit 2C and between the suevitic and grainitoid interface (Unit 3/4). These patterns may reflect preferential movement of fluid and/or availability of nutrients and energy at interfaces. 16S rDNA analysis allows us to rule out contamination of the suevite material since no taxa associated with the drilling mud were observed. Two hundred and fifty microbial enrichments were established using diverse culture media for heterotrophs, autotrophs and chemolithotrophs at temperatures consistent with measured core temperatures. Six yielded growth in the breccia, lower breccia and upper granitoid layer and they affiliated with Acidiphilium, Thermoanaerobacteracea and Desulfohalbiaceae. The latter exhibited visible microbial sulfate-reduction. By contrast, the granitoid material exhibited low cell abundances, most samples were below direct cell detection. DNA extraction revealed pervasive low level contamination by drilling mud taxa, consistent with the highly fractured, high porosity of the impact-shocked granitoids. Few taxa can be attributed to an indigenous biota and no enrichments (at 60 and 70°C) yielded growth. These data show that even with a porosity approximately an order of magnitude greater than most unshocked granites, the uplifted granites have not experienced sufficient fluid flow to establish a significant deep biosphere. Paleosterilisation of the material during impact may have re-set colonisation and the material may have originally been below the depth at which temperatures exceeded the upper temperature limit for life. These data show that the deep biosphere can preserve the imprint of catastrophe long after these events. In this case, the distribution of deep subsurface microbial communities reflects the lithological sequence established during the substantial impact-induced geological rearrangements that occurred in the first hours of the Cenozoic.

Margined winner-take-all: New learning rule for pattern recognition.

PubMed

Fukushima, Kunihiko

2018-01-01

The neocognitron is a deep (multi-layered) convolutional neural network that can be trained to recognize visual patterns robustly. In the intermediate layers of the neocognitron, local features are extracted from input patterns. In the deepest layer, based on the features extracted in the intermediate layers, input patterns are classified into classes. A method called IntVec (interpolating-vector) is used for this purpose. This paper proposes a new learning rule called margined Winner-Take-All (mWTA) for training the deepest layer. Every time when a training pattern is presented during the learning, if the result of recognition by WTA (Winner-Take-All) is an error, a new cell is generated in the deepest layer. Here we put a certain amount of margin to the WTA. In other words, only during the learning, a certain amount of handicap is given to cells of classes other than that of the training vector, and the winner is chosen under this handicap. By introducing the margin to the WTA, we can generate a compact set of cells, with which a high recognition rate can be obtained with a small computational cost. The ability of this mWTA is demonstrated by computer simulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Identity and abundance of active sulfate-reducing bacteria in deep tidal flat sediments determined by directed cultivation and CARD-FISH analysis.

PubMed

Gittel, Antje; Mussmann, Marc; Sass, Henrik; Cypionka, Heribert; Könneke, Martin

2008-10-01

The identity and abundance of potentially active sulfate-reducing bacteria (SRB) in several metre deep sediments of a tidal sand flat in the German Wadden Sea were assessed by directed cultivation and cultivation-independent CARD-FISH analysis (catalysed reporter deposition fluorescence in situ hybridization). Presumably abundant SRB from different sediment layers between 0.5 and 4 m depth were selectively enriched in up to million-fold diluted cultures supplemented with lactate, acetate or hydrogen. Partial 16S rRNA gene sequences obtained from highest dilution steps showing sulfide formation indicated growth of deltaproteobacterial SRB belonging to the Desulfobulbaceae and the Desulfobacteraceae as well as of members of the Firmicutes. Subsequent isolation resulted in 10 novel phylotypes of both litho- and organotrophic sulfate-reducing Deltaproteobacteria. Molecular pre-screening identified six isolates as members of the Desulfobulbaceae, sharing highest identities with either candidatus 'Desulfobacterium corrodens' (95-97%) or Desulfobacterium catecholicum (98%), and four isolates as members of Desulfobacteraceae, being related to either Desulfobacter psychrotolerans (98%) or Desulfobacula phenolica (95-97%). Relatives of D. phenolica were exlusively isolated from 50 and 100 cm deep sediments with 10 and 2 mM of pore water sulfate respectively. In contrast, relatives of D. corrodens, D. psychrotolerans and D. catecholicum were also obtained from layers deeper than 100 cm and with less than 2 mM sulfate. The high in situ abundance of members of both families in sediment layers beneath 50 cm could be confirmed via CARD-FISH analysis performed with a set of six SRB-specific oligonucleotide probes. Moreover, SRB represented a numerically significant fraction of the microbial community throughout the sediment (up to 7%) and reached even higher cell numbers in deep, sulfate-poor layers than in the sulfate-rich surface sediment. This relatively large community size of potentially active SRB in deep sandy sediments might on the one hand be a result of their syntrophic association with other anaerobes. Our results furthermore support the hypothesis that enhanced advective pore water transport might supply nutrients to microbial communities in deep sandy sediments and point to their so far unrecognized contribution to biogeochemical processes in Wadden Sea sediments.

The deep layer of the tractus iliotibialis and its relevance when using the direct anterior approach in total hip arthroplasty: a cadaver study.

PubMed

Putzer, David; Haselbacher, Matthias; Hörmann, Romed; Klima, Günter; Nogler, Michael

2017-12-01

Surgical approaches through smaller incisions reveal less of the underlying anatomy, and therefore, detailed knowledge of the local anatomy and its variations is important in minimally invasive surgery. The aim of this study was to determine the location, extension, and histomorphology of the deep layer of the iliotibial band during minimally invasive hip surgery using the direct anterior approach (DAA). The morphology of the iliotibial tract was determined in this cadaver study on 40 hips with reference to the anterior superior iliac spine and the tibia. The deep layer of the tractus iliotibialis was exposed up to the hip-joint capsule and length and width measurements taken. Sections of the profound iliotibial tract were removed from the hips and the thickness of the sections was determined microscopically after staining. The superficial tractus iliotibialis had a length of 50.1 (SD 3.8) cm, while tensor fasciae latae total length was 18 (SD 2) cm [unattached 15 (SD 2.5) cm]. Length and width of the deep layer of the tractus iliotibialis were 10.4 (SD 1.3) × 3.3 (SD 0.6) cm. The deep iliotibial band always extended from the distal part of the tensor fascia latae (TFL) muscle to the lateral part of the hip capsule (mean maximum thickness 584 μm). Tractus iliotibialis deep layer morphology did not correlate to other measurements taken (body length, thigh length, and TFL length). The length of the deep layer is dependent on the TFL, since the profound part of the iliotibial band reaches from the TFL to the hip-joint capsule. The deep layer covers the hip-joint capsule, rectus, and lateral vastus muscles in the DAA interval. To access the precapsular fat pad and the hip-joint capsule, the deep layer has to be split in all approaches that use the direct anterior interval.

A two-dimensional ocean model for long-term climatic simulations: Stability and coupling to atmospheric and sea ice models

NASA Astrophysics Data System (ADS)

Harvey, L. D. Danny

1992-06-01

A two-dimensional (latitude-depth) deep ocean model is presented which is coupled to a sea ice model and an Energy Balance Climate Model (EBCM), the latter having land-sea and surface-air resolution. The processes which occur in the ocean model are thermohaline overturning driven by the horizontal density gradient, shallow wind-driven overturning cells, convective overturning, and vertical and horizontal diffusion of heat and salt. The density field is determined from the temperature and salinity fields using a nonlinear equation of state. Mixed layer salinity is affected by evaporation, precipitation, runoff from continents, and sea ice freezing and melting, as well as by advective, convective, and diffusive exchanges with the deep ocean. The ocean model is first tested in an uncoupled mode, in which hemispherically symmetric mixed layer temperature and salinity, or salinity flux, are specified as upper boundary conditions. An experiment performed with previous models is repeated in which a mixed layer salinity perturbation is introduced in the polar half of one hemisphere after switching from a fixed salinity to a fixed salinity flux boundary condition. For small values of the vertical diffusion coefficient KV, the model undergoes self-sustained oscillations with a period of about 1500 years. With larger values of KV, the model locks into either an asymmetric mode with a single overturning cell spanning both hemispheres, or a symmetric quiescent state with downwelling near the equator, upwelling at high latitudes, and a warm deep ocean (depending on the value of KV). When the ocean model is forced with observed mixed layer temperature and salinity, no oscillations occur. The model successfully simulates the very weak meridional overturning and strong Antarctic Circumpolar Current at the latitudes of the Drake Passage. The coupled EBCM-deep ocean model displays internal oscillations with a period of 3000 years if the ocean fraction is uniform with latitude and KV and the horizontal diffusion coefficient in the mixed layer are not too large. Globally averaged atmospheric temperature changes of 2 K are driven by oscillations in the heat flux into or out of the deep ocean, with the sudden onset of a heat flux out of the deep ocean associated with the rapid onset of thermohaline overturning after a quiescent period, and the sudden onset of a heat flux into the deep ocean associated with the collapse of thermohaline overturning. When the coupled model is run with prescribed parameters (such as land-sea fraction and precipitation) varying with latitude based on observations, the model does not oscillate and produces a reasonable deep ocean temperature field but a completely unrealistic salinity field. Resetting the mixed layer salinity to observations on each time step (equivalent to the "flux correction" method used in atmosphere-ocean general circulation models) is sufficient to give a realistic salinity field throughout the ocean depth, but dramatically alters the flow field and associated heat transport. Although the model is highly idealized, the finding that the maximum perturbation in globally averaged heat flux from the deep ocean to the surface over a 100-year period is 1.4 W m-2 suggests that effect of continuing greenhouse gas increases, which could result in a heating perturbation of 10 W m-2 by the end of the next century, will swamp possible surface heating perturbations due to changes in oceanic circulation. On the other hand, the extreme sensitivity of the oceanic flow field to variations in precipitation and evaporation suggests that it will not be possible to produce accurate projections of regional climatic change in the near term, if at all.

Size and Carbon Content of Sub-seafloor Microbial Cells at Landsort Deep, Baltic Sea

PubMed Central

Braun, Stefan; Morono, Yuki; Littmann, Sten; Kuypers, Marcel; Aslan, Hüsnü; Dong, Mingdong; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-01-01

The discovery of a microbial ecosystem in ocean sediments has evoked interest in life under extreme energy limitation and its role in global element cycling. However, fundamental parameters such as the size and the amount of biomass of sub-seafloor microbial cells are poorly constrained. Here we determined the volume and the carbon content of microbial cells from a marine sediment drill core retrieved by the Integrated Ocean Drilling Program (IODP), Expedition 347, at Landsort Deep, Baltic Sea. To determine their shape and volume, cells were separated from the sediment matrix by multi-layer density centrifugation and visualized via epifluorescence microscopy (FM) and scanning electron microscopy (SEM). Total cell-carbon was calculated from amino acid-carbon, which was analyzed by high-performance liquid chromatography (HPLC) after cells had been purified by fluorescence-activated cell sorting (FACS). The majority of microbial cells in the sediment have coccoid or slightly elongated morphology. From the sediment surface to the deepest investigated sample (~60 m below the seafloor), the cell volume of both coccoid and elongated cells decreased by an order of magnitude from ~0.05 to 0.005 μm3. The cell-specific carbon content was 19–31 fg C cell−1, which is at the lower end of previous estimates that were used for global estimates of microbial biomass. The cell-specific carbon density increased with sediment depth from about 200 to 1000 fg C μm−3, suggesting that cells decrease their water content and grow small cell sizes as adaptation to the long-term subsistence at very low energy availability in the deep biosphere. We present for the first time depth-related data on the cell volume and carbon content of sedimentary microbial cells buried down to 60 m below the seafloor. Our data enable estimates of volume- and biomass-specific cellular rates of energy metabolism in the deep biosphere and will improve global estimates of microbial biomass. PMID:27630628

Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks

NASA Astrophysics Data System (ADS)

Wang, Yiheng; Liu, Tong; Xu, Dong; Shi, Huidong; Zhang, Chaoyang; Mo, Yin-Yuan; Wang, Zheng

2016-01-01

The hypo- or hyper-methylation of the human genome is one of the epigenetic features of leukemia. However, experimental approaches have only determined the methylation state of a small portion of the human genome. We developed deep learning based (stacked denoising autoencoders, or SdAs) software named “DeepMethyl” to predict the methylation state of DNA CpG dinucleotides using features inferred from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns. We used the experimental data from immortalised myelogenous leukemia (K562) and healthy lymphoblastoid (GM12878) cell lines to train the learning models and assess prediction performance. We have tested various SdA architectures with different configurations of hidden layer(s) and amount of pre-training data and compared the performance of deep networks relative to support vector machines (SVMs). Using the methylation states of sequentially neighboring regions as one of the learning features, an SdA achieved a blind test accuracy of 89.7% for GM12878 and 88.6% for K562. When the methylation states of sequentially neighboring regions are unknown, the accuracies are 84.82% for GM12878 and 72.01% for K562. We also analyzed the contribution of genome topological features inferred from Hi-C. DeepMethyl can be accessed at http://dna.cs.usm.edu/deepmethyl/.

Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks.

PubMed

Wang, Yiheng; Liu, Tong; Xu, Dong; Shi, Huidong; Zhang, Chaoyang; Mo, Yin-Yuan; Wang, Zheng

2016-01-22

The hypo- or hyper-methylation of the human genome is one of the epigenetic features of leukemia. However, experimental approaches have only determined the methylation state of a small portion of the human genome. We developed deep learning based (stacked denoising autoencoders, or SdAs) software named "DeepMethyl" to predict the methylation state of DNA CpG dinucleotides using features inferred from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns. We used the experimental data from immortalised myelogenous leukemia (K562) and healthy lymphoblastoid (GM12878) cell lines to train the learning models and assess prediction performance. We have tested various SdA architectures with different configurations of hidden layer(s) and amount of pre-training data and compared the performance of deep networks relative to support vector machines (SVMs). Using the methylation states of sequentially neighboring regions as one of the learning features, an SdA achieved a blind test accuracy of 89.7% for GM12878 and 88.6% for K562. When the methylation states of sequentially neighboring regions are unknown, the accuracies are 84.82% for GM12878 and 72.01% for K562. We also analyzed the contribution of genome topological features inferred from Hi-C. DeepMethyl can be accessed at http://dna.cs.usm.edu/deepmethyl/.

Integrated plasticity at inhibitory and excitatory synapses in the cerebellar circuit.

PubMed

Mapelli, Lisa; Pagani, Martina; Garrido, Jesus A; D'Angelo, Egidio

2015-01-01

The way long-term potentiation (LTP) and depression (LTD) are integrated within the different synapses of brain neuronal circuits is poorly understood. In order to progress beyond the identification of specific molecular mechanisms, a system in which multiple forms of plasticity can be correlated with large-scale neural processing is required. In this paper we take as an example the cerebellar network, in which extensive investigations have revealed LTP and LTD at several excitatory and inhibitory synapses. Cerebellar LTP and LTD occur in all three main cerebellar subcircuits (granular layer, molecular layer, deep cerebellar nuclei) and correspondingly regulate the function of their three main neurons: granule cells (GrCs), Purkinje cells (PCs) and deep cerebellar nuclear (DCN) cells. All these neurons, in addition to be excited, are reached by feed-forward and feed-back inhibitory connections, in which LTP and LTD may either operate synergistically or homeostatically in order to control information flow through the circuit. Although the investigation of individual synaptic plasticities in vitro is essential to prove their existence and mechanisms, it is insufficient to generate a coherent view of their impact on network functioning in vivo. Recent computational models and cell-specific genetic mutations in mice are shedding light on how plasticity at multiple excitatory and inhibitory synapses might regulate neuronal activities in the cerebellar circuit and contribute to learning and memory and behavioral control.

Correction of cell-induced optical aberrations in a fluorescence fluctuation microscope

PubMed Central

Leroux, Charles-Edouard; Grichine, Alexei; Wang, Irène; Delon, Antoine

2013-01-01

We describe the effect of optical aberrations on fluorescence fluctuations microscopy (FFM), when focusing through a single living cell. FFM measurements are performed in an aqueous fluorescent solution, and prove to be a highly sensitive tool to assess the optical aberrations introduced by the cell. We demonstrate an adaptive optics (AO) system to remove the aberration-related bias in the FFM measurements. Our data show that AO is not only useful when imaging deep in tissues, but also when performing FFM measurements through a single cellular layer. PMID:23939061

Study of relationships of material properties and high efficiency solar cell performance on material composition

NASA Technical Reports Server (NTRS)

Sah, C. T.

1983-01-01

The performance improvements obtainable from extending the traditionally thin back-surface-field (BSF) layer deep into the base of silicon solar cells under terrestrial solar illumination (AM1) are analyzed. This extended BSF cell is also known as the back-drift-field cell. About 100 silicon cells were analyzed, each with a different emitter or base dopant impurity distribution whose selection was based on physically anticipated improvements. The four principal performance parameters (the open-circuit voltage, the short-circuit current, the fill factor, and the maximum efficiency) are computed using a FORTRAN program, called Circuit Technique for Semiconductor-device Analysis, CTSA, which numerically solves the six Shockley Equations under AM1 solar illumination at 88.92 mW/cm, at an optimum cell thickness of 50 um. The results show that very significant performance improvements can be realized by extending the BSF layer thickness from 2 um (18% efficiency) to 40 um (20% efficiency).

Electron Radiation Damage of (alga) As-gaas Solar Cells

NASA Technical Reports Server (NTRS)

Loo, R.; Kamath, G. S.; Knechtli, R.

1979-01-01

Solar cells (2 cm by 2 cm (AlGa) As-GaAs cells) were fabricated and then subjected to irradiation at normal incidence by electrons. The influence of junction depth and n-type buffer layer doping level on the cell's resistance to radiation damage was investigated. The study shows that (1) a 0.3 micrometer deep junction results in lower damage to the cells than does a 0.5 micrometer junction, and (2) lowering the n buffer layer doping density does not improve the radiation resistance of the cell. Rather, lowering the doping density decreases the solar cell's open circuit voltage. Some preliminary thermal annealing experiments in vacuum were performed on the (AlGa)As-GaAs solar cells damaged by 1-MeV electron irradiation. The results show that cell performance can be expected to partially recover at 200 C with more rapid and complete recovery occurring at higher temperature. For a 0.5hr anneal at 400 C, 90% of the initial power is recovered. The characteristics of the (AlGa)As-GaAs cells both before and after irradiation are described.

Parvalbumin and calbindin immunoreactivity in the cerebral cortex of the hedgehog (Erinaceus europaeus).

PubMed Central

Ferrer, I; Zujar, M J; Admella, C; Alcantara, S

1992-01-01

To investigate the morphology and distribution of nonpyramidal neurons in the brain of insectivores, parvalbumin and calbindin 28 kDa immunoreactivity was examined in the cerebral cortex of the hedgehog (Erinaceus europaeus). Parvalbumin-immunoreactive cells were found in all layers of the isocortex, but in contrast to other mammals, a laminar organisation or specific regional distribution was not seen. Characteristic parvalbumin-immunoreactive neurons were multipolar cells with large ascending and descending dendrites extending throughout several layers. Calbindin-immunoreactive neurons were similar to those found in other species, although appearing in smaller numbers than in the cerebral cortex of more advanced mammals. The morphology and distribution of parvalbumin- and calbindin-immunoreactive cells in the piriform and entorhinal cortices were similar in hedgehogs and rodents. Parvalbumin-immunoreactive cells in the hippocampal complex were pyramidal-like and bitufted neurons, which were mainly found in the stratum oriens and stratum pyramidale of the hippocampus, and in the stratum moleculare and hilus of the fascia dentata. Heavily stained cells were found in the deep part of the stratum granulare. Intense calbindin immunoreactivity occurred mainly in the granule cell and molecular layers of the dentate gyrus and in the mossy fibre layer. The most outstanding feature in the hippocampal complex of the hedgehog was the extension of calbindin immunoreactivity to CA1 field of the hippocampus, suggesting, in agreement with other reports, that mossy fibres can establish synaptic contacts throughout the pyramidal cell layer. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:1452472

A Physiological Neural Network for Saccadic Eye Movement Control

DTIC Science & Technology

1994-04-01

cerebellum, substantia nigra, nucleus reticularis tegmenti pontis, the thalamus, the deep layers of the superior colliculus and the oculomotor plant...and pause cells), the vestibular nucleus , abducens nucleus , oculomotor nucleus , cerebellum, substantia nigra, nucleus reticularis tegmenti pontis, the...vestibular nucleus , abducens nucleus , oculomotor nucleus , cerebellum, substantia nigra, nucleus reticularis tegmenti pontis (NRTP), the thalamus, the

On the front and back side quantum efficiency differences in semi-transparent organic solar cells and photodiodes

NASA Astrophysics Data System (ADS)

Bouthinon, B.; Clerc, R.; Verilhac, J. M.; Racine, B.; De Girolamo, J.; Jacob, S.; Lienhard, P.; Joimel, J.; Dhez, O.; Revaux, A.

2018-03-01

The External Quantum Efficiency (EQE) of semi-transparent Bulk Hetero-Junction (BHJ) organic photodiodes processed in air shows significant differences when measured from the front or back side contacts. This difference was found significantly reduced when decreasing the active layer thickness or by applying a negative bias. This work brings new elements to help understanding this effect, providing a large set of experiments featuring different applied voltages, active layers, process conditions, and electron and hole layers. By means of detailed electrical simulations, all these measurements have been found consistent with the mechanisms of irreversible photo-oxidation, modeled as deep trap states (and not as p-type doping). The EQE measurement from front and back sides is thus a simple and efficient way of monitoring the presence and amplitude of oxygen contamination in BHJ organic solar cells and photodiodes.

Histological and morphological observations on tongue of Scincella tsinlingensis (Reptilia, Squamata, Scincidae).

PubMed

Yang, Chun; Wang, Limin

2016-01-01

The histology and morphology characteristics of the tongue in Scincella tsinlingensis were studied by light and electronic microscopy. Under light microscopy, the tongue consists of tip, lingual body and radix in sequence. Numerous lingual papillae widely distribute on the surface of the dorsal and ventral flanks in the tongue, in addition to some regions of the tip. The papillae's surface is covered with the epithelial layer. The lamina propria and dense connective tissue are distinct existing under the epithelial layer. There are many lingual glands spread over the lamina propria. Tongue muscle is developed and composed of distinct intrinsic muscle, hyoglossus and genioglossus. By scanning electron microscopy, at higher magnification, the epithelial cells of the dorsal surface in the divaricate tongue tips show numerous microvilli, micro-ridges and micro-pores. The surface of dorsal side of the papillae in lingual body is covered with abundant of micro-ridges and taste bud lacuna. On the surface of the papillae in radix, micro-facets and micro-ridges are compactly distributed, as well as scattered mucilage-pores. The lingual epithelium is divided into four layers observed by the transmission electron microscope. Cells of basal layer are irregularly elliptical in shape, with sparse organelles in the cytoplasm. The deep intermediate layer is not always distinct. Small numbers of organelles are scattered into the cytoplasm. The cells of the superficial intermediate layer gradually flatten, as do their nuclei. The cytoplasm contains many keratohyalin granules. Cell membranes are formed processes around cells and joined by abundant desmosomes to the cell membranes of adjacent cells. The cells located on the extreme free-surface side of the keratinized layer have fallen off. The basal lamina is intercalated between the basal layer and the lamina propria. The lamina propria of lingual body contains lingual gland. A large part of the cytoplasm is occupied by mucus granules which located in the distal part of the cell. The connective tissue contains myelinated nerve fibers, vessel and muscle cells. Copyright © 2015 Elsevier Ltd. All rights reserved.

Anatomy of the subcutaneous tissue of the trunk and lower extremity.

PubMed

Markman, B; Barton, F E

1987-08-01

Dissections on 8 fresh and 10 embalmed cadavers were used to determine the anatomy of the subcutaneous adipose tissue in the trunk and extremities. These dissections, along with CT scans, confirmed Gray's original description of the subcutaneous tissue consisting of a superficial and deep adipose layer. The superficial adipose layer is contained within organized, compact fascial septa. The deep adipose layer demonstrated regional variations with respect to its fascial framework, but was contained within a relatively loose, less organized, and more widely spaced fascial septa. We observed that the adipose layers are partitioned by a discrete subcutaneous fascia which fuses with the underlying muscle fascia at particular anatomic locations. The deep layer is thus contained by the subcutaneous fascia above and the muscle fascia below to form what we termed the deep adipose compartments. The deep adipose compartments contributed significantly to overall adipose thickness, are bilateral, and are found in the abdomen and paralumbar and gluteal-thigh regions.

Comparison of frailty of primary neurons, embryonic, and aging mouse cortical layers.

PubMed

Fugistier, Patrick; Vallet, Philippe G; Leuba, Geneviève; Piotton, Françoise; Marin, Pascale; Bouras, Constantin; Savioz, Armand

2014-02-01

Superficial layers I to III of the human cerebral cortex are more vulnerable toward Aβ peptides than deep layers V to VI in aging. Three models of layers were used to investigate this pattern of frailty. First, primary neurons from E14 and E17 embryonic murine cortices, corresponding respectively to future deep and superficial layers, were treated either with Aβ(1-42), okadaic acid, or kainic acid. Second, whole E14 and E17 embryonic cortices, and third, in vitro separated deep and superficial layers of young and old C57BL/6J mice, were treated identically. We observed that E14 and E17 neurons in culture were prone to death after the Aβ and particularly the kainic acid treatment. This was also the case for the superficial layers of the aged cortex, but not for the embryonic, the young cortex, and the deep layers of the aged cortex. Thus, the aged superficial layers appeared to be preferentially vulnerable against Aβ and kainic acid. This pattern of vulnerability corresponds to enhanced accumulation of senile plaques in the superficial cortical layers with aging and Alzheimer's disease. Copyright © 2014 Elsevier Inc. All rights reserved.

Molecular analysis of neocortical layer structure in the ferret

PubMed Central

Rowell, Joanna J.; Mallik, Atul K.; Dugas-Ford, Jennifer; Ragsdale, Clifton W.

2010-01-01

Molecular markers that distinguish specific layers of rodent neocortex are increasingly employed to study cortical development and the physiology of cortical circuits. The extent to which these markers represent general features of neocortical cell type identity across mammals is, however, unknown. To assess the conservation of layer markers more broadly, we isolated orthologs for fifteen layer-enriched genes in the ferret, a carnivore with a large, gyrencephalic brain, and analyzed their patterns of neocortical gene expression. Our major findings are: (1) Many but not all layer markers tested show similar patterns of layer-specific gene expression between mouse and ferret cortex, supporting the view that layer-specific cell type identity is conserved at a molecular level across mammalian superorders; (2) Our panel of deep layer markers (ER81/ETV1, SULF2, PCP4, FEZF2/ZNF312, CACNA1H, KCNN2/SK2, SYT6, FOXP2, CTGF) provides molecular evidence that the specific stratifications of layer 5 and 6 into 5a, 5b, 6a and 6b are also conserved between rodents and carnivores. (3) Variations in layer-specific gene expression are more pronounced across areas of ferret cortex than between homologous areas of mouse and ferret cortex; (4) This variation of area gene expression was clearest with the superficial layer markers studied (SERPINE2, MDGA1, CUX1, UNC5D, RORB/NR1F2, EAG2/KCNH5). Most dramatically, the layer 4 markers RORB and EAG2 disclosed a molecular sublamination to ferret visual cortex and demonstrated a molecular dissociation among the so-called agranular areas of the neocortex. Our findings establish molecular markers as a powerful complement to cytoarchitecture for neocortical layer and cell-type comparisons across mammals. PMID:20575059

Molecular analysis of neocortical layer structure in the ferret.

PubMed

Rowell, Joanna J; Mallik, Atul K; Dugas-Ford, Jennifer; Ragsdale, Clifton W

2010-08-15

Molecular markers that distinguish specific layers of rodent neocortex are increasingly employed to study cortical development and the physiology of cortical circuits. The extent to which these markers represent general features of neocortical cell type identity across mammals, however, is unknown. To assess the conservation of layer markers more broadly, we isolated orthologs for 15 layer-enriched genes in the ferret, a carnivore with a large, gyrencephalic brain, and analyzed their patterns of neocortical gene expression. Our major findings are: 1) Many but not all layer markers tested show similar patterns of layer-specific gene expression between mouse and ferret cortex, supporting the view that layer-specific cell type identity is conserved at a molecular level across mammalian superorders; 2) Our panel of deep layer markers (ER81/ETV1, SULF2, PCP4, FEZF2/ZNF312, CACNA1H, KCNN2/SK2, SYT6, FOXP2, CTGF) provides molecular evidence that the specific stratifications of layers 5 and 6 into 5a, 5b, 6a, and 6b are also conserved between rodents and carnivores; 3) Variations in layer-specific gene expression are more pronounced across areas of ferret cortex than between homologous areas of mouse and ferret cortex; 4) This variation of area gene expression was clearest with the superficial layer markers studied (SERPINE2, MDGA1, CUX1, UNC5D, RORB/NR1F2, EAG2/KCNH5). Most dramatically, the layer 4 markers RORB and EAG2 disclosed a molecular sublamination to ferret visual cortex and demonstrated a molecular dissociation among the so-called agranular areas of the neocortex. Our findings establish molecular markers as a powerful complement to cytoarchitecture for neocortical layer and cell-type comparisons across mammals. (c) 2010 Wiley-Liss, Inc.

Automatic classification of ovarian cancer types from cytological images using deep convolutional neural networks.

PubMed

Wu, Miao; Yan, Chuanbo; Liu, Huiqiang; Liu, Qian

2018-06-29

Ovarian cancer is one of the most common gynecologic malignancies. Accurate classification of ovarian cancer types (serous carcinoma, mucous carcinoma, endometrioid carcinoma, transparent cell carcinoma) is an essential part in the different diagnosis. Computer-aided diagnosis (CADx) can provide useful advice for pathologists to determine the diagnosis correctly. In our study, we employed a Deep Convolutional Neural Networks (DCNN) based on AlexNet to automatically classify the different types of ovarian cancers from cytological images. The DCNN consists of five convolutional layers, three max pooling layers, and two full reconnect layers. Then we trained the model by two group input data separately, one was original image data and the other one was augmented image data including image enhancement and image rotation. The testing results are obtained by the method of 10-fold cross-validation, showing that the accuracy of classification models has been improved from 72.76 to 78.20% by using augmented images as training data. The developed scheme was useful for classifying ovarian cancers from cytological images. © 2018 The Author(s).

Cellular and laminar expression of Dab-1 during the postnatal critical period in cat visual cortex and the effects of dark rearing.

PubMed

Kiser, Paul J; Liu, Zijing; Wilt, Steven D; Mower, George D

2011-04-06

This study describes postnatal critical period changes in cellular and laminar expression of Dab-1, a gene shown to play a role in controlling neuronal positioning during embryonic brain development, in cat visual cortex and the effects of dark rearing (DR). At 1week, there is dense cellular staining which is uniform across cortical layers and very light neuropil staining. At the peak of the critical period (5weeks), dense cell staining is largely restricted to large pyramidal cells of deep layer III and layer V, there is faint cell body staining throughout all cortical layers, neuropil staining is markedly increased and uniform in layers III to VI. This dramatic change in laminar and cellular labeling is independent of visual input, since immunostaining is similar in 5-week DR cats. By 10weeks, the mature laminar and cellular staining pattern is established and the major subsequent change is a further reduction in the density of cellular staining in all cortical layers. Neuropil staining is pronounced and uniform across cortical layers. These developmental changes are altered by DR. Quantification by cell counts indicated that age and DR interact such that differences in cellular expression are opposite in direction between 5- and 20-week-old cats. This bidirectional regulation of cellular expression is the same in all cortical laminae. The bidirectional regulation of cellular expression matches the effects of age and DR on physiological plasticity during the critical period as assessed by ocular dominance shifts in response to monocular deprivation. Copyright © 2011 Elsevier B.V. All rights reserved.

Convectively-driven cold layer and its influences on moisture in the UTLS

NASA Astrophysics Data System (ADS)

Kim, J.; Randel, W. J.; Birner, T.

2016-12-01

Characteristics of the cold anomaly in the tropical tropopause layer (TTL) that is commonly observed with deep convection are examined using CloudSat and Constellation Observing System for Meteorology, Ionosphere and Climate (COSMIC) GPS radio occultation measurements. Deep convection is sampled based on the cloud top height (>17 km) from CloudSat 2B-CLDCLASS, and then temperature profiles from COSMIC are composited around the deep convection. The composite temperature shows anomalously warm troposphere (up to 14 km) and a significantly cold layer near the tropopause (at 16-18 km) in the regions of deep convection. Generally in the tropics, the cold layer has very large horizontal scale (2,000 - 6,000 km) compared to that of mesoscale convective cluster, and it lasts one or two weeks with minimum temperature anomaly of - 2K. The cold layer shows slight but clear eastward-tilted vertical structure in the deep tropics indicating a large-scale Kelvin wave response. Further analyses on circulation patterns suggest that the anomaly can be explained as a part of Gill-type response in the TTL to deep convective heating in the troposphere. Response of moisture to the cold layer is also examined in the upper troposphere and lower stratosphere using microwave limb sounder (MLS) measurements. The water vapor anomalies show coherent structures with the temperature and circulation anomalies. A clear dry anomaly is found in the cold layer and its outflow region, implying a large-scale dehydration process due to the convectively driven cold layer in the upper TTL.

Gas Classification Using Deep Convolutional Neural Networks.

PubMed

Peng, Pai; Zhao, Xiaojin; Pan, Xiaofang; Ye, Wenbin

2018-01-08

In this work, we propose a novel Deep Convolutional Neural Network (DCNN) tailored for gas classification. Inspired by the great success of DCNN in the field of computer vision, we designed a DCNN with up to 38 layers. In general, the proposed gas neural network, named GasNet, consists of: six convolutional blocks, each block consist of six layers; a pooling layer; and a fully-connected layer. Together, these various layers make up a powerful deep model for gas classification. Experimental results show that the proposed DCNN method is an effective technique for classifying electronic nose data. We also demonstrate that the DCNN method can provide higher classification accuracy than comparable Support Vector Machine (SVM) methods and Multiple Layer Perceptron (MLP).

Gas Classification Using Deep Convolutional Neural Networks

PubMed Central

Peng, Pai; Zhao, Xiaojin; Pan, Xiaofang; Ye, Wenbin

2018-01-01

In this work, we propose a novel Deep Convolutional Neural Network (DCNN) tailored for gas classification. Inspired by the great success of DCNN in the field of computer vision, we designed a DCNN with up to 38 layers. In general, the proposed gas neural network, named GasNet, consists of: six convolutional blocks, each block consist of six layers; a pooling layer; and a fully-connected layer. Together, these various layers make up a powerful deep model for gas classification. Experimental results show that the proposed DCNN method is an effective technique for classifying electronic nose data. We also demonstrate that the DCNN method can provide higher classification accuracy than comparable Support Vector Machine (SVM) methods and Multiple Layer Perceptron (MLP). PMID:29316723

Sensitivity of complex cells in cat striate cortex to relative motion.

PubMed

Hammond, P; Smith, A T

1984-06-03

Sensitivity of 95 complex cells to relative motion between oriented bars and textured backgrounds was investigated monocularly in the striate cortex of lightly anesthetized, paralyzed cats. Cells were classified conventionally. Those in deep layers were either direction-selective, or strongly preferred one direction of motion, and responded well to background texture motion alone: backgrounds potentiated the response to the bar in the cell's preferred direction when moved in phase, or in the opposite direction when moved in antiphase; other combinations depressed the level of response compared with that for the bar alone. The majority of direction-selective or strongly direction-biased cells in superficial layers behaved similarly. The most interesting superficial-layer cells were bidirectional or weakly direction-biased, and recorded closer to the cortical surface than the direction-selective neurons. A majority showed preference for relative motion, some for antiphase, others for in-phase motion, regardless of the absolute direction of motion across the receptive field, which could not be accounted for on the basis of separate responses to bars and backgrounds alone. Three of the superficial-layer direction-selective cells also showed preference for antiphase relative motion. In a few complex cells from superficial laminae, backgrounds were either without influence on responses to oriented stimuli, or purely suppressive. Visual backgrounds against which objects are perceived are usually neither featureless nor motionless: the results suggest that most complex cells in striate cortex are sensitive to the context in which objects are seen and susceptible to relationships between objects and their backgrounds in relative motion.

The Harderian gland, its secretory duct and porphyrin content in the mongolian gerbil (Meriones unguiculatus).

PubMed Central

Johnston, H S; McGadey, J; Thompson, G G; Moore, M R; Payne, A P

1983-01-01

The Harderian gland, its secretory duct and porphyrin content were examined in the mongolian gerbil (Meriones unguiculatus). The gland consisted of tubules lined by a single layer of epithelial cells and a myoepithelial network. The tubule cells were often binucleate and possessed lipid vacuoles in the apical half of the cell, a corona of granular endoplasmic reticulum surrounding the nucleus, and cytoplasmic 'slashes'. The latter are probably derived from dense membranous couplets and may be precursors of the lipid vacuoles. Holocrine and merocrine secretion was observed. Interstitial cells included plasma cells, mast cells and (predominantly) melanocytes which render the gland black. The gland was surrounded by a collagen capsule and an outer layer of highly attenuated (possibly endothelioid) cells. Within the gland, the secretory duct was lined by a single layer of normal tubule cells. Outside the gland, the duct enlarged to form an ampulla, from which clefts led off to deep crypts. The ampulla and clefts were lined by cells with small dense apical granules and stubby microvilli; some possessed lipid vacuoles. The crypts were lined by serous cells with active Golgi regions. At the duct opening, ampullary cells became squamous and goblet cells occurred. Geometric crystalloid deposits (with a layered structure of 7.6 nm periodicity) occurred at cleft-crypt junctions. Islets of extra-glandular ductal tissue were occasionally found within the gland. Porphyrins were detectable both by chemical assay and fluorescence microscopy. There was a trend for female glands to have a higher content than males. Solid intraluminal accretions of porphyrin and/or lipid were present. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 Fig. 10 Fig. 12 Fig. 13 Fig. 14 Fig. 15 Fig. 16 PMID:6654750

Vertical wind shear characteristics that promote supercell-to-MCS transitions

NASA Astrophysics Data System (ADS)

Peters, J. M.

2017-12-01

What causes supercells to transition into MCSs in some situations, but not others? To explore this question, I first examined observed environmental characteristics of supercell events when MCSs formed, and compared them to the analogous environmental characteristics of supercell events when MCSs did not form. During events when MCS growth occurred, 0-1 km (low-level) vertical wind shear was stronger and 0-10 km (deep-layer) vertical wind shear was weaker than the wind shear during events when MCS growth did not occur. Next, I used idealized simulations of supercell thunderstorms to understand the connections between low-level and deep-layer shear and MCS growth. Compared to simulations with strong deep-layer shear, the simulations with weak deep-layer shear had rain in the storm's forward-flank downdraft (FFD) that fell closer to the updraft, fell through storm-moistened air and evaporated less, and produced a more intense FFD. Compared to simulations with weak low-level shear, the simulations with stronger low-level shear showed enhanced northward low-level hydrometeor transport into the FFD. Environments with strong low-level shear and weak deep-layer shear therefore conspired to produce a storm with a more intense FFD cold pool, when compared to environments with weak low-level shear and/or strong deep-layer shear. This strong FFD periodically disrupted the supercells' mesocyclones, and favorably interacted with westerly wind shear to produce widespread linear convection initiation, which drove MCS growth. These results suggest that increasing low-level wind shear after dark - while commonly assumed to enhance tornado potential - may in fact drive MCS growth and reduce tornado potential, unless it is combined with sufficiently strong deep layer shear.

Hydroxyurea Treatment and Development of the Rat Cerebellum: Effects on the Neurogenetic Profiles and Settled Patterns of Purkinje Cells and Deep Cerebellar Nuclei Neurons.

PubMed

Martí, Joaquín; Santa-Cruz, M C; Serra, Roger; Hervás, José P

2016-11-01

The current paper analyzes the development of the male and female rat cerebellum exposed to hydroxyurea (HU) (300 or 600 mg/kg) as embryo and collected at postnatal day 90. Our study reveals that the administration of this drug compromises neither the cytoarchitecture of the cerebellar cortex nor deep nuclei (DCN). However, in comparison with the saline group, we observed that several cerebellar parameters were lower in the HU injected groups. These parameters included area of the cerebellum, cerebellar cortex length, molecular layer area, Purkinje cell number, granule cell counts, internal granular layer, white matter and cerebellar nuclei areas, and number of deep cerebellar nuclei neurons. These features were larger in the rats injected with saline, smaller in those exposed to 300 mg/kg of HU and smallest in the group receiving 600 mg/kg of this agent. No sex differences in the effect of the HU were observed. In addition, we infer the neurogenetic timetables and the neurogenetic gradients of PCs and DCN neurons in rats exposed to either saline or HU as embryos. For this purpose, 5-bromo-2'-deoxyuridine was injected into pregnant rats previously administered with saline or HU. This thymidine analog was administered following a progressively delayed cumulative labeling method. The data presented here show that systematic differences exist in the pattern of neurogenesis and in the spatial location of cerebellar neurons between rats injected with saline or HU. No sex differences in the effect of the HU were observed. These findings have implications for the administration of this compound to women in gestation as the effects of HU on the development of the cerebellum might persist throughout their offsprings' life.

DeepSynergy: predicting anti-cancer drug synergy with Deep Learning

PubMed Central

Preuer, Kristina; Lewis, Richard P I; Hochreiter, Sepp; Bender, Andreas; Bulusu, Krishna C; Klambauer, Günter

2018-01-01

Abstract Motivation While drug combination therapies are a well-established concept in cancer treatment, identifying novel synergistic combinations is challenging due to the size of combinatorial space. However, computational approaches have emerged as a time- and cost-efficient way to prioritize combinations to test, based on recently available large-scale combination screening data. Recently, Deep Learning has had an impact in many research areas by achieving new state-of-the-art model performance. However, Deep Learning has not yet been applied to drug synergy prediction, which is the approach we present here, termed DeepSynergy. DeepSynergy uses chemical and genomic information as input information, a normalization strategy to account for input data heterogeneity, and conical layers to model drug synergies. Results DeepSynergy was compared to other machine learning methods such as Gradient Boosting Machines, Random Forests, Support Vector Machines and Elastic Nets on the largest publicly available synergy dataset with respect to mean squared error. DeepSynergy significantly outperformed the other methods with an improvement of 7.2% over the second best method at the prediction of novel drug combinations within the space of explored drugs and cell lines. At this task, the mean Pearson correlation coefficient between the measured and the predicted values of DeepSynergy was 0.73. Applying DeepSynergy for classification of these novel drug combinations resulted in a high predictive performance of an AUC of 0.90. Furthermore, we found that all compared methods exhibit low predictive performance when extrapolating to unexplored drugs or cell lines, which we suggest is due to limitations in the size and diversity of the dataset. We envision that DeepSynergy could be a valuable tool for selecting novel synergistic drug combinations. Availability and implementation DeepSynergy is available via www.bioinf.jku.at/software/DeepSynergy. Contact klambauer@bioinf.jku.at Supplementary information Supplementary data are available at Bioinformatics online. PMID:29253077

Fabrication of two-layer poly(dimethyl siloxane) devices for hydrodynamic cell trapping and exocytosis measurement with integrated indium tin oxide microelectrodes arrays

PubMed Central

Gao, Changlu; Sun, Xiuhua; Gillis, Kevin D.

2016-01-01

The design, fabrication and test of a microfluidic cell trapping device to measure single cell exocytosis were reported. Research on the patterning of double layer template based on repetitive standard photolithography of AZ photoresist was investigated. The replicated poly(dimethyl siloxane) devices with 2.5 μm deep channels were proved to be efficient for stopping cells. Quantal exocytosis measurement can be achieved by targeting single or small clumps of chromaffin cells on top of the 10 μm ×10 μm indium tin oxide microelectrodes arrays with the developed microdevice. And about 72% of the trapping sites can be occupied by cells with hydrodynamic trapping method and the recorded amperometric signals are comparable to the results with traditional carbon fiber microelectrodes. The method of manufacturing the microdevices is simple, low-cost and easy to perform. The manufactured device offers a platform for the high throughput detection of quantal catecholamine exocytosis from chromaffin cells with sufficient sensitivity and broad application. PMID:23329291

Neural responses of rat cortical layers due to infrared neural modulation and photoablation of thalamocortical brain slices

NASA Astrophysics Data System (ADS)

Jenkins, J. Logan; Kao, Chris C.; Cayce, Jonathan M.; Mahadevan-Jansen, Anita; Jansen, E. Duco

2017-02-01

Infrared neural modulation (INM) is a label-free method for eliciting neural activity with high spatial selectivity in mammalian models. While there has been an emphasis on INM research towards applications in the peripheral nervous system and the central nervous system (CNS), the biophysical mechanisms by which INM occurs remains largely unresolved. In the rat CNS, INM has been shown to elicit and inhibit neural activity, evoke calcium signals that are dependent on glutamate transients and astrocytes, and modulate inhibitory GABA currents. So far, in vivo experiments have been restricted to layers I and II of the rat cortex which consists mainly of astrocytes, inhibitory neurons, and dendrites from deeper excitatory neurons owing to strong absorption of light in these layers. Deeper cortical layers (III-VI) have vastly different cell type composition, consisting predominantly of excitatory neurons which can be targeted for therapies such as deep brain stimulation. The neural responses to infrared light of deeper cortical cells have not been well defined. Acute thalamocortical brain slices will allow us to analyze the effects of INS on various components of the cortex, including different cortical layers and cell populations. In this study, we present the use of photoablation with an erbium:YAG laser to reduce the thickness of the dead cell zone near the cutting surface of brain slices. This technique will allow for more optical energy to reach living cells, which should contribute the successful transduction of pulsed infrared light to neural activity. In the future, INM-induced neural responses will lead to a finer characterization of the parameter space for the neuromodulation of different cortical cell types and may contribute to understanding the cell populations that are important for allowing optical stimulation of neurons in the CNS.

A case of epidermal cyst with pilomatrical differentiation.

PubMed

Ikoma, Norihiro; Iwashita, Kenichi; Umezawa, Yoshinori; Matsuyama, Takashi; Ohta, Yukinori; Ozawa, Akira; Umemura, Shinobu; Ueyama, Yoshito; Yamazaki, Hitoshi

2004-09-01

A 20-year-old Japanese woman with an epidermal cyst on the back is described. Physical examination revealed a deep blue and round shaped cystic lesion measuring 10 min in diameter. A comedo-like keratotic plug also could be seen at the center. Histologically, the inner surface of the cyst was clearly separated of two types of the cells. The one was layers of epidermal keratinocytes and the other looked like a basal layer of epidermis, which immunohistochemically stained by S-100, HMB-45, cytokeratin (CK19) and Fontana-Masson staining. We diagnosed this case as epidermal cyst with pilomatrical differentiation.

Modification of electron states in CdTe absorber due to a buffer layer in CdTe/CdS solar cells

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

Fedorenko, Y. G., E-mail: y.fedorenko@liverpool.ac.uk; Major, J. D.; Pressman, A.

2015-10-28

By application of the ac admittance spectroscopy method, the defect state energy distributions were determined in CdTe incorporated in thin film solar cell structures concluded on ZnO, ZnSe, and ZnS buffer layers. Together with the Mott-Schottky analysis, the results revealed a strong modification of the defect density of states and the concentration of the uncompensated acceptors as influenced by the choice of the buffer layer. In the solar cells formed on ZnSe and ZnS, the Fermi level and the energy position of the dominant deep trap levels were observed to shift closer to the midgap of CdTe, suggesting the mid-gapmore » states may act as recombination centers and impact the open-circuit voltage and the fill factor of the solar cells. For the deeper states, the broadening parameter was observed to increase, indicating fluctuations of the charge on a microscopic scale. Such changes can be attributed to the grain-boundary strain and the modification of the charge trapped at the grain-boundary interface states in polycrystalline CdTe.« less

Fine structure of the retinal pigment epithelium of the great horned owl (Bubo virginianus).

PubMed

Braekevelt, C R; Thorlakson, I J

1993-01-01

The fine structure of the retinal epithelium (RPE), choriocapillaries and Bruch's membrane (complexus basalis) has been studied by light and electron microscopy in the great horned owl (Bubo virginianus). The RPE consists of a single layer of cuboidal cells joined laterally in the mid to basal region by a series of tight junctions forming part of the blood-ocular barrier. Basally (sclerally) the epithelial cells show numerous deep infoldings while apically (vitreally) a wealth of microvillar processes interdigitate with the photoreceptor cells. Internally the RPE cells display a large vesicular nucleus, plentiful smooth endoplasmic reticulum (SER) and polysomes with only small scattered profiles of rough endoplasmic reticulum (RER). Numerous pleomorphic mitochondria are basally located. In the light-adapted state the melanosomes are located almost exclusively within the apical processes indicating retinomotor movements. Myeloid bodies are numerous and often show ribosomes on their outer surface. Bruch's membrane is typical of avian species in that it is pentalaminate and the lamina densa is displaced towards the choriocapillaris. The choriocapillaris itself is but minimally fenestrated facing Bruch's membrane. Most fenestrations present show a single layered diaphragm while others display a double-layered diaphragm.

Beyond Retinal Layers: A Deep Voting Model for Automated Geographic Atrophy Segmentation in SD-OCT Images

PubMed Central

Ji, Zexuan; Chen, Qiang; Niu, Sijie; Leng, Theodore; Rubin, Daniel L.

2018-01-01

Purpose To automatically and accurately segment geographic atrophy (GA) in spectral-domain optical coherence tomography (SD-OCT) images by constructing a voting system with deep neural networks without the use of retinal layer segmentation. Methods An automatic GA segmentation method for SD-OCT images based on the deep network was constructed. The structure of the deep network was composed of five layers, including one input layer, three hidden layers, and one output layer. During the training phase, the labeled A-scans with 1024 features were directly fed into the network as the input layer to obtain the deep representations. Then a soft-max classifier was trained to determine the label of each individual pixel. Finally, a voting decision strategy was used to refine the segmentation results among 10 trained models. Results Two image data sets with GA were used to evaluate the model. For the first dataset, our algorithm obtained a mean overlap ratio (OR) 86.94% ± 8.75%, absolute area difference (AAD) 11.49% ± 11.50%, and correlation coefficients (CC) 0.9857; for the second dataset, the mean OR, AAD, and CC of the proposed method were 81.66% ± 10.93%, 8.30% ± 9.09%, and 0.9952, respectively. The proposed algorithm was capable of improving over 5% and 10% segmentation accuracy, respectively, when compared with several state-of-the-art algorithms on two data sets. Conclusions Without retinal layer segmentation, the proposed algorithm could produce higher segmentation accuracy and was more stable when compared with state-of-the-art methods that relied on retinal layer segmentation results. Our model may provide reliable GA segmentations from SD-OCT images and be useful in the clinical diagnosis of advanced nonexudative AMD. Translational Relevance Based on the deep neural networks, this study presents an accurate GA segmentation method for SD-OCT images without using any retinal layer segmentation results, and may contribute to improved understanding of advanced nonexudative AMD. PMID:29302382

Beyond Retinal Layers: A Deep Voting Model for Automated Geographic Atrophy Segmentation in SD-OCT Images.

PubMed

Ji, Zexuan; Chen, Qiang; Niu, Sijie; Leng, Theodore; Rubin, Daniel L

2018-01-01

To automatically and accurately segment geographic atrophy (GA) in spectral-domain optical coherence tomography (SD-OCT) images by constructing a voting system with deep neural networks without the use of retinal layer segmentation. An automatic GA segmentation method for SD-OCT images based on the deep network was constructed. The structure of the deep network was composed of five layers, including one input layer, three hidden layers, and one output layer. During the training phase, the labeled A-scans with 1024 features were directly fed into the network as the input layer to obtain the deep representations. Then a soft-max classifier was trained to determine the label of each individual pixel. Finally, a voting decision strategy was used to refine the segmentation results among 10 trained models. Two image data sets with GA were used to evaluate the model. For the first dataset, our algorithm obtained a mean overlap ratio (OR) 86.94% ± 8.75%, absolute area difference (AAD) 11.49% ± 11.50%, and correlation coefficients (CC) 0.9857; for the second dataset, the mean OR, AAD, and CC of the proposed method were 81.66% ± 10.93%, 8.30% ± 9.09%, and 0.9952, respectively. The proposed algorithm was capable of improving over 5% and 10% segmentation accuracy, respectively, when compared with several state-of-the-art algorithms on two data sets. Without retinal layer segmentation, the proposed algorithm could produce higher segmentation accuracy and was more stable when compared with state-of-the-art methods that relied on retinal layer segmentation results. Our model may provide reliable GA segmentations from SD-OCT images and be useful in the clinical diagnosis of advanced nonexudative AMD. Based on the deep neural networks, this study presents an accurate GA segmentation method for SD-OCT images without using any retinal layer segmentation results, and may contribute to improved understanding of advanced nonexudative AMD.

The S-layer Protein DR_2577 Binds Deinoxanthin and under Desiccation Conditions Protects against UV-Radiation in Deinococcus radiodurans

PubMed Central

Farci, Domenica; Slavov, Chavdar; Tramontano, Enzo; Piano, Dario

2016-01-01

Deinococcus radiodurans has the puzzling ability to withstand over a broad range of extreme conditions including high doses of ultraviolet radiation and deep desiccation. This bacterium is surrounded by a surface layer (S-layer) built of a regular repetition of several proteins, assembled to form a paracrystalline structure. Here we report that the deletion of a main constituent of this S-layer, the gene DR_2577, causes a decrease in the UVC resistance, especially in desiccated cells. Moreover, we show that the DR_2577 protein binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium. A further spectroscopical characterization of the deinoxanthin-DR_2577 complex revealed features which could suggest a protective role of DR_2577. We propose that, especially under desiccation, the S-layer shields the bacterium from incident ultraviolet light and could behave as a first lane of defense against UV radiation. PMID:26909071

The S-layer Protein DR_2577 Binds Deinoxanthin and under Desiccation Conditions Protects against UV-Radiation in Deinococcus radiodurans.

PubMed

Farci, Domenica; Slavov, Chavdar; Tramontano, Enzo; Piano, Dario

2016-01-01

Deinococcus radiodurans has the puzzling ability to withstand over a broad range of extreme conditions including high doses of ultraviolet radiation and deep desiccation. This bacterium is surrounded by a surface layer (S-layer) built of a regular repetition of several proteins, assembled to form a paracrystalline structure. Here we report that the deletion of a main constituent of this S-layer, the gene DR_2577, causes a decrease in the UVC resistance, especially in desiccated cells. Moreover, we show that the DR_2577 protein binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium. A further spectroscopical characterization of the deinoxanthin-DR_2577 complex revealed features which could suggest a protective role of DR_2577. We propose that, especially under desiccation, the S-layer shields the bacterium from incident ultraviolet light and could behave as a first lane of defense against UV radiation.

Investigation of solar cells fabricated on low-cost silicon sheet materials using 1 MeV electron irradiation

NASA Technical Reports Server (NTRS)

Kachare, A. H.; Hyland, S. L.; Garlick, G. F. J.

1981-01-01

The use of high energy electron irradiation is investigated as a controlled means to study in more detail the junction depletion layer processes of solar cells made on various low-cost silicon sheet materials. Results show that solar cells made on Czochralski grown silicon exhibit enhancement of spectral response in the shorter wavelength region when irradiated with high energy electrons. The base region damage can be reduced by subsequent annealing at 450 C which restores the degraded longer wavelength response, although the shorter wavelength enhancement persists. The second diode component of the cell dark forward bias current is also reduced by electron irradiation, while thermal annealing at 450 C without electron irradiation can also produce these same effects. Electron irradiation produces small changes in the shorter wavelength spectral responses and junction improvements in solar cells made on WEB, EFG, and HEM silicon. It is concluded that these beneficial effects on cell characteristics are due to the reduction of oxygen associated deep level recombination centers in the N(+) diffused layer and in the junction.

A water-processable organic electron-selective layer for solution-processed inverted organic solar cells

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

Chen, Dongcheng; Zhou, Hu; Cai, Ping

2014-02-03

A triazine- and pyridinium-containing water-soluble material of 1,1′,1″-(4,4′,4″-(1,3,5-triazine-2,4,6-triyl)tris(benzene-4,1-diyl)) tris(methylene)tripyridinium bromide (TzPyBr) was developed as an organic electron-selective layer in solution-processed inverted organic solar cells due to its strong anti-erosion capacity against non-polar organic solvents commonly used for the active layer. Ohmic-like contact with the adjacent active materials like fullerene derivatives is speculated to be formed, as confirmed by the work-function measurements with scanning Kelvin probe and ultraviolet photoelectron spectroscopy techniques. Besides, considering the deep highest occupied molecular orbital energy level of TzPyBr, excellent hole-blocking property of the electron-selective layer is also anticipated. The inverted organic photovoltaic devices based on themore » TzPyBr/ITO (indium tin oxide) bilayer cathode exhibit dramatically enhanced performance compared to the control devices with bare ITO as the cathode and even higher efficiency than the conventional type devices with ITO and Al as the electrodes.« less

Echinococcus granulosus equinus: an ultrastructural study of murine tissue response to hydatid cysts.

PubMed

Richards, K S; Arme, C; Bridges, J F

1983-06-01

Peritoneal hydatids of Echinococcus granulosus equinus of 9 months standing in BALB/c mice occurred as free cysts or cysts within cyst masses. Both showed wide variation in size and in host tissue response, and all had a well-developed laminated layer separating the host tissue response from the germinal layer. In the smallest cyst-mass cysts the host tissue response was present as remnants of the initial cellular attack involving eosinophils. Slightly larger cyst-mass cysts possessed a primary macrophage invasion which phagocytosed the remnants of the initial attack and also, though to little effect, the laminated layer material. In the largest cyst-mass cysts a second macrophage invasion, of monocyte origin, had commenced and transformation stages of these cells to macrophages were observed. No fibroblasts surrounded individual cyst-mass cysts but they were present around the cyst mass, encapsulating it and possibly preventing further host cell invasion. Thus, the host tissue response around individual cyst-mass cysts remained 'preserved' at an early stage such as existed at the time of encapsulation. Small free cysts showed a primary macrophage invasion and transformation stages of cells of a secondary infiltration of peritoneal origin. Peripheral to the macrophages were fibroblasts demonstrating limited fibrinogenesis, and each cyst was surrounded by a layer of mesothelial cells. Large free cysts, also delimited by a mesothelial layer, possessed peripheral connective tissue, a deep fibrous layer and a monolayer of very compressed macrophages lying adjacent to the laminated layer. It is emphasized that an understanding of the host tissue response in cysts of different sizes and from different locations is an essential pre-requisite for the design of experimental studies.

Anatomical verification and designation of the superficial layer of the temporalis muscle.

PubMed

Lee, Ju-Young; Kim, Jeong-Nam; Kim, Soon-Heum; Choi, Hyun-Gon; Hu, Kyung-Seok; Kim, Hee-Jin; Song, Wu-Chul; Koh, Ki-Seok

2012-03-01

The temporalis muscle, which is one of the masticatory muscles, enables elevation and retraction of the mandible. Direct injury to the temporalis muscle, facial nerve, or temporal fat pad during cranial-base surgery can cause temporal hollowing. The temporalis muscle is currently described in almost all atlases and textbooks as comprising a single layer. In this study, a superficial layer of the temporalis muscle is described, clarifying the anatomy of this muscle. Twenty heads of adult cadavers were dissected. The gross anatomy of the temporalis muscle was examined after removing the skin, subcutaneous tissue, superficial temporal fascia, and deep temporal fascia. The superficial layer of the temporalis muscle was clearly distinguishable from the deep layer. The superficial layer originated from the same region as the deep layer, and the muscle fibers of the two layers were intermingled in the superior part of the muscle. The deep layer of the temporalis muscle, which is referred to in textbooks and atlases simply as the temporalis muscle, was exposed after removing the superficial layer. The existence of this superficial layer was confirmed herein both histologically and by magnetic resonance imaging. Henceforth, the superficial layer of the temporalis muscle must be included in descriptions of the temporalis muscle in anatomy textbooks and atlases. The findings of this study are important not only from the perspective of simply acquiring correct anatomical knowledge, but also from the surgical perspective in preventing temporal hollowing during related surgical procedures. Copyright © 2011 Wiley-Liss, Inc.

Convection and the seeding of the North Atlantic bloom

NASA Astrophysics Data System (ADS)

D'Asaro, Eric A.

Observations of vertical velocities in deep wintertime mixed layers using neutrally buoyant floats show that the convectively driven vertical velocities, roughly 1000 m per day, greatly exceed the sinking velocities of phytoplankton, 10 m or less per day. These velocities mix plankton effectively and uniformly across the convective layer and are therefore capable of returning those that have sunk to depth back into the euphotic zone. This mechanism cycles cells through the surface layer during the winter and provides a seed population for the spring bloom. A simple model of this mechanism applied to immortal phytoplankton in the subpolar Labrador Sea predicts that the seed population in early spring will be a few percent of the fall concentration if the plankton sink more slowly than the mean rate at which the surface well-mixed layer grows over the winter. Plankton that sink faster than this will mostly sink into the abyss with only a minute fraction remaining by spring. The shallower mixed layers of mid-latitudes are predicted to be much less effective at maintaining a seed population over the winter, limiting the ability of rapidly sinking cells to survive the winter.

Effects of processing history on the evolution of surface damage layer and dislocation substructure in large grain niobium cavities

DOE PAGES

Kang, D.; Bieler, T. R.; Compton, C.

2015-12-16

Large grain niobium (Nb) is being investigated for fabricating superconducting radiofrequency cavities as an alternative to the traditional approach using fine grain polycrystalline Nb sheets. Past studies have identified a surface damage layer on fine grain cavities due to deep drawing and demonstrated the necessity for chemical etching on the surface. However, the origin of and depth of the damage layer are not well understood, and similar exploration on large grain cavities is lacking. In this work, electron backscatter diffraction (EBSD) was used to examine the cross sections at the equator and iris of a half cell deep drawn frommore » a large grain Nb ingot slice. The results indicate that the damage (identified by a high density of geometrically necessary dislocations) depends on crystal orientations, is different at the equator and iris, and is present through the full thickness of a half cell in some places. After electron backscatter diffraction, the specimens were heat treated at 800 °C or 1000 °C for two hours, and the same areas were reexamined. A more dramatic decrease in dislocation content was observed at the iris than the equator, where some regions exhibited no change. The specimens were then etched and examined again, to determine if the subsurface region behaved differently than the surface. As a result, little change in the dislocation substructure was observed, suggesting that the large grain microstructure is retained with a normal furnace anneal.« less

Cellular uptake and ex vivo urothelial penetration by oligodeoxynucleotides for optimizing treatment of transitional cell carcinoma.

PubMed

Bolenz, Christian; Trojan, Lutz; Gabriel, Ute; Honeck, Patrick; Wendt-Nordahl, Gunnar; Schaaf, Axel; Alken, Peter; Michel, Maurice Stephan

2008-10-01

To evaluate cellular uptake and urothelial penetration of oligodeoxynucleotides (ODNs) in transitional cell carcinoma (TCC) cell lines and in a porcine ex vivo model, respectively. A panel of human TCC cell lines (RT 112, HT 1197 and UM-UC3) were exposed tofluorescein-labeled ODNs. Transfection rates were assessed byfluorescence microscopy and fluorescence-activated cell sorting (FACS). Intravesical treatment with ODNs was performed in a porcine ex vivo model. Urothelial penetration was evaluated using fluorescence microscopy of cryosections. Treatment with ODNs provided transfection rates of at least 96.8% of TCC cells, irrespective of use of a transfection agent. Effective urothelial penetration by ODNs was detected when compared with controls (p = 0.0325). The addition of a liposomal transfection agent significantly increased the penetration depth, allowing affection of deep urothelial cell layers (p = 0.0082). High transfection rates of ODNs can be achieved in TCC cells. Urothelial penetration of ODNs was observed down to the deepest cell layers when a transfection agent is added, suggesting a high potential for complementing the chemoresection effects on residual tumor areas during intravesical therapy of non-muscle-invasive TCC.

Deep Visual Attention Prediction

NASA Astrophysics Data System (ADS)

Wang, Wenguan; Shen, Jianbing

2018-05-01

In this work, we aim to predict human eye fixation with view-free scenes based on an end-to-end deep learning architecture. Although Convolutional Neural Networks (CNNs) have made substantial improvement on human attention prediction, it is still needed to improve CNN based attention models by efficiently leveraging multi-scale features. Our visual attention network is proposed to capture hierarchical saliency information from deep, coarse layers with global saliency information to shallow, fine layers with local saliency response. Our model is based on a skip-layer network structure, which predicts human attention from multiple convolutional layers with various reception fields. Final saliency prediction is achieved via the cooperation of those global and local predictions. Our model is learned in a deep supervision manner, where supervision is directly fed into multi-level layers, instead of previous approaches of providing supervision only at the output layer and propagating this supervision back to earlier layers. Our model thus incorporates multi-level saliency predictions within a single network, which significantly decreases the redundancy of previous approaches of learning multiple network streams with different input scales. Extensive experimental analysis on various challenging benchmark datasets demonstrate our method yields state-of-the-art performance with competitive inference time.

Prediction of Bispectral Index during Target-controlled Infusion of Propofol and Remifentanil: A Deep Learning Approach.

PubMed

Lee, Hyung-Chul; Ryu, Ho-Geol; Chung, Eun-Jin; Jung, Chul-Woo

2018-03-01

The discrepancy between predicted effect-site concentration and measured bispectral index is problematic during intravenous anesthesia with target-controlled infusion of propofol and remifentanil. We hypothesized that bispectral index during total intravenous anesthesia would be more accurately predicted by a deep learning approach. Long short-term memory and the feed-forward neural network were sequenced to simulate the pharmacokinetic and pharmacodynamic parts of an empirical model, respectively, to predict intraoperative bispectral index during combined use of propofol and remifentanil. Inputs of long short-term memory were infusion histories of propofol and remifentanil, which were retrieved from target-controlled infusion pumps for 1,800 s at 10-s intervals. Inputs of the feed-forward network were the outputs of long short-term memory and demographic data such as age, sex, weight, and height. The final output of the feed-forward network was the bispectral index. The performance of bispectral index prediction was compared between the deep learning model and previously reported response surface model. The model hyperparameters comprised 8 memory cells in the long short-term memory layer and 16 nodes in the hidden layer of the feed-forward network. The model training and testing were performed with separate data sets of 131 and 100 cases. The concordance correlation coefficient (95% CI) were 0.561 (0.560 to 0.562) in the deep learning model, which was significantly larger than that in the response surface model (0.265 [0.263 to 0.266], P < 0.001). The deep learning model-predicted bispectral index during target-controlled infusion of propofol and remifentanil more accurately compared to the traditional model. The deep learning approach in anesthetic pharmacology seems promising because of its excellent performance and extensibility.

Effects of Plantar Vibration on Bone and Deep Fascia in a Rat Hindlimb Unloading Model of Disuse

PubMed Central

Huang, Yunfei; Fan, Yubo; Salanova, Michele; Yang, Xiao; Sun, Lianwen; Blottner, Dieter

2018-01-01

The deep fascia of the vertebrate body comprises a biomechanically unique connective cell and tissue layer with integrative functions to support global and regional strain, tension, and even muscle force during motion and performance control. However, limited information is available on deep fascia in relation to bone in disuse. We used rat hindlimb unloading as a model of disuse (21 days of hindlimb unloading) to study biomechanical property as well as cell and tissue changes to deep fascia and bone unloading. Rats were randomly divided into three groups (n = 8, each): hindlimb unloading (HU), HU + vibration (HUV), and cage-control (CON). The HUV group received local vibration applied to the plantar of both hind paws. Micro-computed tomography analyzed decreased bone mineral density (BMD) of vertebra, tibia, and femur in HU vs. CON. Biomechanical parameters (elastic modulus, max stress, yield stress) of spinal and crural fascia in HU were always increased vs. CON. Vibration in HUV only counteracted HU-induced tibia bone loss and crural fascia mechanical changes but failed to show comparable changes in the vertebra and spinal fascia on lumbar back. Tissue and cell morphometry (size and cell nuclear density), immunomarker intensity levels of anti-collagen-I and III, probed on fascia cryosections well correlated with biomechanical changes suggesting crural fascia a prime target for plantar vibration mechano-stimulation in the HU rat. We conclude that the regular biomechanical characteristics as well as tissue and cell properties in crural fascia and quality of tibia bone (BMD) were preserved by local plantar vibration in disuse suggesting common mechanisms in fascia and bone adaptation to local mechanovibration stimulation following hind limb unloading in the HUV rat. PMID:29875702

Effects of Plantar Vibration on Bone and Deep Fascia in a Rat Hindlimb Unloading Model of Disuse.

PubMed

Huang, Yunfei; Fan, Yubo; Salanova, Michele; Yang, Xiao; Sun, Lianwen; Blottner, Dieter

2018-01-01

The deep fascia of the vertebrate body comprises a biomechanically unique connective cell and tissue layer with integrative functions to support global and regional strain, tension, and even muscle force during motion and performance control. However, limited information is available on deep fascia in relation to bone in disuse. We used rat hindlimb unloading as a model of disuse (21 days of hindlimb unloading) to study biomechanical property as well as cell and tissue changes to deep fascia and bone unloading. Rats were randomly divided into three groups ( n = 8, each): hindlimb unloading (HU), HU + vibration (HUV), and cage-control (CON). The HUV group received local vibration applied to the plantar of both hind paws. Micro-computed tomography analyzed decreased bone mineral density (BMD) of vertebra, tibia, and femur in HU vs. CON. Biomechanical parameters (elastic modulus, max stress, yield stress) of spinal and crural fascia in HU were always increased vs. CON. Vibration in HUV only counteracted HU-induced tibia bone loss and crural fascia mechanical changes but failed to show comparable changes in the vertebra and spinal fascia on lumbar back. Tissue and cell morphometry (size and cell nuclear density), immunomarker intensity levels of anti-collagen-I and III, probed on fascia cryosections well correlated with biomechanical changes suggesting crural fascia a prime target for plantar vibration mechano-stimulation in the HU rat. We conclude that the regular biomechanical characteristics as well as tissue and cell properties in crural fascia and quality of tibia bone (BMD) were preserved by local plantar vibration in disuse suggesting common mechanisms in fascia and bone adaptation to local mechanovibration stimulation following hind limb unloading in the HUV rat.

Deep learning

NASA Astrophysics Data System (ADS)

Lecun, Yann; Bengio, Yoshua; Hinton, Geoffrey

2015-05-01

Deep learning allows computational models that are composed of multiple processing layers to learn representations of data with multiple levels of abstraction. These methods have dramatically improved the state-of-the-art in speech recognition, visual object recognition, object detection and many other domains such as drug discovery and genomics. Deep learning discovers intricate structure in large data sets by using the backpropagation algorithm to indicate how a machine should change its internal parameters that are used to compute the representation in each layer from the representation in the previous layer. Deep convolutional nets have brought about breakthroughs in processing images, video, speech and audio, whereas recurrent nets have shone light on sequential data such as text and speech.

Deep learning.

PubMed

LeCun, Yann; Bengio, Yoshua; Hinton, Geoffrey

2015-05-28

Deep learning allows computational models that are composed of multiple processing layers to learn representations of data with multiple levels of abstraction. These methods have dramatically improved the state-of-the-art in speech recognition, visual object recognition, object detection and many other domains such as drug discovery and genomics. Deep learning discovers intricate structure in large data sets by using the backpropagation algorithm to indicate how a machine should change its internal parameters that are used to compute the representation in each layer from the representation in the previous layer. Deep convolutional nets have brought about breakthroughs in processing images, video, speech and audio, whereas recurrent nets have shone light on sequential data such as text and speech.

Axon topography of layer 6 spiny cells to orientation map in the primary visual cortex of the cat (area 18).

PubMed

Karube, Fuyuki; Sári, Katalin; Kisvárday, Zoltán F

2017-04-01

To uncover the functional topography of layer 6 neurons, optical imaging was combined with three-dimensional neuronal reconstruction. Apical dendrite morphology of 23 neurons revealed three distinct types. Type Aa possessed a short apical dendrite with many oblique branches, Type Ab was characterized by a short and less branched apical dendrite, whereas Type B had a long apical dendrite with tufts in layer 2. Each type had a similar number of boutons, yet their spatial distribution differed from each other in both radial and horizontal extent. Boutons of Type Aa and Ab were almost restricted to the column of the parent soma with a laminar preference to layer 4 and 5/6, respectively. Only Type B contributed to long horizontal connections (up to 1.5 mm) mostly in deep layers. For all types, bouton distribution on orientation map showed an almost equal occurrence at iso- (52.6 ± 18.8 %) and non-iso-orientation (oblique, 27.7 ± 14.9 % and cross-orientation 19.7 ± 10.9 %) sites. Spatial convergence of axons of nearby layer 6 spiny neurons depended on soma separation of the parent cells, but only weakly on orientation preference, contrary to orientation dependence of converging axons of layer 4 spiny cells. The results show that layer 6 connections have only a weak dependence on orientation preference compared with those of layers 2/3 (Buzás et al., J Comp Neurol 499:861-881, 2006) and 4 (Karube and Kisvárday, Cereb Cortex 21:1443-1458, 2011).

Comparison of four lasers (λ = 650, 808, 980, and 1075 nm) for noninvasive creation of deep subsurface lesions in tissue

NASA Astrophysics Data System (ADS)

Chang, Chun-Hung; Wilson, Christopher R.; Fried, Nathaniel M.

2015-07-01

Lasers have been used in combination with applied cooling methods to preserve superficial skin layers (100's μm's) during cosmetic surgery. Preservation of a thicker tissue surface layer (millimeters) may also allow development of other noninvasive laser procedures. We are exploring noninvasive therapeutic laser applications in urology (e.g. laser vasectomy and laser treatment of female stress urinary incontinence), which require surface tissue preservation on the millimeter scale. In this preliminary study, four lasers were compared for noninvasive creation of deep subsurface thermal lesions. Laser energy from three diode lasers (650, 808, and 980 nm) and a Ytterbium fiber laser (1075 nm) was delivered through a custom built, side-firing, laser probe with integrated cooling. An alcohol-based solution at -5 °C was circulated through a flow cell, cooling a sapphire window, which in turn cooled the tissue surface. The probe was placed in contact with porcine liver tissue, ex vivo, kept hydrated in saline and maintained at ~ 35 °C. Incident laser power was 4.2 W, spot diameter was 5.3 mm, and treatment time was 60 s. The optimal laser wavelength tested for creation of deep subsurface thermal lesions during contact cooling of tissues was 1075 nm, which preserved a surface layer of ~ 2 mm. The Ytterbium fiber laser provides a compact, low maintenance, and high power alternative laser source to the Neodymium:YAG laser for noninvasive thermal therapy.

Field-Assisted Splitting of Pure Water Based on Deep-Sub-Debye-Length Nanogap Electrochemical Cells.

PubMed

Wang, Yifei; Narayanan, S R; Wu, Wei

2017-08-22

Owing to the low conductivity of pure water, using an electrolyte is common for achieving efficient water electrolysis. In this paper, we have fundamentally broken through this common sense by using deep-sub-Debye-length nanogap electrochemical cells to achieve efficient electrolysis of pure water (without any added electrolyte) at room temperature. A field-assisted effect resulted from overlapped electrical double layers can greatly enhance water molecules ionization and mass transport, leading to electron-transfer limited reactions. We have named this process "virtual breakdown mechanism" (which is completely different from traditional mechanisms) that couples the two half-reactions together, greatly reducing the energy losses arising from ion transport. This fundamental discovery has been theoretically discussed in this paper and experimentally demonstrated in a group of electrochemical cells with nanogaps between two electrodes down to 37 nm. On the basis of our nanogap electrochemical cells, the electrolysis current density from pure water can be significantly larger than that from 1 mol/L sodium hydroxide solution, indicating the much better performance of pure water splitting as a potential for on-demand clean hydrogen production.

The organization of plasticity in the cerebellar cortex: from synapses to control.

PubMed

D'Angelo, Egidio

2014-01-01

The cerebellum is thought to play a critical role in procedural learning, but the relationship between this function and the underlying cellular and synaptic mechanisms remains largely speculative. At present, at least nine forms of long-term synaptic and nonsynaptic plasticity (some of which are bidirectional) have been reported in the cerebellar cortex and deep cerebellar nuclei. These include long-term potentiation (LTP) and long-term depression at the mossy fiber-granule cell synapse, at the synapses formed by parallel fibers, climbing fibers, and molecular layer interneurons on Purkinje cells, and at the synapses formed by mossy fibers and Purkinje cells on deep cerebellar nuclear cells, as well as LTP of intrinsic excitability in granule cells, Purkinje cells, and deep cerebellar nuclear cells. It is suggested that the complex properties of cerebellar learning would emerge from the distribution of plasticity in the network and from its dynamic remodeling during the different phases of learning. Intrinsic and extrinsic factors may hold the key to explain how the different forms of plasticity cooperate to select specific transmission channels and to regulate the signal-to-noise ratio through the cerebellar cortex. These factors include regulation of neuronal excitation by local inhibitory networks, engagement of specific molecular mechanisms by spike bursts and theta-frequency oscillations, and gating by external neuromodulators. Therefore, a new and more complex view of cerebellar plasticity is emerging with respect to that predicted by the original "Motor Learning Theory," opening issues that will require experimental and computational testing. © 2014 Elsevier B.V. All rights reserved.

Shear Strengthening of RC Deep Beam Using Externally Bonded GFRP Fabrics

NASA Astrophysics Data System (ADS)

Kumari, A.; Patel, S. S.; Nayak, A. N.

2018-06-01

This work presents the experimental investigation of RC deep beams wrapped with externally bonded Glass Fibre Reinforced Polymer (GFRP) fabrics in order to study the Load versus deflection behavior, cracking pattern, failure modes and ultimate shear strength. A total number of five deep beams have been casted, which is designed with conventional steel reinforcement as per IS: 456 (Indian standard plain and reinforced concrete—code for practice, Bureau of Indian Standards, New Delhi, 2000). The spans to depth ratio for all RC deep beams have been kept less than 2 as per the above specification. Out of five RC deep beams, one without retrofitting serves as a reference beam and the rest four have been wrapped with GFRP fabrics in multiple layers and tested with two point loading condition. The first cracking load, ultimate load and the shear contribution of GFRP to the deep beams have been observed. A critical discussion is made with respect to the enhancement of the strength, behaviour and performance of retrofitted deep beams in comparison to the deep beam without GFRP in order to explore the potential use of GFRP for strengthening the RC deep beams. Test results have demonstrated that the deep beams retrofitted with GFRP shows a slower development of the diagonal cracks and improves shear carrying capacity of the RC deep beam. A comparative study of the experimental results with the theoretical ones predicted by various researchers available in the literatures has also been presented. It is observed that the ultimate load of the beams retrofitted with GFRP fabrics increases with increase of number of GFRP layers up to a specific number of layers, i.e. 3 layers, beyond which it decreases.

Shear Strengthening of RC Deep Beam Using Externally Bonded GFRP Fabrics

NASA Astrophysics Data System (ADS)

Kumari, A.; Patel, S. S.; Nayak, A. N.

2018-02-01

This work presents the experimental investigation of RC deep beams wrapped with externally bonded Glass Fibre Reinforced Polymer (GFRP) fabrics in order to study the Load versus deflection behavior, cracking pattern, failure modes and ultimate shear strength. A total number of five deep beams have been casted, which is designed with conventional steel reinforcement as per IS: 456 (Indian standard plain and reinforced concrete—code for practice, Bureau of Indian Standards, New Delhi, 2000). The spans to depth ratio for all RC deep beams have been kept less than 2 as per the above specification. Out of five RC deep beams, one without retrofitting serves as a reference beam and the rest four have been wrapped with GFRP fabrics in multiple layers and tested with two point loading condition. The first cracking load, ultimate load and the shear contribution of GFRP to the deep beams have been observed. A critical discussion is made with respect to the enhancement of the strength, behaviour and performance of retrofitted deep beams in comparison to the deep beam without GFRP in order to explore the potential use of GFRP for strengthening the RC deep beams. Test results have demonstrated that the deep beams retrofitted with GFRP shows a slower development of the diagonal cracks and improves shear carrying capacity of the RC deep beam. A comparative study of the experimental results with the theoretical ones predicted by various researchers available in the literatures has also been presented. It is observed that the ultimate load of the beams retrofitted with GFRP fabrics increases with increase of number of GFRP layers up to a specific number of layers, i.e. 3 layers, beyond which it decreases.

Effects of Link Annotations on Search Performance in Layered and Unlayered Hierarchically Organized Information Spaces.

ERIC Educational Resources Information Center

Fraser, Landon; Locatis, Craig

2001-01-01

Investigated the effects of link annotations on high school user search performance in Web hypertext environments having deep (layered) and shallow link structures. Results confirmed previous research that shallow link structures are better than deep (layered) link structures, and also showed that annotations had virtually no effect on search…

DEEP BIOSPHERE. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor.

PubMed

Inagaki, F; Hinrichs, K-U; Kubo, Y; Bowles, M W; Heuer, V B; Hong, W-L; Hoshino, T; Ijiri, A; Imachi, H; Ito, M; Kaneko, M; Lever, M A; Lin, Y-S; Methé, B A; Morita, S; Morono, Y; Tanikawa, W; Bihan, M; Bowden, S A; Elvert, M; Glombitza, C; Gross, D; Harrington, G J; Hori, T; Li, K; Limmer, D; Liu, C-H; Murayama, M; Ohkouchi, N; Ono, S; Park, Y-S; Phillips, S C; Prieto-Mollar, X; Purkey, M; Riedinger, N; Sanada, Y; Sauvage, J; Snyder, G; Susilawati, R; Takano, Y; Tasumi, E; Terada, T; Tomaru, H; Trembath-Reichert, E; Wang, D T; Yamada, Y

2015-07-24

Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~10(4) cells cm(-3). Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed. Copyright © 2015, American Association for the Advancement of Science.

Peering Deep into Jupiter Atmosphere

NASA Image and Video Library

2013-03-14

The dark hot spot in this false-color image from NASA Cassini spacecraft is a window deep into Jupiter atmosphere. All around it are layers of higher clouds, with colors indicating which layer of the atmosphere the clouds are in.

A New Approach to Develop Computer-aided Diagnosis Scheme of Breast Mass Classification Using Deep Learning Technology

PubMed Central

Qiu, Yuchen; Yan, Shiju; Gundreddy, Rohith Reddy; Wang, Yunzhi; Cheng, Samuel; Liu, Hong; Zheng, Bin

2017-01-01

PURPOSE To develop and test a deep learning based computer-aided diagnosis (CAD) scheme of mammograms for classifying between malignant and benign masses. METHODS An image dataset involving 560 regions of interest (ROIs) extracted from digital mammograms was used. After down-sampling each ROI from 512×512 to 64×64 pixel size, we applied an 8 layer deep learning network that involves 3 pairs of convolution-max-pooling layers for automatic feature extraction and a multiple layer perceptron (MLP) classifier for feature categorization to process ROIs. The 3 pairs of convolution layers contain 20, 10, and 5 feature maps, respectively. Each convolution layer is connected with a max-pooling layer to improve the feature robustness. The output of the sixth layer is fully connected with a MLP classifier, which is composed of one hidden layer and one logistic regression layer. The network then generates a classification score to predict the likelihood of ROI depicting a malignant mass. A four-fold cross validation method was applied to train and test this deep learning network. RESULTS The results revealed that this CAD scheme yields an area under the receiver operation characteristic curve (AUC) of 0.696±0.044, 0.802±0.037, 0.836±0.036, and 0.822±0.035 for fold 1 to 4 testing datasets, respectively. The overall AUC of the entire dataset is 0.790±0.019. CONCLUSIONS This study demonstrates the feasibility of applying a deep learning based CAD scheme to classify between malignant and benign breast masses without a lesion segmentation, image feature computation and selection process. PMID:28436410

A new approach to develop computer-aided diagnosis scheme of breast mass classification using deep learning technology.

PubMed

Qiu, Yuchen; Yan, Shiju; Gundreddy, Rohith Reddy; Wang, Yunzhi; Cheng, Samuel; Liu, Hong; Zheng, Bin

2017-01-01

To develop and test a deep learning based computer-aided diagnosis (CAD) scheme of mammograms for classifying between malignant and benign masses. An image dataset involving 560 regions of interest (ROIs) extracted from digital mammograms was used. After down-sampling each ROI from 512×512 to 64×64 pixel size, we applied an 8 layer deep learning network that involves 3 pairs of convolution-max-pooling layers for automatic feature extraction and a multiple layer perceptron (MLP) classifier for feature categorization to process ROIs. The 3 pairs of convolution layers contain 20, 10, and 5 feature maps, respectively. Each convolution layer is connected with a max-pooling layer to improve the feature robustness. The output of the sixth layer is fully connected with a MLP classifier, which is composed of one hidden layer and one logistic regression layer. The network then generates a classification score to predict the likelihood of ROI depicting a malignant mass. A four-fold cross validation method was applied to train and test this deep learning network. The results revealed that this CAD scheme yields an area under the receiver operation characteristic curve (AUC) of 0.696±0.044, 0.802±0.037, 0.836±0.036, and 0.822±0.035 for fold 1 to 4 testing datasets, respectively. The overall AUC of the entire dataset is 0.790±0.019. This study demonstrates the feasibility of applying a deep learning based CAD scheme to classify between malignant and benign breast masses without a lesion segmentation, image feature computation and selection process.

Atomic Layer-Deposited Molybdenum Oxide/Carbon Nanotube Hybrid Electrodes: The Influence of Crystal Structure on Lithium-Ion Capacitor Performance.

PubMed

Fleischmann, Simon; Zeiger, Marco; Quade, Antje; Kruth, Angela; Presser, Volker

2018-06-06

Merging of supercapacitors and batteries promises the creation of electrochemical energy storage devices that combine high specific energy, power, and cycling stability. For that purpose, lithium-ion capacitors (LICs) that store energy by lithiation reactions at the negative electrode and double-layer formation at the positive electrode are currently investigated. In this study, we explore the suitability of molybdenum oxide as a negative electrode material in LICs for the first time. Molybdenum oxide-carbon nanotube hybrid materials were synthesized via atomic layer deposition, and different crystal structures and morphologies were obtained by post-deposition annealing. These model materials are first structurally characterized and electrochemically evaluated in half-cells. Benchmarking in LIC full-cells revealed the influences of crystal structure, half-cell capacity, and rate handling on the actual device level performance metrics. The energy efficiency, specific energy, and power are mainly influenced by the overpotential and kinetics of the lithiation reaction during charging. Optimized LIC cells show a maximum specific energy of about 70 W·h·kg -1 and a high specific power of 4 kW·kg -1 at 34 W·h·kg -1 . The longevity of the LIC cells is drastically increased without significantly reducing the energy by preventing a deep cell discharge, hindering the negative electrode from crossing its anodic potential limit.

Predator-Prey Dynamics in the Mesopelagic: Odontocete Foraging Ecology and Anti-predator Behavior of Prey

NASA Astrophysics Data System (ADS)

Benoit-Bird, K. J.

2016-02-01

We explored the behavior of Risso's dolphins foraging in scattering layers off California using an integrated approach comprising echosounders deployed in a deep-diving autonomous underwater vehicle, ship based acoustics, visual observations, direct prey sampling, and animal-borne tags on deep-diving predators. We identified three distinct prey layers: a persistent layer around 425 m, a vertically migrating layer around 300 m, and a layer intermittently present near 50 m, all of which were used by individual tagged animals. Active acoustic measurements demonstrated that Risso's dolphins dove to discrete prey layers throughout the day and night with only slightly higher detection rates at night. Dolphins were detected in all three layers during the day with over half of detections in the middle layer, 20% of detections in the deepest layer, and 10% falling outside the main layers. Dolphins were found less frequently in areas where the shallow, intermittent layer was absent, suggesting that this layer, while containing the smallest prey and the lowest densities of squid, was an important component of their foraging strategy. The deepest layer was targeted equally both during the day and at night. Using acoustic data collected from the AUV, we found layers were made up of distinct, small patches of animals of similar size and taxonomy adjacent to contrasting patches. Squid made up over 70% of the patches in which dolphins were found and more than 95% of those in deep water. Squid targeted by dolphins in deep water were also relatively large, indicating significant benefit from these relatively rare, physically demanding dives. Within these patches, prey formed tighter aggregations when Risso's dolphins were present. Careful integration of a suite of traditional and novel tools is providing insight into the ecology and dynamics of predator and prey in the mesopelagic.

Crop response to deep tillage - a meta-analysis

NASA Astrophysics Data System (ADS)

Schneider, Florian; Don, Axel; Hennings, Inga; Schmittmann, Oliver; Seidel, Sabine J.

2017-04-01

Subsoil, i.e. the soil layer below the topsoil, stores tremendous stocks of nutrients and can keep water even under drought conditions. Deep tillage may be a method to enhance the plant-availability of subsoil resources. However, in field trials, deep tillage effects on crop yields were inconsistent. Therefore, we conducted a meta-analysis of crop yield response to subsoiling, deep ploughing and deep mixing of soil profiles. Our search resulted in 1530 yield comparisons following deep and conventional control tillage on 67 experimental cropping sites. The vast majority of the data derived from temperate latitudes, from trials conducted in the USA (679 observations) and Germany (630 observations). On average, crop yield response to deep tillage was slightly positive (6% increase). However, individual deep tillage effects were highly scattered including about 40% yield depressions after deep tillage. Deep tillage on soils with root restrictive layers increased crop yields about 20%, while soils containing >70% silt increased the risk of yield depressions following deep tillage. Generally, deep tillage effects increased with drought intensity indicating deep tillage as climate adaptation measure at certain sites. Our results suggest that deep tillage can facilitate the plant-availability of subsoil nutrients, which increases crop yields if (i) nutrients in the topsoil are growth limiting, and (ii) deep tillage does not come at the cost of impairing topsoil fertility. On sites with root restrictive soil layers, deep tillage can be an effective measure to mitigate drought stress and improve the resilience of crops. However, deep tillage should only be performed on soils with a stable structure, i.e. <70% silt content. We will discuss the contribution of deep tillage options to enhance the sustainability of agricultural production by facilitating the uptake of nutrients and water from the subsoil.

Parvalbumin interneurons and calretinin fibers arising from the thalamic nucleus reuniens degenerate in the subiculum after kainic acid-induced seizures

PubMed Central

Drexel, M.; Preidt, A.P.; Kirchmair, E.; Sperk, G.

2011-01-01

The subiculum is the major output area of the hippocampus. It is closely interconnected with the entorhinal cortex and other parahippocampal areas. In animal models of temporal lobe epilepsy (TLE) and in TLE patients it exerts increased network excitability and may crucially contribute to the propagation of limbic seizures. Using immunohistochemistry and in situ-hybridization we now investigated neuropathological changes affecting parvalbumin and calretinin containing neurons in the subiculum and other parahippocampal areas after kainic acid-induced status epilepticus. We observed prominent losses in parvalbumin containing interneurons in the subiculum and entorhinal cortex, and in the principal cell layers of the pre- and parasubiculum. Degeneration of parvalbumin-positive neurons was associated with significant precipitation of parvalbumin-immunoreactive debris 24 h after kainic acid injection. In the subiculum the superficial portion of the pyramidal cell layer was more severely affected than its deep part. In the entorhinal cortex, the deep layers were more severely affected than the superficial ones. The decrease in number of parvalbumin-positive neurons in the subiculum and entorhinal cortex correlated with the number of spontaneous seizures subsequently experienced by the rats. The loss of parvalbumin neurons thus may contribute to the development of spontaneous seizures. On the other hand, surviving parvalbumin neurons revealed markedly increased expression of parvalbumin mRNA notably in the pyramidal cell layer of the subiculum and in all layers of the entorhinal cortex. This indicates increased activity of these neurons aiming to compensate for the partial loss of this functionally important neuron population. Furthermore, calretinin-positive fibers terminating in the molecular layer of the subiculum, in sector CA1 of the hippocampus proper and in the entorhinal cortex degenerated together with their presumed perikarya in the thalamic nucleus reuniens. In addition, a significant loss of calretinin containing interneurons was observed in the subiculum. Notably, the loss in parvalbumin positive neurons in the subiculum equaled that in human TLE. It may result in marked impairment of feed-forward inhibition of the temporo-ammonic pathway and may significantly contribute to epileptogenesis. Similarly, the loss of calretinin-positive fiber tracts originating from the nucleus reuniens thalami significantly contributes to the rearrangement of neuronal circuitries in the subiculum and entorhinal cortex during epileptogenesis. PMID:21616128

Deep Learning Method for Denial of Service Attack Detection Based on Restricted Boltzmann Machine.

PubMed

Imamverdiyev, Yadigar; Abdullayeva, Fargana

2018-06-01

In this article, the application of the deep learning method based on Gaussian-Bernoulli type restricted Boltzmann machine (RBM) to the detection of denial of service (DoS) attacks is considered. To increase the DoS attack detection accuracy, seven additional layers are added between the visible and the hidden layers of the RBM. Accurate results in DoS attack detection are obtained by optimization of the hyperparameters of the proposed deep RBM model. The form of the RBM that allows application of the continuous data is used. In this type of RBM, the probability distribution of the visible layer is replaced by a Gaussian distribution. Comparative analysis of the accuracy of the proposed method with Bernoulli-Bernoulli RBM, Gaussian-Bernoulli RBM, deep belief network type deep learning methods on DoS attack detection is provided. Detection accuracy of the methods is verified on the NSL-KDD data set. Higher accuracy from the proposed multilayer deep Gaussian-Bernoulli type RBM is obtained.

Deep RNNs for video denoising

NASA Astrophysics Data System (ADS)

Chen, Xinyuan; Song, Li; Yang, Xiaokang

2016-09-01

Video denoising can be described as the problem of mapping from a specific length of noisy frames to clean one. We propose a deep architecture based on Recurrent Neural Network (RNN) for video denoising. The model learns a patch-based end-to-end mapping between the clean and noisy video sequences. It takes the corrupted video sequences as the input and outputs the clean one. Our deep network, which we refer to as deep Recurrent Neural Networks (deep RNNs or DRNNs), stacks RNN layers where each layer receives the hidden state of the previous layer as input. Experiment shows (i) the recurrent architecture through temporal domain extracts motion information and does favor to video denoising, and (ii) deep architecture have large enough capacity for expressing mapping relation between corrupted videos as input and clean videos as output, furthermore, (iii) the model has generality to learned different mappings from videos corrupted by different types of noise (e.g., Poisson-Gaussian noise). By training on large video databases, we are able to compete with some existing video denoising methods.

Warming trend in the western Mediterranean deep water

NASA Astrophysics Data System (ADS)

Bethoux, J. P.; Gentili, B.; Raunet, J.; Tailliez, D.

1990-10-01

THE western Mediterranean Sea comprises three water masses: a surface layer (from 0 to ~150 m depth), an intermediate layer (~150-400 m) issuing from the eastern basin, and a deep water mass at depths below 400 m. The deep water is homogeneous and has maintained a more or less constant temperature and salinity from the start of the century until recently1. Here we report measurements from the Medatlante cruises of December 1988 and August 1989, which show the deep layer to be 0.12 °C warmer and ~0.03 p.s.u. more saline than in 1959. Taking these data together with those from earlier cruises, we find a trend of continuously increasing temperatures over the past three decades. These deep-water records reflect the averaged evolution of climate conditions at the surface during the winter, when the deep water is formed. Consideration of the heat budget and water flux in the Mediterranean2,3 leads to the possibility that the deep-water temperature trend may be the result of greenhouse-gas-induced local warming.

Congo red agar, a differential medium for Aeromonas salmonicida, detects the presence of the cell surface protein array involved in virulence.

PubMed Central

Ishiguro, E E; Ainsworth, T; Trust, T J; Kay, W W

1985-01-01

Strains of the fish pathogen Aeromonas salmonicida which possess the cell surface protein array known as the A-layer (A+) involved in virulence formed deep red colonies on tryptic soy agar containing 30 micrograms of Congo red per ml. These were readily distinguished from colorless or light orange colonies of avirulent mutants lacking A-layer (A-). The utility of Congo red agar for quantifying A+ and A- cells in the routine assessment of culture virulence was demonstrated. Intact A+ cells adsorbed Congo red, whereas A- mutants did not bind Congo red unless first permeabilized with EDTA. The dye-binding component of A+ cells was shown to be the 50,000-Mr A-protein component of the surface array. Purified A-protein avidly bound Congo red at a dye-to-protein molar ratio of about 30 by a nonspecific hydrophobic mechanism enhanced by high salt concentrations. Neither A+ nor A- cells adsorbed to Congo red-Sepharose columns at low salt concentrations. On the other hand, A+ (but not A-) cells were avidly bound at high salt concentrations. Images PMID:3934141

Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma.

PubMed

Young, Jonathan D; Cai, Chunhui; Lu, Xinghua

2017-10-03

One approach to improving the personalized treatment of cancer is to understand the cellular signaling transduction pathways that cause cancer at the level of the individual patient. In this study, we used unsupervised deep learning to learn the hierarchical structure within cancer gene expression data. Deep learning is a group of machine learning algorithms that use multiple layers of hidden units to capture hierarchically related, alternative representations of the input data. We hypothesize that this hierarchical structure learned by deep learning will be related to the cellular signaling system. Robust deep learning model selection identified a network architecture that is biologically plausible. Our model selection results indicated that the 1st hidden layer of our deep learning model should contain about 1300 hidden units to most effectively capture the covariance structure of the input data. This agrees with the estimated number of human transcription factors, which is approximately 1400. This result lends support to our hypothesis that the 1st hidden layer of a deep learning model trained on gene expression data may represent signals related to transcription factor activation. Using the 3rd hidden layer representation of each tumor as learned by our unsupervised deep learning model, we performed consensus clustering on all tumor samples-leading to the discovery of clusters of glioblastoma multiforme with differential survival. One of these clusters contained all of the glioblastoma samples with G-CIMP, a known methylation phenotype driven by the IDH1 mutation and associated with favorable prognosis, suggesting that the hidden units in the 3rd hidden layer representations captured a methylation signal without explicitly using methylation data as input. We also found differentially expressed genes and well-known mutations (NF1, IDH1, EGFR) that were uniquely correlated with each of these clusters. Exploring these unique genes and mutations will allow us to further investigate the disease mechanisms underlying each of these clusters. In summary, we show that a deep learning model can be trained to represent biologically and clinically meaningful abstractions of cancer gene expression data. Understanding what additional relationships these hidden layer abstractions have with the cancer cellular signaling system could have a significant impact on the understanding and treatment of cancer.

Three-dimensional assembly of tissue-engineered cartilage constructs results in cartilaginous tissue formation without retainment of zonal characteristics.

PubMed

Schuurman, W; Harimulyo, E B; Gawlitta, D; Woodfield, T B F; Dhert, W J A; van Weeren, P R; Malda, J

2016-04-01

Articular cartilage has limited regenerative capabilities. Chondrocytes from different layers of cartilage have specific properties, and regenerative approaches using zonal chondrocytes may yield better replication of the architecture of native cartilage than when using a single cell population. To obtain high seeding efficiency while still mimicking zonal architecture, cell pellets of expanded deep zone and superficial zone equine chondrocytes were seeded and cultured in two layers on poly(ethylene glycol)-terephthalate-poly(butylene terephthalate) (PEGT-PBT) scaffolds. Scaffolds seeded with cell pellets consisting of a 1:1 mixture of both cell sources served as controls. Parallel to this, pellets of superficial or deep zone chondrocytes, and combinations of the two cell populations, were cultured without the scaffold. Pellet cultures of zonal chondrocytes in scaffolds resulted in a high seeding efficiency and abundant cartilaginous tissue formation, containing collagen type II and glycosaminoglycans (GAGs) in all groups, irrespective of the donor (n = 3), zonal population or stratified scaffold-seeding approach used. However, whereas total GAG production was similar, the constructs retained significantly more GAG compared to pellet cultures, in which a high percentage of the produced GAGs were secreted into the culture medium. Immunohistochemistry for zonal markers did not show any differences between the conditions. We conclude that spatially defined pellet culture in 3D scaffolds is associated with high seeding efficiency and supports cartilaginous tissue formation, but did not result in the maintenance or restoration of the original zonal phenotype. The use of pellet-assembled constructs leads to a better retainment of newly produced GAGs than the use of pellet cultures alone. Copyright © 2013 John Wiley & Sons, Ltd.

Investigation of defect properties in Cu(In,Ga)Se 2 solar cells by deep-level transient spectroscopy

NASA Astrophysics Data System (ADS)

Kerr, L. L.; Li, Sheng S.; Johnston, S. W.; Anderson, T. J.; Crisalle, O. D.; Kim, W. K.; Abushama, J.; Noufi, R. N.

2004-09-01

The performance of the chalcopyrite material Cu(In,Ga)Se 2 (CIGS) used as an absorber layer in thin-film photovoltaic devices is significantly affected by the presence of native defects. The deep-level transient spectroscopy (DLTS) technique is used in this work to characterize the defect properties, yielding relevant information about the defect types, their capture cross-sections, and energy levels and densities in the CIGS cells. Three solar cells developed using different absorber growth technologies were analyzed using DLTS, capacitance-voltage ( C- V), and capacitance-temperature ( C- T) techniques. It was found that CIS cells grown at the University of Florida exhibits a middle-gap defect level that may relate to the cell's low fill factor and open-circuit voltage values observed. A high efficiency ( ηc>18%) CIGS cell produced by the National Renewable Energy Laboratory (NREL) was found to contain three minority-carrier (electron) traps and a 13% CIGS cell produced by the Energy Photovoltaics Inc. (EPV) exhibited one majority (hole) trap. The approach followed using the DLTS technique serves as a paradigm for revealing the presence of significant defect levels in absorber materials, and may be used to support the identification of remedial processing operations.

Deep Retinal Layer Microvasculature Dropout detected by the Optical Coherence Tomography Angiography in Glaucoma

PubMed Central

Suh, Min Hee; Zangwill, Linda M.; Manalastas, Patricia Isabel C.; Belghith, Akram; Yarmohammadi, Adeleh; Medeiros, Felipe A.; Diniz-Filho, Alberto; Saunders, Luke J.; Weinreb, Robert N.

2016-01-01

Purpose To investigate factors associated with dropout of the deep retinal layer microvasculature within the β-zone parapapillary atrophy (βPPA) assessed by optical coherence tomography angiography (OCT-A) in glaucomatous eyes. Design Cross-sectional study. Participants Seventy-one eyes from 71 primary open angle glaucoma (POAG) patients with βPPA enrolled in the Diagnostic Innovations in Glaucoma Study. Methods βPPA deep layer microvasculature dropout was defined as a complete loss of the microvasculature located within deep retinal layer of the βPPA from OCT-A-derived optic nerve head vessel density maps by standardized qualitative assessment. Circumpapillary vessel density (cpVD) within the retinal nerve fiber layer (RNFL) was also calculated using OCT-A. Choroidal thickness and presence of the focal lamina cribrosa (LC) defect were determined using swept-source OCT. Main Outcome Measures Presence of the βPPA deep layer microvasculature dropout. Parameters including age, systolic and diastolic blood pressure, axial length, intraocular pressure, disc hemorrhage, cpVD, visual field (VF) mean deviation (MD), focal LC defect, βPPA area, and choroidal thickness were analyzed. Results βPPA deep layer microvasculature dropout was detected in 37 eyes (52.1%) of eyes with POAG. Eyes with dropouts had a higher prevalence of LC defect (70.3 vs. 32.4%), lower cpVD (52.7 vs. 58.8%), worse VF MD (-9.06 vs. -3.83dB), thinner total choroidal thickness (126.5 vs. 169.1/μm), longer axial length (24.7 vs. 24.0mm), larger βPPA (1.2 vs. 0.76mm2) and lower diastolic blood pressure (74.7 vs. 81.7mmHg) than those without dropouts (P< 0.05, respectively). In the multivariate logistic regression, higher prevalence of focal LC defect (odds ratio [OR], 6.27; P = 0.012), reduced cpVD (OR, 1.27; P = 0.002), worse VF MD (OR, 1.27; P = 0.001), thinner choroidal thickness (OR, 1.02; P = 0.014), and lower diastolic blood pressure (OR, 1.16; P = 0.003) were significantly associated with the dropout. Conclusions Certain systemic and ocular factors such as focal LC defect, more advanced disease status, reduced RNFL vessel density, thinner choroidal thickness, and lower diastolic blood pressure were factors associated with the βPPA deep layer microvasculature dropout in glaucomatous eyes. Longitudinal studies are required to elucidate the temporal relationship between βPPA deep layer dropout and these factors. PMID:27769587

Deep Retinal Layer Microvasculature Dropout Detected by the Optical Coherence Tomography Angiography in Glaucoma.

PubMed

Suh, Min Hee; Zangwill, Linda M; Manalastas, Patricia Isabel C; Belghith, Akram; Yarmohammadi, Adeleh; Medeiros, Felipe A; Diniz-Filho, Alberto; Saunders, Luke J; Weinreb, Robert N

2016-12-01

To investigate factors associated with dropout of the parapapillary deep retinal layer microvasculature assessed by optical coherence tomography angiography (OCTA) in glaucomatous eyes. Cross-sectional study. Seventy-one eyes from 71 primary open-angle glaucoma (POAG) patients with β-zone parapapillary atrophy (βPPA) enrolled in the Diagnostic Innovations in Glaucoma Study. Parapapillary deep-layer microvasculature dropout was defined as a complete loss of the microvasculature located within the deep retinal layer of the βPPA from OCTA-derived optic nerve head vessel density maps by standardized qualitative assessment. Circumpapillary vessel density (cpVD) within the retinal nerve fiber layer (RNFL) also was calculated using OCTA. Choroidal thickness and presence of focal lamina cribrosa (LC) defects were determined using swept-source optical coherence tomography. Presence of parapapillary deep-layer microvasculature dropout. Parameters including age, systolic and diastolic blood pressure, axial length, intraocular pressure, disc hemorrhage, cpVD, visual field (VF) mean deviation (MD), focal LC defects βPPA area, and choroidal thickness were analyzed. Parapapillary deep-layer microvasculature dropout was detected in 37 POAG eyes (52.1%). Eyes with microvasculature dropout had a higher prevalence of LC defects (70.3% vs. 32.4%), lower cpVD (52.7% vs. 58.8%), worse VF MD (-9.06 dB vs. -3.83 dB), thinner total choroidal thickness (126.5 μm vs. 169.1 μm), longer axial length (24.7 mm vs. 24.0 mm), larger βPPA (1.2 mm 2 vs. 0.76 mm 2 ), and lower diastolic blood pressure (74.7 mmHg vs. 81.7 mmHg) than those without dropout (P < 0.05, respectively). In the multivariate logistic regression analysis, higher prevalence of focal LC defects (odds ratio [OR], 6.27; P = 0.012), reduced cpVD (OR, 1.27; P = 0.002), worse VF MD (OR, 1.27; P = 0.001), thinner choroidal thickness (OR, 1.02; P = 0.014), and lower diastolic blood pressure (OR, 1.16; P = 0.003) were associated significantly with the dropout. Systemic and ocular factors including focal LC defects more advanced glaucoma, reduced RNFL vessel density, thinner choroidal thickness, and lower diastolic blood pressure were factors associated with the parapapillary deep-layer microvasculature dropout in glaucomatous eyes. Longitudinal studies are required to elucidate the temporal relationship between parapapillary deep-layer microvasculature dropout and systemic and ocular factors. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Deep sediment resuspension and thick nepheloid layer generation by open-ocean convection

NASA Astrophysics Data System (ADS)

Durrieu de Madron, X.; Ramondenc, S.; Berline, L.; Houpert, L.; Bosse, A.; Martini, S.; Guidi, L.; Conan, P.; Curtil, C.; Delsaut, N.; Kunesch, S.; Ghiglione, J. F.; Marsaleix, P.; Pujo-Pay, M.; Séverin, T.; Testor, P.; Tamburini, C.

2017-03-01

The Gulf of Lions in the northwestern Mediterranean is one of the few sites around the world ocean exhibiting deep open-ocean convection. Based on 6 year long (2009-2015) time series from a mooring in the convection region, shipborne measurements from repeated cruises, from 2012 to 2015, and glider measurements, we report evidence of bottom thick nepheloid layer formation, which is coincident with deep sediment resuspension induced by bottom-reaching convection events. This bottom nepheloid layer, which presents a maximum thickness of more than 2000 m in the center of the convection region, probably results from the action of cyclonic eddies that are formed during the convection period and can persist within their core while they travel through the basin. The residence time of this bottom nepheloid layer appears to be less than a year. In situ measurements of suspended particle size further indicate that the bottom nepheloid layer is primarily composed of aggregates between 100 and 1000 µm in diameter, probably constituted of fine silts. Bottom-reaching open ocean convection, as well as deep dense shelf water cascading that occurred concurrently some years, lead to recurring deep sediments resuspension episodes. They are key mechanisms that control the concentration and characteristics of the suspended particulate matter in the basin, and in turn affect the bathypelagic biological activity.

Quantum state engineering with ultra-short-period (AlN)m/(GaN)n superlattices for narrowband deep-ultraviolet detection.

PubMed

Gao, Na; Lin, Wei; Chen, Xue; Huang, Kai; Li, Shuping; Li, Jinchai; Chen, Hangyang; Yang, Xu; Ji, Li; Yu, Edward T; Kang, Junyong

2014-12-21

Ultra-short-period (AlN)m/(GaN)n superlattices with tunable well and barrier atomic layer numbers were grown by metal-organic vapour phase epitaxy, and employed to demonstrate narrowband deep ultraviolet photodetection. High-resolution transmission electron microscopy and X-ray reciprocal space mapping confirm that superlattices containing well-defined, coherently strained GaN and AlN layers as thin as two atomic layers (∼ 0.5 nm) were grown. Theoretical and experimental results demonstrate that an optical absorption band as narrow as 9 nm (210 meV) at deep-ultraviolet wavelengths can be produced, and is attributable to interband transitions between quantum states along the [0001] direction in ultrathin GaN atomic layers isolated by AlN barriers. The absorption wavelength can be precisely engineered by adjusting the thickness of the GaN atomic layers because of the quantum confinement effect. These results represent a major advance towards the realization of wavelength selectable and narrowband photodetectors in the deep-ultraviolet region without any additional optical filters.

PRISM3 DOT1 Atlantic Basin Reconstruction

USGS Publications Warehouse

Dowsett, Harry; Robinson, Marci; Dwyer, Gary S.; Chandler, Mark; Cronin, Thomas

2006-01-01

PRISM3 DOT1 (Pliocene Research, Interpretation and Synoptic Mapping 3, Deep Ocean Temperature 1) provides a three-dimensional temperature reconstruction for the mid-Pliocene Atlantic basin, the first of several regional data sets that will comprise a global mid-Pliocene reconstruction. DOT1 is an alteration of modern temperature values for the Atlantic Ocean in 4 degree x 5 degree cells in 13 depth layers for December 1 based on Mg/Ca-derived BWT estimates from seventeen DSDP and ODP Sites and SST estimates from the PRISM2 reconstruction (Dowsett et al., 1999). DOT1 reflects a vaguely modern circulation system, assuming similar processes of deep-water formation; however, North Atlantic Deep Water (NADW) production is increased, and Antarctic Bottom Water (AABW) production is decreased. Pliocene NADW was approximately 2 degreesC warmer than modern temperatures, and Pliocene AABW was approximately 0.3 degreesC warmer than modern temperatures.

Vertical Mixing Effects on Phytoplankton Dynamics and Organic Carbon Export in the Western Mediterranean Sea

NASA Astrophysics Data System (ADS)

Kessouri, Faycal; Ulses, Caroline; Estournel, Claude; Marsaleix, Patrick; D'Ortenzio, Fabrizio; Severin, Tatiana; Taillandier, Vincent; Conan, Pascal

2018-03-01

A 3-D high-resolution coupled hydrodynamic-biogeochemical model of the western Mediterranean was used to study phytoplankton dynamics and organic carbon export in three regions with contrasting vertical regimes, ranging from deep convection to a shallow mixed layer. One month after the initial increase in surface chlorophyll (caused by the erosion of the deep chlorophyll maximum), the autumnal bloom was triggered in all three regions by the upward flux of nutrients resulting from mixed layer deepening. In contrast, at the end of winter, the end of turbulent mixing favored the onset of the spring bloom in the deep convection region. Low grazing pressure allowed rapid phytoplankton growth during the bloom. Primary production in the shallow mixed layer region, the Algerian subbasin, was characterized by a long period (4 months) of sustained phytoplankton development, unlike the deep convection region where primary production was inhibited during 2 months in winter. Despite seasonal variations, annual primary production in all three regions is similar. In the deep convection region, total organic carbon export below the photic layer (150 m) and transfer to deep waters (800 m) was 5 and 8 times, respectively, higher than in the Algerian subbasin. Although some of the exported material will be injected back into the surface layer during the next convection event, lateral transport, and strong interannual variability of MLD in this region suggest that a significant amount of exported material is effectively sequestrated.

Social Isolation During the Critical Period Reduces Synaptic and Intrinsic Excitability of a Subtype of Pyramidal Cell in Mouse Prefrontal Cortex.

PubMed

Yamamuro, Kazuhiko; Yoshino, Hiroki; Ogawa, Yoichi; Makinodan, Manabu; Toritsuka, Michihiro; Yamashita, Masayuki; Corfas, Gabriel; Kishimoto, Toshifumi

2018-03-01

Juvenile social experience is crucial for the functional development of forebrain regions, especially the prefrontal cortex (PFC). We previously reported that social isolation for 2 weeks after weaning induces prefrontal cortex dysfunction and hypomyelination. However, the effect of social isolation on physiological properties of PFC neuronal circuit remained unknown. Since hypomyelination due to isolation is prominent in deep-layer of medial PFC (mPFC), we focused on 2 types of Layer-5 pyramidal cells in the mPFC: prominent h-current (PH) cells and nonprominent h-current (non-PH) cells. We found that a 2-week social isolation after weaning leads to a specific deterioration in action potential properties and reduction in excitatory synaptic inputs in PH cells. The effects of social isolation on PH cells, which involve reduction in functional glutamatergic synapses and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid/N-methyl-d-aspartate charge ratio, are specific to the 2 weeks after weaning and to the mPFC. We conclude that juvenile social experience plays crucial roles in the functional development in a subtype of Layer-5 pyramidal cells in the mPFC. Since these neurons project to subcortical structures, a deficit in social experience during the critical period may result in immature neural circuitry between mPFC and subcortical targets. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Observations of a two-layer soil moisture influence on surface energy dynamics and planetary boundary layer characteristics in a semiarid shrubland

NASA Astrophysics Data System (ADS)

Sanchez-Mejia, Zulia Mayari; Papuga, Shirley A.

2014-01-01

We present an observational analysis examining soil moisture control on surface energy dynamics and planetary boundary layer characteristics. Understanding soil moisture control on land-atmosphere interactions will become increasingly important as climate change continues to alter water availability. In this study, we analyzed 4 years of data from the Santa Rita Creosote Ameriflux site. We categorized our data independently in two ways: (1) wet or dry seasons and (2) one of the four cases within a two-layer soil moisture framework for the root zone based on the presence or absence of moisture in shallow (0-20 cm) and deep (20-60 cm) soil layers. Using these categorizations, we quantified the soil moisture control on surface energy dynamics and planetary boundary layer characteristics using both average responses and linear regression. Our results highlight the importance of deep soil moisture in land-atmosphere interactions. The presence of deep soil moisture decreased albedo by about 10%, and significant differences were observed in evaporative fraction even in the absence of shallow moisture. The planetary boundary layer height (PBLh) was largest when the whole soil profile was dry, decreasing by about 1 km when the whole profile was wet. Even when shallow moisture was absent but deep moisture was present the PBLh was significantly lower than when the entire profile was dry. The importance of deep moisture is likely site-specific and modulated through vegetation. Therefore, understanding these relationships also provides important insights into feedbacks between vegetation and the hydrologic cycle and their consequent influence on the climate system.

The remarkable chemical uniformity of Apollo 16 layered deep drill core section 60002

NASA Technical Reports Server (NTRS)

Nava, D. F.; Philpotts, J. A.; Lindstrom, M. M.; Schuhmann, P. J.; Lindstrom, D. J.

1976-01-01

Atomic absorption and colorimetric spectrophotometers were used to determine major- and minor-element abundances in 12 samples from layered section 60002 of the Apollo 16 deep drill core. It is suggested that gardening of a relatively thick local unit produced the layering in this section in such a manner that the proportions of materials of different compositions remained virtually unchanged.

Localization of P-type calcium channels in the central nervous system.

PubMed Central

Hillman, D; Chen, S; Aung, T T; Cherksey, B; Sugimori, M; Llinás, R R

1991-01-01

The distribution of the P-type calcium channel in the mammalian central nervous system has been demonstrated immunohistochemically by using a polyclonal specific antibody. This antibody was generated after P-channel isolation via a fraction from funnel-web spider toxin (FTX) that blocks the voltage-gated P channels in cerebellar Purkinje cells. In the cerebellar cortex, immunolabeling to the antibody appeared throughout the molecular layer, while all the other regions were negative. Intensely labeled patches of reactivity were seen on Purkinje cell dendrites, especially at bifurcations; much weaker reactivity was present in the soma and stem segment. Electron microscopic localization revealed labeled patches of plasma membrane on the soma, main dendrites, spiny branchlets, and spines; portions of the smooth endoplasmic reticulum were also labeled. Strong labeling was present in the periglomerular cells of the olfactory bulb and scattered neurons in the deep layer of the entorhinal and pyriform cortices. Neurons in the brainstem, habenula, nucleus of the trapezoid body and inferior olive and along the floor of the fourth ventricle were also labeled intensely. Medium-intensity reactions were observed in layer II pyramidal cells of the frontal cortex, the CA1 cells of the hippocampus, the lateral nucleus of the substantia nigra, lateral reticular nucleus, and spinal fifth nucleus. Light labeling was seen in the neocortex, striatum, and in some brainstem neurons. Images PMID:1651493

Localization of P-type calcium channels in the central nervous system.

PubMed

Hillman, D; Chen, S; Aung, T T; Cherksey, B; Sugimori, M; Llinás, R R

1991-08-15

The distribution of the P-type calcium channel in the mammalian central nervous system has been demonstrated immunohistochemically by using a polyclonal specific antibody. This antibody was generated after P-channel isolation via a fraction from funnel-web spider toxin (FTX) that blocks the voltage-gated P channels in cerebellar Purkinje cells. In the cerebellar cortex, immunolabeling to the antibody appeared throughout the molecular layer, while all the other regions were negative. Intensely labeled patches of reactivity were seen on Purkinje cell dendrites, especially at bifurcations; much weaker reactivity was present in the soma and stem segment. Electron microscopic localization revealed labeled patches of plasma membrane on the soma, main dendrites, spiny branchlets, and spines; portions of the smooth endoplasmic reticulum were also labeled. Strong labeling was present in the periglomerular cells of the olfactory bulb and scattered neurons in the deep layer of the entorhinal and pyriform cortices. Neurons in the brainstem, habenula, nucleus of the trapezoid body and inferior olive and along the floor of the fourth ventricle were also labeled intensely. Medium-intensity reactions were observed in layer II pyramidal cells of the frontal cortex, the CA1 cells of the hippocampus, the lateral nucleus of the substantia nigra, lateral reticular nucleus, and spinal fifth nucleus. Light labeling was seen in the neocortex, striatum, and in some brainstem neurons.

Convection in a volatile nitrogen-ice-rich layer drives Pluto's geological vigour

NASA Astrophysics Data System (ADS)

McKinnon, William B.; Nimmo, Francis; Wong, Teresa; Schenk, Paul M.; White, Oliver L.; Roberts, J. H.; Moore, J. M.; Spencer, J. R.; Howard, A. D.; Umurhan, O. M.; Stern, S. A.; Weaver, H. A.; Olkin, C. B.; Young, L. A.; Smith, K. E.; Moore, J. M.; McKinnon, W. B.; Spencer, J. R.; Beyer, R.; Buie, M.; Buratti, B.; Cheng, A.; Cruikshank, D.; Dalle Ore, C.; Gladstone, R.; Grundy, W.; Howard, A.; Lauer, T.; Linscott, I.; Nimmo, F.; Olkin, C.; Parker, J.; Porter, S.; Reitsema, H.; Reuter, D.; Roberts, J. H.; Robbins, S.; Schenk, P. M.; Showalter, M.; Singer, K.; Strobel, D.; Summers, M.; Tyler, L.; Weaver, H.; White, O. L.; Umurhan, O. M.; Banks, M.; Barnouin, O.; Bray, V.; Carcich, B.; Chaikin, A.; Chavez, C.; Conrad, C.; Hamilton, D.; Howett, C.; Hofgartner, J.; Kammer, J.; Lisse, C.; Marcotte, A.; Parker, A.; Retherford, K.; Saina, M.; Runyon, K.; Schindhelm, E.; Stansberry, J.; Steffl, A.; Stryk, T.; Throop, H.; Tsang, C.; Verbiscer, A.; Winters, H.; Zangari, A.; New Horizons Geology, Geophysics and Imaging Theme Team

2016-06-01

The vast, deep, volatile-ice-filled basin informally named Sputnik Planum is central to Pluto's vigorous geological activity. Composed of molecular nitrogen, methane, and carbon monoxide ices, but dominated by nitrogen ice, this layer is organized into cells or polygons, typically about 10 to 40 kilometres across, that resemble the surface manifestation of solid-state convection. Here we report, on the basis of available rheological measurements, that solid layers of nitrogen ice with a thickness in excess of about one kilometre should undergo convection for estimated present-day heat-flow conditions on Pluto. More importantly, we show numerically that convective overturn in a several-kilometre-thick layer of solid nitrogen can explain the great lateral width of the cells. The temperature dependence of nitrogen-ice viscosity implies that the ice layer convects in the so-called sluggish lid regime, a unique convective mode not previously definitively observed in the Solar System. Average surface horizontal velocities of a few centimetres a year imply surface transport or renewal times of about 500,000 years, well under the ten-million-year upper-limit crater retention age for Sputnik Planum. Similar convective surface renewal may also occur on other dwarf planets in the Kuiper belt, which may help to explain the high albedos shown by some of these bodies.

Convection in a volatile nitrogen-ice-rich layer drives Pluto's geological vigour.

PubMed

McKinnon, William B; Nimmo, Francis; Wong, Teresa; Schenk, Paul M; White, Oliver L; Roberts, J H; Moore, J M; Spencer, J R; Howard, A D; Umurhan, O M; Stern, S A; Weaver, H A; Olkin, C B; Young, L A; Smith, K E

2016-06-02

The vast, deep, volatile-ice-filled basin informally named Sputnik Planum is central to Pluto's vigorous geological activity. Composed of molecular nitrogen, methane, and carbon monoxide ices, but dominated by nitrogen ice, this layer is organized into cells or polygons, typically about 10 to 40 kilometres across, that resemble the surface manifestation of solid-state convection. Here we report, on the basis of available rheological measurements, that solid layers of nitrogen ice with a thickness in excess of about one kilometre should undergo convection for estimated present-day heat-flow conditions on Pluto. More importantly, we show numerically that convective overturn in a several-kilometre-thick layer of solid nitrogen can explain the great lateral width of the cells. The temperature dependence of nitrogen-ice viscosity implies that the ice layer convects in the so-called sluggish lid regime, a unique convective mode not previously definitively observed in the Solar System. Average surface horizontal velocities of a few centimetres a year imply surface transport or renewal times of about 500,000 years, well under the ten-million-year upper-limit crater retention age for Sputnik Planum. Similar convective surface renewal may also occur on other dwarf planets in the Kuiper belt, which may help to explain the high albedos shown by some of these bodies.

Preparation and photovoltaic properties of perovskite solar cell based on ZnO nanorod arrays

NASA Astrophysics Data System (ADS)

Xu, Yang; Liu, Tian; Li, Zhaosong; Feng, Bingjie; Li, Siqian; Duan, Jinxia; Ye, Cong; Zhang, Jun; Wang, Hao

2016-12-01

A careful control of ZnO nanorod arrays with various densities and thickness were achieved by hydrothermal method. An obvious increase in the ZnO nanorod density is observed as the concentrations of zinc acetate dropped as expected through the surface SEM images. On the other hand, samples with and without TiO2 compact layer were also studied and results had been analyzed to seek for an optimized substrate structure for light absorbing layer and increase the efficiency. What's more, a deep research for the drying temperature for perovskite layer was also conducted. As a result, SEM images discribe a promising surface appearance of perovskite layer which is finely attached onto the nanorod structure. Final power conversion efficiency (PCE) of FTO/ZnO seed layer/ZnO nanorods/perovskite/spiro-OMe-TAD/Au electrode photovoltaic device reached ∼9.15% together with open-circuit voltage of 957 mV, short-circuit current density of 17.8 mA/cm2 and fill factor of 0.537.

The Structure of Microbial Community and Degradation of Diatoms in the Deep Near-Bottom Layer of Lake Baikal

PubMed Central

Zakharova, Yulia R.; Galachyants, Yuri P.; Kurilkina, Maria I.; Likhoshvay, Alexander V.; Petrova, Darya P.; Shishlyannikov, Sergey M.; Ravin, Nikolai V.; Mardanov, Andrey V.; Beletsky, Alexey V.; Likhoshway, Yelena V.

2013-01-01

Insight into the role of bacteria in degradation of diatoms is important for understanding the factors and components of silica turnover in aquatic ecosystems. Using microscopic methods, it has been shown that the degree of diatom preservation and the numbers of diatom-associated bacteria in the surface layer of bottom sediments decrease with depth; in the near-bottom water layer, the majority of bacteria are associated with diatom cells, being located either on the cell surface or within the cell. The structure of microbial community in the near-bottom water layer has been characterized by pyrosequencing of the 16S rRNA gene, which has revealed 149 208 unique sequences. According to the results of metagenomic analysis, the community is dominated by representatives of Proteobacteria (41.9%), Actinobacteria (16%); then follow Acidobacteria (6.9%), Cyanobacteria (5%), Bacteroidetes (4.7%), Firmicutes (2.8%), Nitrospira (1.6%), and Verrucomicrobia (1%); other phylotypes account for less than 1% each. For 18.7% of the sequences, taxonomic identification has been possible only to the Bacteria domain level. Many bacteria identified to the genus level have close relatives occurring in other aquatic ecosystems and soils. The metagenome of the bacterial community from the near-bottom water layer also contains 16S rRNA gene sequences found in previously isolated bacterial strains possessing hydrolytic enzyme activity. These data show that potential degraders of diatoms occur among the vast variety of microorganisms in the near-bottom water of Lake Baikal. PMID:23560063

Characterisation of retention properties of charge-trapping memory cells at low temperatures

NASA Astrophysics Data System (ADS)

Yurchuk, E.; Bollmann, J.; Mikolajick, T.

2009-09-01

The density of states of deep level centers in silicon oxynitride layer of SONOS memory cells are calculated from temperature dependent retention measurement. The dominating charge loss mechanisms are direct trap-to-band tunneling (TB) and thermally stimulated emission (TE). Retention measurements at low temperatures (80 - 300K) will be dominated by TE from more "shallow" traps with energies below 1eV and by TB. Taking into account both independent and rival processes the density of states could be calculated self consisting. The results are in excellent agreement with elsewhere published data.

Design of an elastin-layered dermal regeneration template.

PubMed

Mithieux, Suzanne M; Weiss, Anthony S

2017-04-01

We demonstrate a novel approach for the production of tunable quantities of elastic fibers. We also show that exogenous tropoelastin is rate-limiting for elastin synthesis regardless of the age of the dermal fibroblast donor. Additionally, we provide a strategy to further enhance synthesis by older cells through the application of conditioned media. We show that this approach delivers an elastin layer on one side of the leading dermal repair template for contact with the deep dermis in order to deliver prefabricated elastic fibers to a physiologically appropriate site during subsequent surgery. This system is attractive because it provides for the first time a viable path for sufficient, histologically detectable levels of patient elastin into full-thickness wound sites that have until now lacked this elastic underlayer. The scars of full thickness wounds typically lack elasticity. Elastin is essential for skin elasticity and is enriched in the deep dermis. This paper is significant because it shows that: (1) we can generate elastic fibers in tunable quantities, (2) tropoelastin is the rate-limiting component in elastin synthesis in vitro, (3) we can generate elastin fibers regardless of donor age, (4) we describe a novel approach to further increase the numbers and thickness of elastic fibers for older donors, (5) we improve on Integra Dermal Regeneration Template and generate a new hybrid biomaterial intended to subsequently surgically deliver these elastic fibers, (6) the elastic fiber layer is presented on the side of Integra that is intended for delivery into its physiologically appropriate site i.e. the deep dermis. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Early Postnatal Lesion of the Medial Dorsal Nucleus Leads to Loss of Dendrites and Spines in Adult Prefrontal Cortex

PubMed Central

Marmolejo, Naydu; Paez, Jesse; Levitt, Jonathan B.; Jones, Liesl B.

2013-01-01

Research suggests that the medial dorsal nucleus (MD) of the thalamus influences pyramidal cell development in the prefrontal cortex (PFC) in an activity-dependent manner. The MD is reciprocally connected to the PFC. Many psychiatric disorders, such as schizophrenia, affect the PFC, and one of the most consistent findings in schizophrenia is a decrease in volume and neuronal number in the MD. Therefore, understanding the role the MD plays in the development of the PFC is important and may help in understanding the progression of psychiatric disorders that have their root in development. Focusing on the interplay between the MD and the PFC, this study examined the hypothesis that the MD plays a role in the dendritic development of pyramidal cells in the PFC. Unilateral electrolytic lesions of the MD in Long-Evans rat pups were made on postnatal day 4 (P4), and the animals developed to P60. We then examined dendritic morphology by examining MAP2 immunostaining and by using Golgi techniques to determine basilar dendrite number and spine density. Additionally, we examined pyramidal cell density in cingulate area 1 (Cg1), prelimbic region, and dorsolateral anterior cortex, which receive afferents from the MD. Thalamic lesions caused a mean MD volume decrease of 12.4% which led to a significant decrease in MAP2 staining in both superficial and deep layers in all 3 cortical areas. The lesions also caused a significant decrease in spine density and in the number of primary and secondary basilar dendrites on superficial and deep layer pyramidal neurons in all 3 regions. No significant difference was observed in pyramidal cell density in any of the regions or layers, but a nonsignificant increase in cell density was observed in 2 regions. Our data are thus consistent with the hypothesis that the MD plays a role in the development of the PFC and, therefore, may be a good model to begin to examine neurodevelopmental disorders such as autism and schizophrenia. PMID:23406908

Ionotropic glutamate receptor GluR2/3-immunoreactive neurons in the cat, rabbit, and hamster superficial superior colliculus.

PubMed

Park, Won-Mee; Kim, Min-Jeong; Jeon, Chang-Jin

2004-06-01

Ionotropic glutamate receptor (GluR) subtypes occur in various types of cells in the central nervous system. We studied the distribution of AMPA glutamate receptor subtype GluR2/3 in the superficial layers of cat, rabbit, and hamster superior colliculus (SC) with antibody immunocytochemistry and the effect of enucleation on this distribution. Furthermore, we compared this labeling to that of calbindin D28K and parvalbumin. Anti-GluR2/3-immunoreactive (IR) cells formed a dense band of labeled cells within the lower superficial gray layer (SGL) and upper optic layer (OL) in the cat SC. By contrast, GluR2/3-IR cells formed a dense band within the upper OL in the rabbit and within the OL in the hamster SC. Calbindin D28K-IR cells are located in three layers in the SC: one within the zonal layer (ZL) and the upper SGL in all three animals, a second within the lower OL and upper IGL in the cat, within the IGL in the rabbit and within the OL in the hamster, and a third within the deep gray layer (DGL) in all three animals. Many parvalbumin-IR neurons were found within the lower SGL and upper OL. Thus, the GluR2/3-IR band was sandwiched between the first and second layers of calbindin D28K-IR cells in the cat and rabbit SC while the distribution of GluR2/3-IR cells in the hamster matches the second layer of calbindin D28K-IR cells. The patterned distribution of GluR2/3-IR cells overlapped the tier of parvalbumin-IR neurons in cat, but only partially overlapped in hamster and rabbit. Two-color immunofluorescence revealed that more than half (55.1%) of the GluR2/3-IR cells in the hamster SC expressed calbindin D28K. By contrast, only 9.9% of GluR2/3-IR cells expressed calbindin D28K in the cat. Double-labeled cells were not found in the rabbit SC. Some (4.8%) GluR2/3-IR cells in the cat SC also expressed parvalbumin, while no GluR2/3-IR cells in rabbit and hamster SC expressed parvalbumin. In this dense band of GluR2/3, the majority of labeled cells were small to medium-sized round/oval or stellate cells. Immunoreactivity for the GluR2/3 was clearly reduced in the contralateral SC following unilateral enucleation in the hamster. By contrast, enucleation appeared to have had no effect on the GluR2/3 immunoreactivity in the cat and rabbit SC. The results indicate that neurons in the mammalian SC express GluR2/3 in specific layers, which does not correlate with the expression of calbindin D28K and parvalbumin among the animals.

Reduction in interface defect density in p-BaSi2/n-Si heterojunction solar cells by a modified pretreatment of the Si substrate

NASA Astrophysics Data System (ADS)

Yamashita, Yudai; Yachi, Suguru; Takabe, Ryota; Sato, Takuma; Emha Bayu, Miftahullatif; Toko, Kaoru; Suemasu, Takashi

2018-02-01

We have investigated defects that occurred at the interface of p-BaSi2/n-Si heterojunction solar cells that were fabricated by molecular beam epitaxy. X-ray diffraction measurements indicated that BaSi2 (a-axis-oriented) was subjected to in-plane compressive strain, which relaxed when the thickness of the p-BaSi2 layer exceeded 50 nm. Additionally, transmission electron microscopy revealed defects in the Si layer near steps that were present on the Si(111) substrate. Deep level transient spectroscopy revealed two different electron traps in the n-Si layer that were located at 0.33 eV (E1) and 0.19 eV (E2) below the conduction band edge. The densities of E1 and E2 levels in the region close to the heterointerface were approximately 1014 cm-3. The density of these electron traps decreased below the limits of detection following Si pretreatment to remove the oxide layers from the n-Si substrate, which involved heating the substrate to 800 °C for 30 min under ultrahigh vacuum while depositing a layer of Si (1 nm). The remaining traps in the n-Si layer were hole traps located at 0.65 eV (H1) and 0.38 eV (H2) above the valence band edge. Their densities were as low as 1010 cm-3. Following pretreatment, the current versus voltage characteristics of the p-BaSi2/n-Si solar cells under AM1.5 illumination were reproducible with conversion efficiencies beyond 5% when using a p-BaSi2 layer thickness of 100 nm. The origin of the H2 level is discussed.

Coupling with ocean mixed layer leads to intraseasonal variability in tropical deep convection: Evidence from cloud-resolving simulations

NASA Astrophysics Data System (ADS)

Anber, Usama; Wang, Shuguang; Sobel, Adam

2017-03-01

The effect of coupling a slab ocean mixed layer to atmospheric convection is examined in cloud-resolving model (CRM) simulations in vertically sheared and unsheared environments without Coriolis force, with the large-scale circulation parameterized using the Weak Temperature Gradient (WTG) approximation. Surface fluxes of heat and moisture as well as radiative fluxes are fully interactive, and the vertical profile of domain-averaged horizontal wind is strongly relaxed toward specified profiles with vertical shear that varies from one simulation to the next. Vertical wind shear is found to play a critical role in the simulated behavior. There exists a threshold value of the shear strength above which the coupled system develops regular oscillations between deep convection and dry nonprecipitating states, similar to those found earlier in a much more idealized model which did not consider wind shear. The threshold value of the vertical shear found here varies with the depth of the ocean mixed layer. The time scale of the spontaneously generated oscillations also varies with mixed layer depth, from 10 days with a 1 m deep mixed layer to 50 days with a 10 m deep mixed layer. The results suggest the importance of the interplay between convection organized by vertical wind shear, radiative feedbacks, large-scale dynamics, and ocean mixed layer heat storage in real intraseasonal oscillations.

The effects of interfacial recombination and injection barrier on the electrical characteristics of perovskite solar cells

NASA Astrophysics Data System (ADS)

Shi, Lin Xing; Wang, Zi Shuai; Huang, Zengguang; Sha, Wei E. I.; Wang, Haoran; Zhou, Zhen

2018-02-01

Charge carrier recombination in the perovskite solar cells (PSCs) has a deep influence on the electrical performance, such as open circuit voltage, short circuit current, fill factor and ultimately power conversion efficiency. The impacts of injection barrier, recombination channels, doping properties of carrier transport layers and light intensity on the performance of PSCs are theoretically investigated by drift-diffusion model in this work. The results indicate that due to the injection barrier at the interfaces of perovskite and carrier transport layer, the accumulated carriers modify the electric field distribution throughout the PSCs. Thus, a zero electric field is generated at a specific applied voltage, with greatly increases the interfacial recombination, resulting in a local kink of current density-voltage (J-V) curve. This work provides an effective strategy to improve the efficiency of PSCs by pertinently reducing both the injection barrier and interfacial recombination.

[Effects of snow pack on soil nitrogen transformation enzyme activities in a subalpine Abies faxioniana forest of western Sichuan, China].

PubMed

Xiong, Li; Xu, Zhen-Feng; Wu, Fu-Zhong; Yang, Wan-Qin; Yin, Rui; Li, Zhi-Ping; Gou, Xiao-Lin; Tang, Shi-Shan

2014-05-01

This study characterized the dynamics of the activities of urease, nitrate reductase and nitrite reductase in both soil organic layer and mineral soil layer under three depths of snow pack (deep snowpack, moderate snowpack and shallow snowpack) over the three critical periods (snow formed period, snow stable period, and snow melt period) in the subalpine Abies faxoniana forest of western Sichuan in the winter of 2012 and 2013. Throughout the winter, soil temperature under deep snowpack increased by 46.2% and 26.2%, respectively in comparison with moderate snowpack and shallow snowpack. In general, the three nitrogen-related soil enzyme activities under shallow snowpack were 0.8 to 3.9 times of those under deep snowpack during the winter. In the beginning and thawing periods of seasonal snow pack, shallow snowpack significantly increased the activities of urease, nitrate and nitrite reductase enzyme in both soil organic layer and mineral soil layer. Although the activities of the studied enzymes in soil organic layer and mineral soil layer were observed to be higher than those under deep- and moderate snowpacks in deep winter, no significant difference was found under the three snow packs. Meanwhile, the effects of snowpack on the activities of the measured enzymes were related with season, soil layer and enzyme type. Significant variations of the activities of nitrogen-related enzymes were found in three critical periods over the winter, and the three measured soil enzymes were significantly higher in organic layer than in mineral layer. In addition, the activities of the three measured soil enzymes were closely related with temperature and moisture in soils. In conclusion, the decrease of snow pack induced by winter warming might increase the activities of soil enzymes related with nitrogen transformation and further stimulate the process of wintertime nitrogen transformation in soils of the subalpine forest.

Nanophotonic light-trapping theory for solar cells

NASA Astrophysics Data System (ADS)

Yu, Zongfu; Raman, Aaswath; Fan, Shanhui

2011-11-01

Conventional light-trapping theory, based on a ray-optics approach, was developed for standard thick photovoltaic cells. The classical theory established an upper limit for possible absorption enhancement in this context and provided a design strategy for reaching this limit. This theory has become the foundation for light management in bulk silicon PV cells, and has had enormous influence on the optical design of solar cells in general. This theory, however, is not applicable in the nanophotonic regime. Here we develop a statistical temporal coupled-mode theory of light trapping based on a rigorous electromagnetic approach. Our theory reveals that the standard limit can be substantially surpassed when optical modes in the active layer are confined to deep-subwavelength scale, opening new avenues for highly efficient next-generation solar cells.

Deep water characteristics and circulation in the South China Sea

NASA Astrophysics Data System (ADS)

Wang, Aimei; Du, Yan; Peng, Shiqiu; Liu, Kexiu; Huang, Rui Xin

2018-04-01

This study investigates the deep circulation in the South China Sea (SCS) using oceanographic observations combined with results from a bottom layer reduced gravity model. The SCS water, 2000 m below the surface, is quite different from that in the adjacent Pacific Ocean, and it is characterized by its low dissolved oxygen (DO), high temperature and low salinity. The horizontal distribution of deep water properties indicates a basin-scale cyclonic circulation driven by the Luzon overflow. The results of the bottom layer reduced gravity model are consistent with the existence of the cyclonic circulation in the deep SCS. The circulation is stronger at the northern/western boundary. After overflowing the sill of the Luzon Strait, the deep water moves broadly southwestward, constrained by the 3500 m isobath. The broadening of the southward flow is induced by the downwelling velocity in the interior of the deep basin. The main deep circulation bifurcates into two branches after the Zhongsha Islands. The southward branch continues flowing along the 3500 m isobath, and the eastward branch forms the sub-basin scale cyclonic circulation around the seamounts in the central deep SCS. The returning flow along the east boundary is fairly weak. The numerical experiments of the bottom layer reduced gravity model reveal the important roles of topography, bottom friction, and the upwelling/downwelling pattern in controlling the spatial structure, particularly the strong, deep western boundary current.

Seasonal and inter-annual variations of dissolved oxygen in the northwestern Mediterranean Sea (DYFAMED site)

NASA Astrophysics Data System (ADS)

Coppola, Laurent; Legendre, Louis; Lefevre, Dominique; Prieur, Louis; Taillandier, Vincent; Diamond Riquier, Emilie

2018-03-01

Dissolved oxygen (O2) is a relevant tracer to interpret variations of both water mass properties in the open ocean and biological production in the surface layer of both coastal and open waters. Deep-water formation is very active in the northwestern Mediterranean Sea, where it influences intermediate and deep waters properties, nutrients replenishment and biological production. This study analyses, for the first time, the 20-year time series of monthly O2 concentrations at the DYFAMED long-term sampling site in the Ligurian Sea. Until the winters of 2005 and 2006, a thick and strong oxygen minimum layer was present between 200 and 1300 m because dense water formation was then local, episodic and of low intensity. In 2005-2006, intense and rapid deep convection injected 24 mol O2 m-2 between 350 and 2000 m from December 2005 to March 2006. Since this event, the deep layer has been mostly ventilated during winter time by newly formed deep water spreading from the Gulf of Lion 250 km to the west and by some local deep mixing in early 2010, 2012 and 2013. In the context of climate change, it is predicted that the intensity of deep convection will become weaker in the Mediterranean, which could potentially lead to hypoxia in intermediate and deep layers with substantial impact on marine ecosystems. With the exception of winters 2005 and 2006, the O2 changes in surface waters followed a seasonal trend that reflected the balance between air-sea O2 exchanges, changes in the depth of the mixed layer and phytoplankton net photosynthesis. We used the 20-year O2 time series to estimate monthly and annual net community production. The latter was 7.1 mol C m-2 yr-1, consistent with C-14 primary production determinations and sediment-trap carbon export fluxes at DYFAMED.

Parvalbumin interneuron mediated feedforward inhibition controls signal output in the deep layers of the perirhinal‐entorhinal cortex

PubMed Central

Willems, Janske G. P.; Wadman, Wytse J.

2018-01-01

Abstract The perirhinal (PER) and lateral entorhinal (LEC) cortex form an anatomical link between the neocortex and the hippocampus. However, neocortical activity is transmitted through the PER and LEC to the hippocampus with a low probability, suggesting the involvement of the inhibitory network. This study explored the role of interneuron mediated inhibition, activated by electrical stimulation in the agranular insular cortex (AiP), in the deep layers of the PER and LEC. Activated synaptic input by AiP stimulation rarely evoked action potentials in the PER‐LEC deep layer excitatory principal neurons, most probably because the evoked synaptic response consisted of a small excitatory and large inhibitory conductance. Furthermore, parvalbumin positive (PV) interneurons—a subset of interneurons projecting onto the axo‐somatic region of principal neurons—received synaptic input earlier than principal neurons, suggesting recruitment of feedforward inhibition. This synaptic input in PV interneurons evoked varying trains of action potentials, explaining the fast rising, long lasting synaptic inhibition received by deep layer principal neurons. Altogether, the excitatory input from the AiP onto deep layer principal neurons is overruled by strong feedforward inhibition. PV interneurons, with their fast, extensive stimulus‐evoked firing, are able to deliver this fast evoked inhibition in principal neurons. This indicates an essential role for PV interneurons in the gating mechanism of the PER‐LEC network. PMID:29341361

What if the Diatoms of the Deep Chlorophyll Maximum Can Ascend?

NASA Astrophysics Data System (ADS)

Villareal, T. A.

2016-02-01

Buoyancy regulation is an integral part of diatom ecology via its role in sinking rates and is fundamental to understanding their distribution and abundance. Numerous studies have documented the effects of size and nutrition on sinking rates. Many pelagic diatoms have low intrinsic sinking rates when healthy and nutrient-replete (< 1-2 meters per day). Physiological control of buoyancy via ion regulation and osmolyte control can easily result in cell sap densities less than seawater, resulting in near-zero sinking rates across a large size spectrum of diatoms as well as positive buoyancy in giant diatoms with their low surface:volume ratio. Ascent by smaller diatoms is much less described although predicted in cells as small as 200 cubic microns. Decreased sedimentation rates have long been linked to formation of layers in the water column, particularly at the low light and nutricline conditions of the deep chlorophyll maximum. The potential for ascending behavior adds an additional layer of complexity by allowing both active depth regulation similar to that observed in flagellated taxa and upward transport by some fraction of deep euphotic zone diatom blooms supported by nutrient injection. In this talk, I review the data documenting positive buoyancy in small diatoms, offer direct visual evidence of ascending behavior in common diatoms typical of both oceanic and coastal zones, and note the characteristics of sinking rate distributions within a single species. Buoyancy control leads to bidirectional movement at similar rates across a wide size spectrum of diatoms although the frequency of ascending behavior may be only a small portion of the individual species' abundance. While much remains to be learned, the paradigm of unidirectional downward movement by diatoms is both inaccurate and an oversimplification.

On the glacial and inter-glacial thermohaline circulation and the associated transports of heat and freshwater

NASA Astrophysics Data System (ADS)

Ballarotta, M.; Falahat, S.; Brodeau, L.; Döös, K.

2014-03-01

The change of the thermohaline circulation (THC) between the Last Glacial Maximum (LGM, ≈ 21 kyr ago) and the present day climate are explored using an Ocean General Circulation Model and stream functions projected in various coordinates. Compared to the present day period, the LGM circulation is reorganised in the Atlantic Ocean, in the Southern Ocean and particularly in the abyssal ocean, mainly due to the different haline stratification. Due to stronger wind stress, the LGM tropical circulation is more vigorous than under modern conditions. Consequently, the maximum tropical transport of heat is slightly larger during the LGM. In the North Atlantic basin, the large sea-ice extent during the LGM constrains the Gulf Stream to propagate in a more zonal direction, reducing the transport of heat towards high latitudes and reorganising the freshwater transport. The LGM circulation is represented as a large intrusion of saline Antarctic Bottom Water into the Northern Hemisphere basins. As a result, the North Atlantic Deep Water is shallower in the LGM simulation. The stream functions in latitude-salinity coordinates and thermohaline coordinates point out the different haline regimes between the glacial and interglacial period, as well as a LGM Conveyor Belt circulation largely driven by enhanced salinity contrast between the Atlantic and the Pacific basin. The thermohaline structure in the LGM simulation is the result of an abyssal circulation that lifts and deviates the Conveyor Belt cell from the area of maximum volumetric distribution, resulting in a ventilated upper layer above a deep stagnant layer, and an Atlantic circulation more isolated from the Pacific. An estimation of the turnover times reveal a deep circulation almost sluggish during the LGM, and a Conveyor Belt cell more vigorous due to the combination of stronger wind stress and shortened circulation route.

Deep kernel learning method for SAR image target recognition

NASA Astrophysics Data System (ADS)

Chen, Xiuyuan; Peng, Xiyuan; Duan, Ran; Li, Junbao

2017-10-01

With the development of deep learning, research on image target recognition has made great progress in recent years. Remote sensing detection urgently requires target recognition for military, geographic, and other scientific research. This paper aims to solve the synthetic aperture radar image target recognition problem by combining deep and kernel learning. The model, which has a multilayer multiple kernel structure, is optimized layer by layer with the parameters of Support Vector Machine and a gradient descent algorithm. This new deep kernel learning method improves accuracy and achieves competitive recognition results compared with other learning methods.

Focusing on optic tectum circuitry through the lens of genetics.

PubMed

Nevin, Linda M; Robles, Estuardo; Baier, Herwig; Scott, Ethan K

2010-09-28

The visual pathway is tasked with processing incoming signals from the retina and converting this information into adaptive behavior. Recent studies of the larval zebrafish tectum have begun to clarify how the 'micro-circuitry' of this highly organized midbrain structure filters visual input, which arrives in the superficial layers and directs motor output through efferent projections from its deep layers. The new emphasis has been on the specific function of neuronal cell types, which can now be reproducibly labeled, imaged and manipulated using genetic and optical techniques. Here, we discuss recent advances and emerging experimental approaches for studying tectal circuits as models for visual processing and sensorimotor transformation by the vertebrate brain.

Retinyl palmitate flexible polymeric nanocapsules: characterization and permeation studies.

PubMed

Teixeira, Zaine; Zanchetta, Beatriz; Melo, Bruna A G; Oliveira, Luciana L; Santana, Maria H A; Paredes-Gamero, Edgar J; Justo, Giselle Z; Nader, Helena B; Guterres, Sílvia S; Durán, Nelson

2010-11-01

Polymeric nanocapsules with elastic characteristics were prepared by the pre-formed polymer interfacial deposition method. The system consists of an oily core of retinyl palmitate with Span 60 and a polymeric wall of poly(D,L-lactide) (PLA). A narrow size distribution (215 nm, P.D.I. 0.10) was showed by dynamic light scattering (DLS) analyses. Particle deformability was observed by transmission electron microscopy (TEM) images and permeation of the particles through two superposed membranes of smaller pore diameters. Permeation studies were achieved using plastic surgery abdominal human skin by Franz diffusion cell. Retinyl palmitate permeates into deep skin layers. Besides, a PLA fluorescent derivative conjugated with Nile blue dye by an amide covalent bound was additionally obtained. Permeation profile of the nanocapsules with the fluorescent polymer was evaluated by confocal laser scanning microscopy (CLSM). The CLSM showed that nanocapsules were distributed uniformly, suggesting that the permeation mechanism through skin is intercellular. Thus, the use of these nanocapsules may be a feasible strategy to enhance the permeation of actives into the skin when delivery to deep layers is aimed. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Spin and valence dependence of iron partitioning in Earth’s deep mantle

PubMed Central

Piet, Hélène; Badro, James; Nabiei, Farhang; Dennenwaldt, Teresa; Shim, Sang-Heon; Cantoni, Marco; Hébert, Cécile; Gillet, Philippe

2016-01-01

We performed laser-heated diamond anvil cell experiments combined with state-of-the-art electron microanalysis (focused ion beam and aberration-corrected transmission electron microscopy) to study the distribution and valence of iron in Earth’s lower mantle as a function of depth and composition. Our data reconcile the apparently discrepant existing dataset, by clarifying the effects of spin (high/low) and valence (ferrous/ferric) states on iron partitioning in the deep mantle. In aluminum-bearing compositions relevant to Earth’s mantle, iron concentration in silicates drops above 70 GPa before increasing up to 110 GPa with a minimum at 85 GPa; it then dramatically drops in the postperovskite stability field above 116 GPa. This compositional variation should strengthen the lowermost mantle between 1,800 km depth and 2,000 km depth, and weaken it between 2,000 km depth and the D” layer. The succession of layers could dynamically decouple the mantle above 2,000 km from the lowermost mantle, and provide a rheological basis for the stabilization and nonentrainment of large low-shear-velocity provinces below that depth. PMID:27647917

Computer-aided classification of mammographic masses using the deep learning technology: a preliminary study

NASA Astrophysics Data System (ADS)

Qiu, Yuchen; Yan, Shiju; Tan, Maxine; Cheng, Samuel; Liu, Hong; Zheng, Bin

2016-03-01

Although mammography is the only clinically acceptable imaging modality used in the population-based breast cancer screening, its efficacy is quite controversy. One of the major challenges is how to help radiologists more accurately classify between benign and malignant lesions. The purpose of this study is to investigate a new mammographic mass classification scheme based on a deep learning method. In this study, we used an image dataset involving 560 regions of interest (ROIs) extracted from digital mammograms, which includes 280 malignant and 280 benign mass ROIs, respectively. An eight layer deep learning network was applied, which employs three pairs of convolution-max-pooling layers for automatic feature extraction and a multiple layer perception (MLP) classifier for feature categorization. In order to improve robustness of selected features, each convolution layer is connected with a max-pooling layer. A number of 20, 10, and 5 feature maps were utilized for the 1st, 2nd and 3rd convolution layer, respectively. The convolution networks are followed by a MLP classifier, which generates a classification score to predict likelihood of a ROI depicting a malignant mass. Among 560 ROIs, 420 ROIs were used as a training dataset and the remaining 140 ROIs were used as a validation dataset. The result shows that the new deep learning based classifier yielded an area under the receiver operation characteristic curve (AUC) of 0.810+/-0.036. This study demonstrated the potential superiority of using a deep learning based classifier to distinguish malignant and benign breast masses without segmenting the lesions and extracting the pre-defined image features.

Photosystem II efficiency of the palisade and spongy mesophyll in Quercus coccifera using adaxial/abaxial illumination and excitation light sources with wavelengths varying in penetration into the leaf tissue.

PubMed

Peguero-Pina, José Javier; Gil-Pelegrín, Eustaquio; Morales, Fermín

2009-01-01

The existence of major vertical gradients within the leaf is often overlooked in studies of photosynthesis. These gradients, which involve light heterogeneity, cell composition, and CO(2) concentration across the mesophyll, can generate differences in the maximum potential PSII efficiency (F (V)/F (M) or F (V)/F (P)) of the different cell layers. Evidence is presented for a step gradient of F (V)/F (P) ratios across the mesophyll, from the adaxial (palisade parenchyma, optimal efficiencies) to the abaxial (spongy parenchyma, sub-optimal efficiencies) side of Quercus coccifera leaves. For this purpose, light sources with different wavelengths that penetrate more or less deep within the leaf were employed, and measurements from the adaxial and abaxial sides were performed. To our knowledge, this is the first report where a low photosynthetic performance in the abaxial side of leaves is accompanied by impaired F (V)/F (P) ratios. This low photosynthetic efficiency of the abaxial side could be related to the occurrence of bundle sheath extensions, which facilitates the penetration of high light intensities deep within the mesophyll. Also, leaf morphology (twisted in shape) and orientation (with a marked angle from the horizontal plane) imply direct sunlight illumination of the abaxial side. The existence of cell layers within leaves with different photosynthetic efficiencies makes appropriate the evaluation of how light penetrates within the mesophyll when using Chl fluorescence or gas exchange techniques that use different wavelengths for excitation and/or for driving photosynthesis.

Curative effects of microneedle fractional radiofrequency system on skin laxity in Asian patients: A prospective, double-blind, randomized, controlled face-split study.

PubMed

Lu, Wenli; Wu, Pinru; Zhang, Zhen; Chen, Jinan; Chen, Xiangdong; Ewelina, Biskup

2017-04-01

To date, no studies compared curative effects of thermal lesions in deep and superficial dermal layers in the same patient (face-split study). To evaluate skin laxity effects of microneedle fractional radiofrequency induced thermal lesions in different dermal layers. 13 patients underwent three sessions of a randomized face-split microneedle fractional radiofrequency system (MFRS) treatment of deep dermal and superficial dermal layer. Skin laxity changes were evaluated objectively (digital images, 2 independent experts) and subjectively (patients' satisfaction numerical rating). 12 of 13 subjects completed a course of 3 treatments and a 1-year follow-up. Improvement of nasolabial folds in deep dermal approach was significantly better than that in superficial approach at three months (P=.0002) and 12 months (P=.0057) follow-up. Effects on infraorbital rhytides were only slightly better (P=.3531). MFRS is an effective method to improve skin laxity. Thermal lesion approach seems to provide better outcomes when applied to deep dermal layers. It is necessary to consider the skin thickness of different facial regions when choosing the treatment depth.

BIG1 is required for the survival of deep layer neurons, neuronal polarity, and the formation of axonal tracts between the thalamus and neocortex in developing brain

PubMed Central

Teoh, Jia-Jie; Iwano, Tomohiko; Kunii, Masataka; Atik, Nur; Avriyanti, Erda; Yoshimura, Shin-ichiro; Moriwaki, Kenta

2017-01-01

BIG1, an activator protein of the small GTPase, Arf, and encoded by the Arfgef1 gene, is one of candidate genes for epileptic encephalopathy. To know the involvement of BIG1 in epileptic encephalopathy, we analyzed BIG1-deficient mice and found that BIG1 regulates neurite outgrowth and brain development in vitro and in vivo. The loss of BIG1 decreased the size of the neocortex and hippocampus. In BIG1-deficient mice, the neuronal progenitor cells (NPCs) and the interneurons were unaffected. However, Tbr1+ and Ctip2+ deep layer (DL) neurons showed spatial-temporal dependent apoptosis. This apoptosis gradually progressed from the piriform cortex (PIR), peaked in the neocortex, and then progressed into the hippocampus from embryonic day 13.5 (E13.5) to E17.5. The upper layer (UL) and DL order in the neocortex was maintained in BIG1-deficient mice, but the excitatory neurons tended to accumulate before their destination layers. Further pulse-chase migration assay showed that the migration defect was non-cell autonomous and secondary to the progression of apoptosis into the BIG1-deficient neocortex after E15.5. In BIG1-deficient mice, we observed an ectopic projection of corticothalamic axons from the primary somatosensory cortex (S1) into the dorsal lateral geniculate nucleus (dLGN). The thalamocortical axons were unable to cross the diencephalon–telencephalon boundary (DTB). In vitro, BIG1-deficient neurons showed a delay in neuronal polarization. BIG1-deficient neurons were also hypersensitive to low dose glutamate (5 μM), and died via apoptosis. This study showed the role of BIG1 in the survival of DL neurons in developing embryonic brain and in the generation of neuronal polarity. PMID:28414797

Characterization of focal cortical dysplasia with balloon cells by layer-specific markers: Evidence for differential vulnerability of interneurons.

PubMed

Nakagawa, Julia M; Donkels, Catharina; Fauser, Susanne; Schulze-Bonhage, Andreas; Prinz, Marco; Zentner, Josef; Haas, Carola A

2017-04-01

Focal cortical dysplasia (FCD) is a major cause of pharmacoresistant focal epilepsy. Little is known about the pathomechanisms underlying the characteristic cytoarchitectural abnormalities associated with FCD. In the present study, a broad panel of markers identifying layer-specific neuron subpopulations was applied to characterize dyslamination and structural alterations in FCD with balloon cells (FCD 2b). Pan-neuronal neuronal nuclei (NeuN) and layer-specific protein expression (Reelin, Calbindin, Calretinin, SMI32 (nonphosphorylated neurofilament H), Parvalbumin, transducin-like enhancer protein 4 (TLE4), and Vimentin) was studied by immunohistochemistry on paraffin sections of FCD2b cases (n = 22) and was compared to two control groups with (n = 7) or without epilepsy (n = 4 postmortem cases). Total and layer-specific neuron densities were systematically quantified by cell counting considering age at surgery and brain region. We show that in FCD2b total neuron densities across all six cortical layers were not significantly different from controls. In addition, we present evidence that a basic laminar arrangement of layer-specific neuron subtypes was preserved despite the severe disturbance of cortical structure. SMI32-positive pyramidal neurons showed no significant difference in total numbers, but a reduction in layers III and V. The densities of supragranular Calbindin- and Calretinin-positive interneurons in layers II and III were not different from controls, whereas Parvalbumin-expressing interneurons, primarily located in layer IV, were significantly reduced in numbers when compared to control cases without epilepsy. In layer VI, the density of TLE4-positive projection neurons was significantly increased. Altogether, these data show that changes in cellular composition mainly affect deep cortical layers in FCD2b. The application of a broad panel of markers defining layer-specific neuronal subpopulations revealed that in FCD2b neuronal diversity and a basic laminar arrangement are maintained despite the severe disturbance of cytoarchitecture. Moreover, it showed that Parvalbumin-positive, inhibitory interneurons are highly vulnerable in contrast to other interneuron subtypes, possibly related to the epileptic condition. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

Linear shoaling of free-surface waves in multi-layer non-hydrostatic models

NASA Astrophysics Data System (ADS)

Bai, Yefei; Cheung, Kwok Fai

2018-01-01

The capability to describe shoaling over sloping bottom is fundamental to modeling of coastal wave transformation. The linear shoaling gradient provides a metric to measure this property in non-hydrostatic models with layer-integrated formulations. The governing equations in Boussinesq form facilitate derivation of the linear shoaling gradient, which is in the form of a [ 2 P + 2 , 2 P ] expansion of the water depth parameter kd with P equal to 1 for a one-layer model and (4 N - 4) for an N-layer model. The expansion reproduces the analytical solution from Airy wave theory at the shallow water limit and maintains a reasonable approximation up to kd = 1.2 and 2 for the one and two-layer models. Additional layers provide rapid and monotonic convergence of the shoaling gradient into deep water. Numerical experiments of wave propagation over a plane slope illustrate manifestation of the shoaling errors through the transformation processes from deep to shallow water. Even though outside the zone of active wave transformation, shoaling errors from deep to intermediate water are cumulative to produce appreciable impact to the wave amplitude in shallow water.

An Algorithm to Generate Deep-Layer Temperatures from Microwave Satellite Observations for the Purpose of Monitoring Climate Change. Revised

NASA Technical Reports Server (NTRS)

Goldberg, Mitchell D.; Fleming, Henry E.

1994-01-01

An algorithm for generating deep-layer mean temperatures from satellite-observed microwave observations is presented. Unlike traditional temperature retrieval methods, this algorithm does not require a first guess temperature of the ambient atmosphere. By eliminating the first guess a potentially systematic source of error has been removed. The algorithm is expected to yield long-term records that are suitable for detecting small changes in climate. The atmospheric contribution to the deep-layer mean temperature is given by the averaging kernel. The algorithm computes the coefficients that will best approximate a desired averaging kernel from a linear combination of the satellite radiometer's weighting functions. The coefficients are then applied to the measurements to yield the deep-layer mean temperature. Three constraints were used in deriving the algorithm: (1) the sum of the coefficients must be one, (2) the noise of the product is minimized, and (3) the shape of the approximated averaging kernel is well-behaved. Note that a trade-off between constraints 2 and 3 is unavoidable. The algorithm can also be used to combine measurements from a future sensor (i.e., the 20-channel Advanced Microwave Sounding Unit (AMSU)) to yield the same averaging kernel as that based on an earlier sensor (i.e., the 4-channel Microwave Sounding Unit (MSU)). This will allow a time series of deep-layer mean temperatures based on MSU measurements to be continued with AMSU measurements. The AMSU is expected to replace the MSU in 1996.

Greater contribution of cerebral than extracerebral hemodynamics to near-infrared spectroscopy signals for functional activation and resting-state connectivity in infants.

PubMed

Funane, Tsukasa; Homae, Fumitaka; Watanabe, Hama; Kiguchi, Masashi; Taga, Gentaro

2014-10-01

While near-infrared spectroscopy (NIRS) has been increasingly applied to neuroimaging and functional connectivity studies in infants, it has not been quantitatively examined as to what extent the deep tissue (such as cerebral tissue) as opposed to shallow tissue (such as scalp), contributes to NIRS signals measured in infants. A method for separating the effects of deep- and shallow-tissue layers was applied to data of nine sleeping three-month-old infants who had been exposed to 3-s speech sounds or silence (i.e., resting state) and whose hemodynamic changes over their bilateral temporal cortices had been measured by using an NIRS system with multiple source-detector (S-D) distances. The deep-layer contribution was found to be large during resting [67% at S-D 20 mm, 78% at S-D 30 mm for oxygenated hemoglobin (oxy-Hb)] as well as during the speech condition (72% at S-D 20 mm, 82% at S-D 30 mm for oxy-Hb). A left-right connectivity analysis showed that correlation coefficients between left and right channels did not differ between original- and deep-layer signals under no-stimulus conditions and that of original- and deep-layer signals were larger than those of the shallow layer. These results suggest that NIRS signals obtained in infants with appropriate S-D distances largely reflected cerebral hemodynamic changes.

Greater contribution of cerebral than extracerebral hemodynamics to near-infrared spectroscopy signals for functional activation and resting-state connectivity in infants

PubMed Central

Funane, Tsukasa; Homae, Fumitaka; Watanabe, Hama; Kiguchi, Masashi; Taga, Gentaro

2014-01-01

Abstract. While near-infrared spectroscopy (NIRS) has been increasingly applied to neuroimaging and functional connectivity studies in infants, it has not been quantitatively examined as to what extent the deep tissue (such as cerebral tissue) as opposed to shallow tissue (such as scalp), contributes to NIRS signals measured in infants. A method for separating the effects of deep- and shallow-tissue layers was applied to data of nine sleeping three-month-old infants who had been exposed to 3-s speech sounds or silence (i.e., resting state) and whose hemodynamic changes over their bilateral temporal cortices had been measured by using an NIRS system with multiple source-detector (S-D) distances. The deep-layer contribution was found to be large during resting [67% at S-D 20 mm, 78% at S-D 30 mm for oxygenated hemoglobin (oxy-Hb)] as well as during the speech condition (72% at S-D 20 mm, 82% at S-D 30 mm for oxy-Hb). A left-right connectivity analysis showed that correlation coefficients between left and right channels did not differ between original- and deep-layer signals under no-stimulus conditions and that of original- and deep-layer signals were larger than those of the shallow layer. These results suggest that NIRS signals obtained in infants with appropriate S-D distances largely reflected cerebral hemodynamic changes. PMID:26157977

Alaskan Arctic Soils: Relationship between Microbial Carbon Usage and Soil Composition

NASA Astrophysics Data System (ADS)

Li, H.; Ziolkowski, L. A.

2015-12-01

Carbon stored in Arctic permafrost carbon is sensitive to climate change. Microbes are known to degrade Arctic soil organic carbon (OC) and potentially release vast quantitates of CO2 and CH4. Previously, it has been shown that warming of Arctic soils leads to microbes respiring older carbon. To examine this process, we studied the microbial carbon usage and its relationship to the soil OC composition in active layer soils at five locations along a latitudinal transect on the North Slope of Alaska using the compound specific radiocarbon signatures of the viable microbial community using phospholipid fatty acids (PLFA). Additional geochemical parameters (C/N, 13C, 15N and 14C) of bulk soils were measured. Overall there was a greater change with depth than location. Organic rich surface soils are rich in vegetation and have high PLFA based cell densities, while deeper in the active layer geochemical parameters indicated soil OC was degraded and cell densities decreased. As expected, PLFA indicative of Fungi and Protozoa species dominated in surface soils, methyl-branched PLFAs, indicative of bacterial origin, increased in deeper in the active layer. A group of previously unreported PLFAs, believed to correlate to anaerobic microbes, increased at the transition between the surface and deep microbial communities. Cluster analysis based on individual PLFAs of samples confirmed compositional differences as a function of depth dominated with no site to site differences. Radiocarbon data of soil OC and PLFA show the preferential consumption of younger soil OC by microbes at all sites and older OC being eaten in deep soils. However, in deeper soil, where the C/N ratio suggests lower bioavailability, less soil OC was incorporated into the microbes as indicating by greater differences between bulk and PLFA radiocarbon ages.

Fundamental limit of nanophotonic light trapping in solar cells.

PubMed

Yu, Zongfu; Raman, Aaswath; Fan, Shanhui

2010-10-12

Establishing the fundamental limit of nanophotonic light-trapping schemes is of paramount importance and is becoming increasingly urgent for current solar cell research. The standard theory of light trapping demonstrated that absorption enhancement in a medium cannot exceed a factor of 4n(2)/sin(2)θ, where n is the refractive index of the active layer, and θ is the angle of the emission cone in the medium surrounding the cell. This theory, however, is not applicable in the nanophotonic regime. Here we develop a statistical temporal coupled-mode theory of light trapping based on a rigorous electromagnetic approach. Our theory reveals that the conventional limit can be substantially surpassed when optical modes exhibit deep-subwavelength-scale field confinement, opening new avenues for highly efficient next-generation solar cells.

Differential rotation in solar-like stars from global simulations

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

Guerrero, G.; Kosovichev, A. G.; Smolarkiewicz, P. K.

2013-12-20

To explore the physics of large-scale flows in solar-like stars, we perform three-dimensional anelastic simulations of rotating convection for global models with stratification resembling the solar interior. The numerical method is based on an implicit large-eddy simulation approach designed to capture effects from non-resolved small scales. We obtain two regimes of differential rotation, with equatorial zonal flows accelerated either in the direction of rotation (solar-like) or in the opposite direction (anti-solar). While the models with the solar-like differential rotation tend to produce multiple cells of meridional circulation, the models with anti-solar differential rotation result in only one or two meridionalmore » cells. Our simulations indicate that the rotation and large-scale flow patterns critically depend on the ratio between buoyancy and Coriolis forces. By including a sub-adiabatic layer at the bottom of the domain, corresponding to the stratification of a radiative zone, we reproduce a layer of strong radial shear similar to the solar tachocline. Similarly, enhanced super-adiabaticity at the top results in a near-surface shear layer located mainly at lower latitudes. The models reveal a latitudinal entropy gradient localized at the base of the convection zone and in the stable region, which, however, does not propagate across the convection zone. In consequence, baroclinicity effects remain small, and the rotation isocontours align in cylinders along the rotation axis. Our results confirm the alignment of large convective cells along the rotation axis in the deep convection zone and suggest that such 'banana-cell' pattern can be hidden beneath the supergranulation layer.« less

Longitudinal analysis of MR spin-spin relaxation times (T2) in medial femorotibial cartilage of adolescent vs mature athletes: dependence of deep and superficial zone properties on sex and age.

PubMed

Wirth, W; Eckstein, F; Boeth, H; Diederichs, G; Hudelmaier, M; Duda, G N

2014-10-01

Cartilage spin-spin magnetic resonance imaging (MRI) relaxation time (T2) represents a promising imaging biomarker of "early" osteoarthritis (OA) known to be associated with cartilage composition (collagen integrity, orientation, and hydration). However, no longitudinal imaging studies have been conducted to examine cartilage maturation in healthy subjects thus far. Therefore, we explore T2 change in the deep and superficial cartilage layers at the end of adolescence. Twenty adolescent and 20 mature volleyball athletes were studied (each 10 men and 10 women). Multi-echo spin-echo (MESE) images were acquired at baseline and 2-year follow-up. After segmentation, cartilage T2 was calculated in the deep and superficial cartilage layers of the medial tibial (MT) and the central, weight-bearing part of the medial femoral condyle (cMF), using five echoes (TE 19.4-58.2 ms). 16 adolescent (6 men, 10 women, baseline age 15.8 ± 0.5 years) and 17 mature (nine men, eight women, age 46.5 ± 5.2 years) athletes had complete baseline and follow-up images of sufficient quality to compute T2. In adolescents, a longitudinal decrease in T2 was observed in the deep layers of MT (-2.0 ms; 95% confidence interval (CI): [-3.4, -0.6] ms; P < 0.01) and cMF (-1.3 ms; [-2.4, -0.3] ms; P < 0.05), without obvious differences between males and females. No significant change was observed in the superficial layers, or in the deep or superficial layers of the mature athletes. In this first pilot study on quantitative imaging of cartilage maturation in healthy, athletic subjects, we find evidence of cartilage compositional change in deep cartilage layers of the medial femorotibial compartment in adolescents, most likely related to organizational changes in the collagen matrix. Copyright © 2014 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Correlation of Pliocene and Pleistocene tephra layers between the Turkana Basin of East Africa and the Gulf of Aden

USGS Publications Warehouse

Brown, F.H.; Sarna-Wojcicki, A. M.; Meyer, C.E.; Haileab, B.

1992-01-01

Electron-microprobe analyses of glass shards from volcanic ash in Pliocene and Pleistocene deep-sea sediments in the Gulf of Aden and the Somali Basin demonstrate that most of the tephra layers correlate with tephra layers known on land in the Turkana Basin of northern Kenya and southern Ethiopia. Previous correlations are reviewed, and new correlations proposed. Together these data provide correlations between the deep-sea cores, and to the land-based sections at eight levels ranging in age from about 4 to 0.7 Ma. Specifically, we correlate the Moiti Tuff (???4.1 Ma) with a tephra layer at 188.6 m depth in DSDP hole 231 and with a tephra layer at 150 m depth in DSDP hole 241, the Wargolo Tuff with a tephra layer at 179.7 m in DSDP Hole 231 and with a tephra layer at 155.3 m depth in DSDP Hole 232, the Lomogol Tuff (defined here) with a tephra layer at 165 m in DSDP Hole 232A, the Lokochot Tuff with a tephra layer at 140.1 m depth in DSDP Hole 232, the Tulu Bor Tuff with a tephra layer at 160.8 m depth in DSDP Hole 231, the Kokiselei Tuff with a tephra layer at 120 m depth in DSDP Hole 231 and with a tephra layer at 90.3 m depth in DSDP Hole 232, the Silbo Tuff (0.74 Ma) with a tephra layer at 35.5 m depth in DSDP Hole 231 and possibly with a tephra layer at 10.9 m depth in DSDP Hole 241. We also present analyses of other tephra from the deep sea cores for which correlative units on land are not yet known. The correlated tephra layers provide eight chronostratigraphic horizons that make it possible to temporally correlate paleoecological and paleoclimatic data between the terrestrial and deep-sea sites. Such correlations may make it possible to interpret faunal evolution in the Lake Turkana basin and other sites in East Africa within a broader regional or global paleoclimatic context. ?? 1992.

Effect of potential vorticity flux on the circulation in the South China Sea

NASA Astrophysics Data System (ADS)

Zhu, Yaohua; Sun, Junchuan; Wang, Yonggang; Wei, Zexun; Yang, Dezhou; Qu, Tangdong

2017-08-01

This study analyzes temperature and salinity products from the U.S. Navy Generalized Digital Environment Model. To avoid the fictitious assumption of no-motion reference level, a P-vector inverse method is employed to derive geostrophic velocity. Line integral of geostrophic velocity shows evidence for the existence of a sandwiched circulation in the South China Sea (SCS), i.e., cyclonic circulation in the subsurface and deep layers and anticyclonic in the intermediate layer. To reveal the factors responsible for the sandwiched circulation, we derive the potential vorticity equation based on a four-and-a-half-layer quasi-geostrophic model and apply theoretical potential vorticity constraint to density layers. The result shows that the sandwiched circulation is largely induced by planetary potential vorticity flux through lateral boundaries, mainly the Luzon Strait. This dynamical mechanism lies in the fact that the net potential vorticity inflow in the subsurface and deep layers leads to a positive layer-average vorticity in the SCS basin, yielding vortex stretching and a cyclonic basin-wide circulation. On the contrary, the net potential vorticity outflow in the intermediate layer induces a negative layer-average vorticity, generating an anticyclonic basin-wide circulation in the SCS. Furthermore, by illustrating different consequence from depth/density layers, we clarify that density layers are essential for applying theoretical potential vorticity constraint to the isolated deep SCS basin.

Thermohaline variability in the Adriatic and Northern Ionian Seas observed from the Argo floats during 2010-2014

NASA Astrophysics Data System (ADS)

Kovačević, Vedrana; Ursella, Laura; Gačić, Miroslav; Notarstefano, Giulio; Menna, Milena; Bensi, Manuel; Civitarese, Giuseppe; Poulain, Pierre-Marie

2015-04-01

The Adriatic Sea is the northernmost basin of the Eastern Mediterranean Sea (EMed). At its southern end, the basin communicates with the adjacent Ionian Sea through the 80 km wide and 850 m deep Strait of Otranto. Due to the river discharge in the north and due to the strong winter cooling, the Adriatic is both a dilution basin and the dense water formation region. The basin-wide circulation is cyclonic. The circulation is however, energetic also at smaller spatial and temporal scales, and several circulation cells and mesoscale features are regularly observed equally along the littoral and in the open sea. The North Adriatic Dense Water (NAdDW) formed during winter is the densest water of the whole Mediterranean Sea (up to 1060 kg/m3). It flows as a density driven bottom current from the northern shelf toward south, filling the deep layers of the middle and southern Adriatic pits. The deep open-sea area of the South Adriatic Pit (SAP, 1200 m) feels the influence of a water mass exchange through the Strait of Otranto. Specifically, it receives salty and warm surface and Levantine Intermediate Waters from the Ionian Sea. Through the open-sea winter convection that homogenizes and ventilates 400-800 m thick upper water column, this salty water contributes to the formation of the Adriatic Deep Water (AdDW, 1029.17-1029.20 kg/m3), which is not as dense as the NAdDW. Both dense waters eventually mix and spill across the sill ventilating the deep and bottom layers of the Ionian Sea, and driving the deep thermohaline cell of the EMed. Thermohaline properties of the Adriatic Sea vary at wide spatial and temporal scales, and this in turn affects the properties of its dense waters. The long-term scales are of a particular interest, as they are often associated with the biogeochemical and biotic variability such as intrusion of alien species into the Adriatic Sea and interconnection with the adjacent Ionian basin. Due to the extremely variable meteo- and climatic conditions, the signal of the Adriatic dense waters can be fairly irregular and impulsive. Sporadic in-situ surveys by research vessels are not always sufficient to capture this irregularity and its consequences on the circulation. The Lagrangian platforms are disseminated within the whole Mediterranean through the international Argo program. They are a useful tool to assess some of the spatial and temporal variability in the two basins. Combining the information from the floats and in-situ CTD profiles from oceanographic campaigns, we picture the inter-annual variability of the thermohaline properties in general during 2010-2014. In addition, the peculiarities of the very dense water overflow that during 2012 spilled out form the Strait of Otranto into the Northern Ionian is evidenced. Also, by the remotely sensed sea surface topography, we depict the most prominent circulation features of the upper layer.

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

Windisch, C.F. Jr.; Strachan, D.M.; Henager, C.H. Jr.

Cermet anodes were evaluated as nonconsumable substitutes for carbon anodes using a pilot-scale reduction cell at the Reynolds Manufacturing Technology Laboratory. After pilot cell testing, tile anodes were subjected to extensive materials characterization and physical properties measurements at the Pacific Northwest Laboratory. Significant changes in the composition of the cermet anodes were observed including the growth of a reaction layer and penetration of electrolyte deep into the cermet matrix. Fracture strength and toughness were measured as a function of temperature and the ductile-brittle transition wasreduced by 500C following pilot cell testing. These results imply difficulties with anode material and controlmore » of operating conditions in the pilot cell, and suggest that additional development work be performed before the cermet anodes are used in commercial reduction cells. The results also highlight specific fabrication and operational considerations that should be addressed in future testing.« less

Development of high-efficiency solar cells on silicon web

NASA Technical Reports Server (NTRS)

Meier, D. L.

1986-01-01

Achievement of higher efficiency cells by directing efforts toward identifying carrier loss mechanisms; design of cell structures; and development of processing techniques are described. Use of techniques such as deep-level transient spectroscopy (DLTS), laser-beam-induced current (LBIC), and transmission electron microscopy (TEM) indicated that dislocations in web material rather than twin planes were primarily responsible for limiting diffusion lengths in the web. Lifetimes and cell efficiencies can be improved from 19 to 120 microns, and 8 to 10.3% (no AR), respectively, by implanting hydrogen at 1500 eV and a beam current density of 2.0 mA/sq cm. Some of the processing improvements included use of a double-layer AR coating (ZnS and MgF2) and an addition of an aluminum back surface reflectors. Cells of more than 16% efficiency were achieved.

Alexandrium fundyense cyst viability and germling survival in light vs. dark at a constant low temperature

NASA Astrophysics Data System (ADS)

Vahtera, Emil; Crespo, Bibiana G.; McGillicuddy, Dennis J.; Olli, Kalle; Anderson, Donald M.

2014-05-01

Both observations and models suggest that large-scale coastal blooms of Alexandrium fundyense in the Gulf of Maine are seeded by deep-bottom cyst accumulation zones (“seed beds”) where cysts germinate from the sediment surface or the overlying near-bottom nepheloid layers at water depths exceeding 100 m. The germling cells and their vegetative progeny are assumed to be subject to mortality while in complete darkness, as they swim to illuminated surface waters. To test the validity of this assumption we conducted laboratory investigations of cyst viability and the survival of the germling cells and their vegetative progeny during prolonged exposure to darkness at a temperature of 6 °C, simulating the conditions in deep Gulf of Maine waters. We isolated cysts from bottom sediments collected in the Gulf of Maine under low red light and incubated them in 96-well tissue culture-plates in culture medium under a 10:14 h light:dark cycle and under complete darkness. Cyst viability was high, with excystment frequency reaching 90% in the illuminated treatment after 30 days and in the dark treatment after 50 days. Average germination rates were 0.062 and 0.038 d-1 for light and dark treatments, respectively. The dark treatment showed an approximately 2-week time lag in maximum germination rates compared to the light treatment. Survival of germlings was considerably lower in the dark treatment. In the light treatments, 47% of germinated cysts produced germlings that were able to survive for 7 days and produce vegetative progeny, i.e., there were live cells in the well along with an empty cyst at least once during the experiment. In the dark treatments 12% of the cysts produced germlings that were able to survive for the same length of time. When dark treatments are scaled to take into account non-darkness related mortality, approximately 28% of the cysts produced germlings that were able to survive for at least 7 days. Even though cysts are able to germinate in darkness, the lack of illumination considerably reduces survival rate of germling cells. In addition to viability of cysts in surface sediments and the near-bottom nepheloid layer, survivability of germling cells and their vegetative progeny at aphotic depths is an important consideration in assessing the quantitative role of deep-coastal cyst seed beds in bloom formation.

Hot and sour in the deep ocean

NASA Astrophysics Data System (ADS)

Sabine, Christopher L.

2017-12-01

Stable layering in the ocean limits the rate that human-derived carbon dioxide can acidify the deep ocean. Now observations show that ocean warming, however, can enhance deep-ocean acidification through increased organic matter decomposition.

Histamine up-regulates fibroblast growth factor receptor 1 and increases FOXP2 neurons in cultured neural precursors by histamine type 1 receptor activation: conceivable role of histamine in neurogenesis during cortical development in vivo.

PubMed

Molina-Hernández, Anayansi; Rodríguez-Martínez, Griselda; Escobedo-Ávila, Itzel; Velasco, Iván

2013-03-07

During rat development, histamine (HA) is one of the first neuroactive molecules to appear in the brain, reaching its maximal value at embryonic day 14, a period when neurogenesis of deep layers is occurring in the cerebral cortex, suggesting a role of this amine in neuronal specification. We previously reported, using high-density cerebrocortical neural precursor cultures, that micromolar HA enhanced the effect of fibroblast growth factor (FGF)-2 on proliferation, and that HA increased neuronal differentiation, due to HA type 1 receptor (H(1)R) activation. Clonal experiments performed here showed that HA decreased colony size and caused a significant increase in the percentage of clones containing mature neurons through H(1)R stimulation. In proliferating precursors, we studied whether HA activates G protein-coupled receptors linked to intracellular calcium increases. Neural cells presented an increase in cytoplasmic calcium even in the absence of extracellular calcium, a response mediated by H(1)R. Since FGF receptors (FGFRs) are known to be key players in cell proliferation and differentiation, we determined whether HA modifies the expression of FGFRs1-4 by using RT-PCR. An important transcriptional increase in FGFR1 was elicited after H(1)R activation. We also tested whether HA promotes differentiation specifically to neurons with molecular markers of different cortical layers by immunocytochemistry. HA caused significant increases in cells expressing the deep layer neuronal marker FOXP2; this induction of FOXP2-positive neurons elicited by HA was blocked by the H(1)R antagonist chlorpheniramine in vitro. Finally, we found a notable decrease in FOXP2+ cortical neurons in vivo, when chlorpheniramine was infused in the cerebral ventricles through intrauterine injection. These results show that HA, by activating H(1)R, has a neurogenic effect in clonal conditions and suggest that intracellular calcium elevation and transcriptional up-regulation of FGFR1 participate in HA-induced neuronal differentiation to FOXP2 cells in vitro; furthermore, H(1)R blockade in vivo resulted in decreased cortical FOXP2+ neurons.

Distribution of enkephalin-like immunoreactivity in the cat digestive tract.

PubMed

Bagnol, D; Henry, M; Cupo, A; Julé, Y

1997-05-12

Immunohistochemical investigations were carried out to determine the pattern of distribution of methionine- and leucine-enkephalin-like materials in the cat pylorus, duodenum, ileum and proximal and distal colon. The present results indicate that leucine-enkephalin-like materials are less densely distributed than methionine-enkephalin-like materials, but that the two patterns of distribution show some similarities. Considerable regional differences exist however in the distribution of these enkephalin-like materials in the muscular layers. In the duodenum, ileum and proximal colon, the immunoreactivity was mainly confined to the myenteric plexus and the circular muscle layer, where it was present in nerve cell bodies and in numerous fibres. In the longitudinal muscle and submucous layers, a few immunoreactive fibres were observed which sometimes surrounded blood vessels. In the pylorus and the distal colon, however, numerous immunoreactive fibres were observed in the longitudinal and circular muscle layers; the immunoreactivity was detected in the cell bodies of numerous myenteric plexus neurons but those of only a few submucous plexus neurons. In addition, the pylorus tissues contained immunoreactive plexi which were localized either within the longitudinal muscle or between the serosa and the longitudinal muscle layer. These plexi were connected to the myenteric plexus by immunoreactive nerve strands. In all the small intestinal segments studied, numerous immunoreactive varicosities were present in the deep muscular plexus, in the inner part of the circular muscle layer. Our results suggest that in cats, the nervous control of external muscular layers mediated by enkephalins shows regional differences. In the pylorus and the distal colon, it involves both the longitudinal and circular muscle layers, whereas in other intestinal segments, only the circular muscle layer is involved.

Deep Learning for ECG Classification

NASA Astrophysics Data System (ADS)

Pyakillya, B.; Kazachenko, N.; Mikhailovsky, N.

2017-10-01

The importance of ECG classification is very high now due to many current medical applications where this problem can be stated. Currently, there are many machine learning (ML) solutions which can be used for analyzing and classifying ECG data. However, the main disadvantages of these ML results is use of heuristic hand-crafted or engineered features with shallow feature learning architectures. The problem relies in the possibility not to find most appropriate features which will give high classification accuracy in this ECG problem. One of the proposing solution is to use deep learning architectures where first layers of convolutional neurons behave as feature extractors and in the end some fully-connected (FCN) layers are used for making final decision about ECG classes. In this work the deep learning architecture with 1D convolutional layers and FCN layers for ECG classification is presented and some classification results are showed.

Deep Convolutional Extreme Learning Machine and Its Application in Handwritten Digit Classification

PubMed Central

Yang, Xinyi

2016-01-01

In recent years, some deep learning methods have been developed and applied to image classification applications, such as convolutional neuron network (CNN) and deep belief network (DBN). However they are suffering from some problems like local minima, slow convergence rate, and intensive human intervention. In this paper, we propose a rapid learning method, namely, deep convolutional extreme learning machine (DC-ELM), which combines the power of CNN and fast training of ELM. It uses multiple alternate convolution layers and pooling layers to effectively abstract high level features from input images. Then the abstracted features are fed to an ELM classifier, which leads to better generalization performance with faster learning speed. DC-ELM also introduces stochastic pooling in the last hidden layer to reduce dimensionality of features greatly, thus saving much training time and computation resources. We systematically evaluated the performance of DC-ELM on two handwritten digit data sets: MNIST and USPS. Experimental results show that our method achieved better testing accuracy with significantly shorter training time in comparison with deep learning methods and other ELM methods. PMID:27610128

Deep Convolutional Extreme Learning Machine and Its Application in Handwritten Digit Classification.

PubMed

Pang, Shan; Yang, Xinyi

2016-01-01

In recent years, some deep learning methods have been developed and applied to image classification applications, such as convolutional neuron network (CNN) and deep belief network (DBN). However they are suffering from some problems like local minima, slow convergence rate, and intensive human intervention. In this paper, we propose a rapid learning method, namely, deep convolutional extreme learning machine (DC-ELM), which combines the power of CNN and fast training of ELM. It uses multiple alternate convolution layers and pooling layers to effectively abstract high level features from input images. Then the abstracted features are fed to an ELM classifier, which leads to better generalization performance with faster learning speed. DC-ELM also introduces stochastic pooling in the last hidden layer to reduce dimensionality of features greatly, thus saving much training time and computation resources. We systematically evaluated the performance of DC-ELM on two handwritten digit data sets: MNIST and USPS. Experimental results show that our method achieved better testing accuracy with significantly shorter training time in comparison with deep learning methods and other ELM methods.

Energy Levels of Defects Created in Silicon Supersaturated with Transition Metals

NASA Astrophysics Data System (ADS)

García, H.; Castán, H.; Dueñas, S.; García-Hemme, E.; García-Hernansaz, R.; Montero, D.; González-Díaz, G.

2018-03-01

Intermediate-band semiconductors have attracted much attention for use in silicon-based solar cells and infrared detectors. In this work, n-Si substrates have been implanted with very high doses (1013 cm-2 and 1014 cm-2) of vanadium, which gives rise to a supersaturated layer inside the semiconductor. However, the Mott limit was not exceeded. The energy levels created in the supersaturated silicon were studied in detail by means of thermal admittance spectroscopy. We found a single deep center at energy near E C - 200 meV. This value agrees with one of the levels found for vanadium in silicon. The capture cross-section values of the deep levels were also calculated, and we found a relationship between the capture cross-section and the energy position of the deep levels which follows the Meyer-Neldel rule. This process usually appears in processes involving multiple excitations. The Meyer-Neldel energy values agree with those previously obtained for silicon supersaturated with titanium and for silicon contaminated with iron.

Pathologic findings in human scabies.

PubMed

Fernandez, N; Torres, A; Ackerman, A B

1977-03-01

The histologic findings in the papular, vesicular, nodular, and Norwegian variant of scabies have in common a superficial and deep perivascular mixed inflammatory cell infiltrate of lymphocytes, histiocytes, and numerous eosinophils. A spongiotic vesicle occurs in the papulovesicular type, a dense cellular infiltrate in the nodular type, and a hyperkeratotic psoriasiform dermatitis in the Norwegian type. Eggs, larvae, and adult mites are abundant in the cornified layer of Norwegian scabies, are practically never found in biopsy specimens from lesions of nodular scabies, and are discovered only episodically in papulovesicular lesions.

Towards deep learning with segregated dendrites

PubMed Central

Guerguiev, Jordan; Lillicrap, Timothy P

2017-01-01

Deep learning has led to significant advances in artificial intelligence, in part, by adopting strategies motivated by neurophysiology. However, it is unclear whether deep learning could occur in the real brain. Here, we show that a deep learning algorithm that utilizes multi-compartment neurons might help us to understand how the neocortex optimizes cost functions. Like neocortical pyramidal neurons, neurons in our model receive sensory information and higher-order feedback in electrotonically segregated compartments. Thanks to this segregation, neurons in different layers of the network can coordinate synaptic weight updates. As a result, the network learns to categorize images better than a single layer network. Furthermore, we show that our algorithm takes advantage of multilayer architectures to identify useful higher-order representations—the hallmark of deep learning. This work demonstrates that deep learning can be achieved using segregated dendritic compartments, which may help to explain the morphology of neocortical pyramidal neurons. PMID:29205151

Towards deep learning with segregated dendrites.

PubMed

Guerguiev, Jordan; Lillicrap, Timothy P; Richards, Blake A

2017-12-05

Deep learning has led to significant advances in artificial intelligence, in part, by adopting strategies motivated by neurophysiology. However, it is unclear whether deep learning could occur in the real brain. Here, we show that a deep learning algorithm that utilizes multi-compartment neurons might help us to understand how the neocortex optimizes cost functions. Like neocortical pyramidal neurons, neurons in our model receive sensory information and higher-order feedback in electrotonically segregated compartments. Thanks to this segregation, neurons in different layers of the network can coordinate synaptic weight updates. As a result, the network learns to categorize images better than a single layer network. Furthermore, we show that our algorithm takes advantage of multilayer architectures to identify useful higher-order representations-the hallmark of deep learning. This work demonstrates that deep learning can be achieved using segregated dendritic compartments, which may help to explain the morphology of neocortical pyramidal neurons.

Sensing deep extreme environments: the receptor cell types, brain centers, and multi-layer neural packaging of hydrothermal vent endemic worms.

PubMed

Shigeno, Shuichi; Ogura, Atsushi; Mori, Tsukasa; Toyohara, Haruhiko; Yoshida, Takao; Tsuchida, Shinji; Fujikura, Katsunori

2014-01-01

Deep-sea alvinellid worm species endemic to hydrothermal vents, such as Alvinella and Paralvinella, are considered to be among the most thermotolerant animals known with their adaptability to toxic heavy metals, and tolerance of highly reductive and oxidative stressful environments. Despite the number of recent studies focused on their overall transcriptomic, proteomic, and metabolic stabilities, little is known regarding their sensory receptor cells and electrically active neuro-processing centers, and how these can tolerate and function in such harsh conditions. We examined the extra- and intracellular organizations of the epidermal ciliated sensory cells and their higher centers in the central nervous system through immunocytochemical, ultrastructural, and neurotracing analyses. We observed that these cells were rich in mitochondria and possessed many electron-dense granules, and identified specialized glial cells and serial myelin-like repeats in the head sensory systems of Paralvinella hessleri. Additionally, we identified the major epidermal sensory pathways, in which a pair of distinct mushroom bodies-like or small interneuron clusters was observed. These sensory learning and memory systems are commonly found in insects and annelids, but the alvinellid inputs are unlikely derived from the sensory ciliary cells of the dorsal head regions. Our evidence provides insight into the cellular and system-wide adaptive structure used to sense, process, and combat the deep-sea hydrothermal vent environment. The alvinellid sensory cells exhibit characteristics of annelid ciliary types, and among the most unique features were the head sensory inputs and structure of the neural cell bodies of the brain, which were surrounded by multiple membranes. We speculated that such enhanced protection is required for the production of normal electrical signals, and to avoid the breakdown of the membrane surrounding metabolically fragile neurons from oxidative stress. Such pivotal acquisition is not broadly found in the all body parts, suggesting the head sensory inputs are specific, and these heterogenetic protection mechanisms may be present in alvinellid worms.

An Expanded Analysis of Nitrogen Ice Convection in Sputnik Planum

NASA Astrophysics Data System (ADS)

Umurhan, Orkan M.; Lyra, Wladimir; Wong, Teresa; McKinnon, William B.; Nimmo, Francis; Howard, Alan D.; Moore, Jeffrey M.; Binzel, Richard; White, Oliver; Stern, S. Alan; Ennico, Kimberly; Olkin, Catherine B.; Weaver, Harold A.; Young, Leslie; New Horizons Geology and Geophysics Science Team

2016-10-01

The New Horizons close-encounter flyby of Pluto revealed 20-35 km scale ovoid patterns on the informally named Sputnik Planum. These features have been recently interpreted and shown to arise from the action of solid-state convection of (predominantly) nitrogen ice driven by Pluto's geothermal gradient. One of the major uncertainties in the convection physics centers on the temperature and grain-size dependency of nitrogen ice rheology, which has strong implications for the overturn times of the convecting ice. Assuming nitrogen ice in Sputnik Planum rests on a passive water ice bedrock that conducts Pluto's interior heat flux, and, given the uncertainty of the grain-size distribution of the nitrogen ice in Sputnik Planum, we examine a suite of two-dimensional convection models that take into account the thermal contact between the nitrogen ice layer and the conducting water-ice bedrock for a given emergent geothermal flux. We find for nitrogen ice layers several km deep, the emerging convection efficiently cools the nitrogen-ice water-ice bedrock interface resulting in temperature differences across the convecting layer of 10-20 K (at most) regardless of layer depth. For grain sizes ranging from 0.01 mm to 5 mm the resulting horizontal size to depth ratios of the emerging convection patterns go from 4:1 up to 6:1, suggesting that the nitrogen ice layer in Sputnik Planum may be anywhere between 3.5 and 8 km deep. Such depths are consistent with Sputnik Planum being a large impact basin (in a relative sense) analogous to Hellas on Mars. In this grain-size range we also find, (i) the calculated cell overturn times are anywhere from 1e4 to 5e5 yrs and, (ii) there is a distinct transition from steady state to time dependent convection.

CT analysis of fat distribution superficial and deep to the Scarpa's fascial layer in the mid and lower abdomen.

PubMed

Harley, O J H; Pickford, M A

2013-04-01

Mismatches in the thickness of subcutaneous fat at the level of the umbilicus and suprapubic region can result in an unsightly bulge and an unfavourable result following standard abdominoplasty. This problem can be avoided by thinning the abdominoplasty flap. This study was carried out to assess the thickness of the subcutaneous fat layer at the level of the umbilicus and the supra-pubic region. Measurements of full thickness fat and the depth of Scarpa's fascia separating superficial and sub-Scarpa fat layers were taken from the CT scans in 69 women; mean age 52 years (range 30-79). The thickness of the skin and abdominal wall fat was an average of 7 mm thicker (max 22 mm; p < 0.05). The thickness of the fat layer superficial to Scarpa's fascia was an average of 19 mm at mid abdomen and 22 mm in the lower abdomen (p < 0.05). The thickness of the fat layer deep to Scarpa's fascia was 14 mm in the mid abdomen and 5 mm in the lower abdomen (p < 0.05). In 55% of patients the difference in thickness of the mid abdominal and lower abdominal fat was greater than 5 mm, a difference that could lead to a noticeable mismatch and therefore an unfavourable outcome. Results of this study suggest that selectively thinning the fat layer deep to Scarpa's fascia would address potential mismatches and preserve the Scarpa's fascia layer in more than 50% of cases, therefore allowing wounds to be closed with an effective deep tension layer. Copyright © 2012 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

Total Mercury and Methylmercury Response in Water, Sediment, and Biota to Destratification of the Great Salt Lake, Utah, United States.

PubMed

Valdes, Carla; Black, Frank J; Stringham, Blair; Collins, Jeffrey N; Goodman, James R; Saxton, Heidi J; Mansfield, Christopher R; Schmidt, Joshua N; Yang, Shu; Johnson, William P

2017-05-02

Measurements of chemical and physical parameters made before and after sealing of culverts in the railroad causeway spanning the Great Salt Lake in late 2013 documented dramatic alterations in the system in response to the elimination of flow between the Great Salt Lake's north and south arms. The flow of denser, more-saline water through the culverts from the north arm (Gunnison Bay) to the south arm (Gilbert Bay) previously drove the perennial stratification of the south arm and the existence of oxic shallow brine and anoxic deep brine layers. Closure of the causeway culverts occurred concurrently with a multiyear drought that resulted in a decrease in the lake elevation and a concomitant increase in top-down erosion of the upper surface of the deep brine layer by wind-forced mixing. The combination of these events resulted in the replacement of the formerly stratified water column in the south arm with one that was vertically homogeneous and oxic. Total mercury concentrations in the deep waters of the south arm decreased by approximately 81% and methylmercury concentrations in deep waters decreased by roughly 86% due to destratification. Methylmercury concentrations decreased by 77% in underlying surficial sediment, whereas there was no change observed in total mercury. The dramatic mercury loss from deep waters and methylmercury loss from underlying sediment in response to causeway sealing provides new understanding of the potential role of the deep brine layer in the accumulation and persistence of methylmercury in the Great Salt Lake. Additional mercury measurements in biota appear to contradict the previously implied connection between elevated methylmercury concentrations in the deep brine layer and elevated mercury in avian species reported prior to causeway sealing.

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling.

PubMed

Mehrshad, Maliheh; Rodriguez-Valera, Francisco; Amoozegar, Mohammad Ali; López-García, Purificación; Ghai, Rohit

2018-03-01

The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat.

PubMed

Borrel, Guillaume; Colombet, Jonathan; Robin, Agnès; Lehours, Anne-Catherine; Prangishvili, David; Sime-Ngando, Télesphore

2012-11-01

Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0-10 cm) could be discriminated from those of the intermediate (11-27 cm) and deep (28-40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth.

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

PubMed Central

Borrel, Guillaume; Colombet, Jonathan; Robin, Agnès; Lehours, Anne-Catherine; Prangishvili, David; Sime-Ngando, Télesphore

2012-01-01

Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0–10 cm) could be discriminated from those of the intermediate (11–27 cm) and deep (28–40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth. PMID:22648129

Segregation of Visual Response Properties in the Mouse Superior Colliculus and Their Modulation during Locomotion

PubMed Central

2017-01-01

The superior colliculus (SC) receives direct input from the retina and integrates it with information about sound, touch, and state of the animal that is relayed from other parts of the brain to initiate specific behavioral outcomes. The superficial SC layers (sSC) contain cells that respond to visual stimuli, whereas the deep SC layers (dSC) contain cells that also respond to auditory and somatosensory stimuli. Here, we used a large-scale silicon probe recording system to examine the visual response properties of SC cells of head-fixed and alert male mice. We found cells with diverse response properties including: (1) orientation/direction-selective (OS/DS) cells with a firing rate that is suppressed by drifting sinusoidal gratings (negative OS/DS cells); (2) suppressed-by-contrast cells; (3) cells with complex-like spatial summation nonlinearity; and (4) cells with Y-like spatial summation nonlinearity. We also found specific response properties that are enriched in different depths of the SC. The sSC is enriched with cells with small RFs, high evoked firing rates (FRs), and sustained temporal responses, whereas the dSC is enriched with the negative OS/DS cells and with cells with large RFs, low evoked FRs, and transient temporal responses. Locomotion modulates the activity of the SC cells both additively and multiplicatively and changes the preferred spatial frequency of some SC cells. These results provide the first description of the negative OS/DS cells and demonstrate that the SC segregates cells with different response properties and that the behavioral state of a mouse affects SC activity. SIGNIFICANCE STATEMENT The superior colliculus (SC) receives visual input from the retina in its superficial layers (sSC) and induces eye/head-orientating movements and innate defensive responses in its deeper layers (dSC). Despite their importance, very little is known about the visual response properties of dSC neurons. Using high-density electrode recordings and novel model-based analysis, we found several novel visual response properties of the SC cells, including encoding of a cell's preferred orientation or direction by suppression of the firing rate. The sSC and the dSC are enriched with cells with different visual response properties. Locomotion modulates the cells in the SC. These findings contribute to our understanding of how the SC processes visual inputs, a critical step in comprehending visually guided behaviors. PMID:28760858

An improved advertising CTR prediction approach based on the fuzzy deep neural network

PubMed Central

Gao, Shu; Li, Mingjiang

2018-01-01

Combining a deep neural network with fuzzy theory, this paper proposes an advertising click-through rate (CTR) prediction approach based on a fuzzy deep neural network (FDNN). In this approach, fuzzy Gaussian-Bernoulli restricted Boltzmann machine (FGBRBM) is first applied to input raw data from advertising datasets. Next, fuzzy restricted Boltzmann machine (FRBM) is used to construct the fuzzy deep belief network (FDBN) with the unsupervised method layer by layer. Finally, fuzzy logistic regression (FLR) is utilized for modeling the CTR. The experimental results show that the proposed FDNN model outperforms several baseline models in terms of both data representation capability and robustness in advertising click log datasets with noise. PMID:29727443

An improved advertising CTR prediction approach based on the fuzzy deep neural network.

PubMed

Jiang, Zilong; Gao, Shu; Li, Mingjiang

2018-01-01

Combining a deep neural network with fuzzy theory, this paper proposes an advertising click-through rate (CTR) prediction approach based on a fuzzy deep neural network (FDNN). In this approach, fuzzy Gaussian-Bernoulli restricted Boltzmann machine (FGBRBM) is first applied to input raw data from advertising datasets. Next, fuzzy restricted Boltzmann machine (FRBM) is used to construct the fuzzy deep belief network (FDBN) with the unsupervised method layer by layer. Finally, fuzzy logistic regression (FLR) is utilized for modeling the CTR. The experimental results show that the proposed FDNN model outperforms several baseline models in terms of both data representation capability and robustness in advertising click log datasets with noise.

Wishart Deep Stacking Network for Fast POLSAR Image Classification.

PubMed

Jiao, Licheng; Liu, Fang

2016-05-11

Inspired by the popular deep learning architecture - Deep Stacking Network (DSN), a specific deep model for polarimetric synthetic aperture radar (POLSAR) image classification is proposed in this paper, which is named as Wishart Deep Stacking Network (W-DSN). First of all, a fast implementation of Wishart distance is achieved by a special linear transformation, which speeds up the classification of POLSAR image and makes it possible to use this polarimetric information in the following Neural Network (NN). Then a single-hidden-layer neural network based on the fast Wishart distance is defined for POLSAR image classification, which is named as Wishart Network (WN) and improves the classification accuracy. Finally, a multi-layer neural network is formed by stacking WNs, which is in fact the proposed deep learning architecture W-DSN for POLSAR image classification and improves the classification accuracy further. In addition, the structure of WN can be expanded in a straightforward way by adding hidden units if necessary, as well as the structure of the W-DSN. As a preliminary exploration on formulating specific deep learning architecture for POLSAR image classification, the proposed methods may establish a simple but clever connection between POLSAR image interpretation and deep learning. The experiment results tested on real POLSAR image show that the fast implementation of Wishart distance is very efficient (a POLSAR image with 768000 pixels can be classified in 0.53s), and both the single-hidden-layer architecture WN and the deep learning architecture W-DSN for POLSAR image classification perform well and work efficiently.

Quantifying the influence of deep soil moisture on ecosystem albedo: The role of vegetation

NASA Astrophysics Data System (ADS)

Sanchez-Mejia, Zulia Mayari; Papuga, Shirley Anne; Swetish, Jessica Blaine; van Leeuwen, Willem Jan Dirk; Szutu, Daphne; Hartfield, Kyle

2014-05-01

As changes in precipitation dynamics continue to alter the water availability in dryland ecosystems, understanding the feedbacks between the vegetation and the hydrologic cycle and their influence on the climate system is critically important. We designed a field campaign to examine the influence of two-layer soil moisture control on bare and canopy albedo dynamics in a semiarid shrubland ecosystem. We conducted this campaign during 2011 and 2012 within the tower footprint of the Santa Rita Creosote Ameriflux site. Albedo field measurements fell into one of four Cases within a two-layer soil moisture framework based on permutations of whether the shallow and deep soil layers were wet or dry. Using these Cases, we identified differences in how shallow and deep soil moisture influence canopy and bare albedo. Then, by varying the number of canopy and bare patches within a gridded framework, we explore the influence of vegetation and soil moisture on ecosystem albedo. Our results highlight the importance of deep soil moisture in land surface-atmosphere interactions through its influence on aboveground vegetation characteristics. For instance, we show how green-up of the vegetation is triggered by deep soil moisture, and link deep soil moisture to a decrease in canopy albedo. Understanding relationships between vegetation and deep soil moisture will provide important insights into feedbacks between the hydrologic cycle and the climate system.

An Advanced Deep Learning Approach for Ki-67 Stained Hotspot Detection and Proliferation Rate Scoring for Prognostic Evaluation of Breast Cancer.

PubMed

Saha, Monjoy; Chakraborty, Chandan; Arun, Indu; Ahmed, Rosina; Chatterjee, Sanjoy

2017-06-12

Being a non-histone protein, Ki-67 is one of the essential biomarkers for the immunohistochemical assessment of proliferation rate in breast cancer screening and grading. The Ki-67 signature is always sensitive to radiotherapy and chemotherapy. Due to random morphological, color and intensity variations of cell nuclei (immunopositive and immunonegative), manual/subjective assessment of Ki-67 scoring is error-prone and time-consuming. Hence, several machine learning approaches have been reported; nevertheless, none of them had worked on deep learning based hotspots detection and proliferation scoring. In this article, we suggest an advanced deep learning model for computerized recognition of candidate hotspots and subsequent proliferation rate scoring by quantifying Ki-67 appearance in breast cancer immunohistochemical images. Unlike existing Ki-67 scoring techniques, our methodology uses Gamma mixture model (GMM) with Expectation-Maximization for seed point detection and patch selection and deep learning, comprises with decision layer, for hotspots detection and proliferation scoring. Experimental results provide 93% precision, 0.88% recall and 0.91% F-score value. The model performance has also been compared with the pathologists' manual annotations and recently published articles. In future, the proposed deep learning framework will be highly reliable and beneficial to the junior and senior pathologists for fast and efficient Ki-67 scoring.

A Study of Complex Deep Learning Networks on High Performance, Neuromorphic, and Quantum Computers

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

Potok, Thomas E; Schuman, Catherine D; Young, Steven R

Current Deep Learning models use highly optimized convolutional neural networks (CNN) trained on large graphical processing units (GPU)-based computers with a fairly simple layered network topology, i.e., highly connected layers, without intra-layer connections. Complex topologies have been proposed, but are intractable to train on current systems. Building the topologies of the deep learning network requires hand tuning, and implementing the network in hardware is expensive in both cost and power. In this paper, we evaluate deep learning models using three different computing architectures to address these problems: quantum computing to train complex topologies, high performance computing (HPC) to automatically determinemore » network topology, and neuromorphic computing for a low-power hardware implementation. Due to input size limitations of current quantum computers we use the MNIST dataset for our evaluation. The results show the possibility of using the three architectures in tandem to explore complex deep learning networks that are untrainable using a von Neumann architecture. We show that a quantum computer can find high quality values of intra-layer connections and weights, while yielding a tractable time result as the complexity of the network increases; a high performance computer can find optimal layer-based topologies; and a neuromorphic computer can represent the complex topology and weights derived from the other architectures in low power memristive hardware. This represents a new capability that is not feasible with current von Neumann architecture. It potentially enables the ability to solve very complicated problems unsolvable with current computing technologies.« less

Cartilage canals in the distal intermediate ridge of the tibia of fetuses and foals are surrounded by different types of collagen.

PubMed

Hellings, Ingunn Risnes; Dolvik, Nils Ivar; Ekman, Stina; Olstad, Kristin

2017-10-01

Some epiphyseal growth cartilage canals are surrounded by a ring of hypereosinophilic matrix consisting of collagen type I. Absence of the collagen type I ring may predispose canal vessels to failure and osteochondrosis, which can lead to fragments in joints (osteochondrosis dissecans). It is not known whether the ring develops in response to programming or biomechanical force. The distribution that may reveal the function of the ring has only been described in the distal femur of a limited number of foals. It is also not known which cells are responsible for producing the collagen ring. The aims of the current study were to examine fetuses and foals to infer whether the ring forms in response to biomechanical force or programming, to describe distribution and to investigate which cell type produces the ring. The material consisted of 46 fetuses and foals from 293 days of gestation to 142 days old, of both sexes and different breeds, divided into three groups, designated the naïve group up to and including the day of birth, the adapting group from 2 days up to and including 14 days old, and the loaded group from 15 days and older. The distal tibia was sawn into parasagittal slabs and the cranial half of the central slab from the intermediate ridge was examined by light microscopy and immunohistochemical staining for collagen type I. Presence, completeness and location of the collagen ring was compared, as was the quantity of perivascular mesenchymal cells. An eosinophilic ring present on HE-stained sections was seen in every single fetus and foal examined, which corresponded to collagen type I in immunostained sections. A higher proportion of cartilage canals were surrounded by an eosinophilic ring in the naïve and adapting groups at 73 and 76%, respectively, compared with the loaded group at 51%. When considering only patent canals, the proportion of canals with an eosinophilic ring was higher in the adapting and loaded than the naïve group of foals. The ring was present around 90 and 81% of patent canals in the deep and middle layers, respectively, compared with 58% in the superficial layer, and the ring was more often complete around deep compared with superficial canals. The ring was absent or partial around chondrifying canals. When an eosinophilic ring was present around patent canals, it was more common for the canal to contain one or more layers of perivascular mesenchymal cells rather than few to no layers. It was also more common for the collagen ring to be more complete around canals that contained many as opposed to few mesenchymal cells. In conclusion, the proportion of cartilage canals that had an eosinophilic ring was similar in all three groups of fetuses and foals, indicating that the presence of the collagen ring was mostly programmed, although some adaptation was evident. The ring was more often present around deep, compared with superficial canals, indicating a role in preparation for ossification. The collagen ring appeared to be produced by perivascular mesenchymal cells. © 2017 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.

Hydrophilic Conjugated Polymers with Large Bandgaps and Deep-Lying HOMO Levels as an Efficient Cathode Interlayer in Inverted Polymer Solar Cells.

PubMed

Kan, Yuanyuan; Zhu, Yongxiang; Liu, Zhulin; Zhang, Lianjie; Chen, Junwu; Cao, Yong

2015-08-01

Two hydrophilic conjugated polymers, PmP-NOH and PmP36F-NOH, with polar diethanol-amine on the side chains and main chain structures of poly(meta-phenylene) and poly(meta-phenylene-alt-3,6-fluorene), respectively, are successfully synthesized. The films of PmP-NOH and PmP36F-NOH show absorption edges at 340 and 343 nm, respectively. The calculated optical bandgaps of the two polymers are 3.65 and 3.62 eV, respectively, the largest ones so far reported for hydrophilic conjugated polymers. PmP-NOH and PmP36F-NOH also possess deep-lying highest occupied molecular orbital levels of -6.19 and -6.15 eV, respectively. Inserting PmP-NOH and PmP36F-NOH as a cathode interlayer in inverted polymer solar cells with a PTB7/PC71 BM blend as the active layer, high power conversion efficiencies of 8.58% and 8.33%, respectively, are achieved, demonstrating that the two hydrophilic polymers are excellent interlayers for efficient inverted polymer solar cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stability of organic carbon in deep soil layers controlled by fresh carbon supply.

PubMed

Fontaine, Sébastien; Barot, Sébastien; Barré, Pierre; Bdioui, Nadia; Mary, Bruno; Rumpel, Cornelia

2007-11-08

The world's soils store more carbon than is present in biomass and in the atmosphere. Little is known, however, about the factors controlling the stability of soil organic carbon stocks and the response of the soil carbon pool to climate change remains uncertain. We investigated the stability of carbon in deep soil layers in one soil profile by combining physical and chemical characterization of organic carbon, soil incubations and radiocarbon dating. Here we show that the supply of fresh plant-derived carbon to the subsoil (0.6-0.8 m depth) stimulated the microbial mineralization of 2,567 +/- 226-year-old carbon. Our results support the previously suggested idea that in the absence of fresh organic carbon, an essential source of energy for soil microbes, the stability of organic carbon in deep soil layers is maintained. We propose that a lack of supply of fresh carbon may prevent the decomposition of the organic carbon pool in deep soil layers in response to future changes in temperature. Any change in land use and agricultural practice that increases the distribution of fresh carbon along the soil profile could however stimulate the loss of ancient buried carbon.

Microfluidic Chips Controlled with Elastomeric Microvalve Arrays

PubMed Central

Li, Nianzhen; Sip, Chris; Folch, Albert

2007-01-01

Miniaturized microfluidic systems provide simple and effective solutions for low-cost point-of-care diagnostics and high-throughput biomedical assays. Robust flow control and precise fluidic volumes are two critical requirements for these applications. We have developed microfluidic chips featuring elastomeric polydimethylsiloxane (PDMS) microvalve arrays that: 1) need no extra energy source to close the fluidic path, hence the loaded device is highly portable; and 2) allow for microfabricating deep (up to 1 mm) channels with vertical sidewalls and resulting in very precise features. The PDMS microvalves-based devices consist of three layers: a fluidic layer containing fluidic paths and microchambers of various sizes, a control layer containing the microchannels necessary to actuate the fluidic path with microvalves, and a middle thin PDMS membrane that is bound to the control layer. Fluidic layer and control layers are made by replica molding of PDMS from SU-8 photoresist masters, and the thin PDMS membrane is made by spinning PDMS at specified heights. The control layer is bonded to the thin PDMS membrane after oxygen activation of both, and then assembled with the fluidic layer. The microvalves are closed at rest and can be opened by applying negative pressure (e.g., house vacuum). Microvalve closure and opening are automated via solenoid valves controlled by computer software. Here, we demonstrate two microvalve-based microfluidic chips for two different applications. The first chip allows for storing and mixing precise sub-nanoliter volumes of aqueous solutions at various mixing ratios. The second chip allows for computer-controlled perfusion of microfluidic cell cultures. The devices are easy to fabricate and simple to control. Due to the biocompatibility of PDMS, these microchips could have broad applications in miniaturized diagnostic assays as well as basic cell biology studies. PMID:18989408

Predicting The Intrusion Layer From Deep Ocean Oil Spills

NASA Astrophysics Data System (ADS)

Wang, Dayang; Chow, Aaron; Adams, E. Eric

2015-11-01

Oil spills from deep ocean blowout events motivate our study of multiphase plumes in a water column. Key to understanding the long-term fate of these plumes is the ability to predict the depth and persistence of intrusion layers. While intrusion layers from multiphase plumes have been studied under stagnant conditions, their behavior in the presence of crossflow, especially in mild crossflow, remains poorly understood. The classical classification of plume behavior identifies two regimes: crossflow-dominant and stratification-dominant--but it does not account for the interplay between the two effects, leaving the transition region unexplored. We conduct laboratory tank experiments to investigate the behavior of intrusion layers under the simultaneous action of crossflow and stratification. Our experiments use an inverted frame of reference, using glass beads with a range of sizes to simulate oil droplets. We find that crossflow creates enhanced mixing, which in turn leads to a shallower intrusion layer of the released fluid (correspondingly, a deeper layer in the case of a deep ocean blowout). We develop a mathematical formulation that extends previous models to account for crossflow effects, and use field observations to validate the analytical and experimental findings.

Developmental Markers Expressed in Neocortical Layers Are Differentially Exhibited in Olfactory Cortex

PubMed Central

Brunjes, Peter C.; Osterberg, Stephen K.

2015-01-01

Neurons in the cerebral cortex stratify on the basis of their time of origin, axonal terminations and the molecular identities assigned during early development. Olfactory cortices share many feature with the neocortex, including clear lamination and similar cell types. The present study demonstrates that the markers differentially expressed in the projection neurons of the cerebral cortex are also found in olfactory areas. Three of the four regions examined (pars principalis of the anterior olfactory nucleus: AONpP, anterior and posterior piriform cortices: APC, PPC, and the olfactory tubercle) expressed transcription factors found in deep or superficial neurons in the developing neocortex, though large differences were found between areas. For example, while the AONpP, APC and PPC all broadly expressed the deep cortical marker CTIP2, NOR1 (NR4a3) levels were higher in AONpP and DAARP-32 was more prevalent in the APC and PPC. Similar findings were encountered for superficial cortical markers: all three regions broadly expressed CUX1, but CART was only observed in the APC and PPC. Furthermore, regional variations were observed even within single structures (e.g., NOR1 was found primarily in in the dorsal region of AONpP and CART expression was observed in a discrete band in the middle of layer 2 of both the APC and PPC). Experiments using the mitotic marker EDU verified that the olfactory cortices and neocortex share similar patterns of neuronal production: olfactory cells that express markers found in the deep neocortex are produced earlier than those that express superficial makers. Projection neurons were filled by retrograde tracers injected into the olfactory bulb to see if olfactory neurons with deep and superficial markers had different axonal targets. Unlike the cerebral cortex, no specificity was observed: neurons with each of the transcription factors examined were found to be labelled. Together the results indicate that olfactory cortices are complex: they differ from each other and each is formed from a variable mosaic of neurons. The results suggest that the olfactory cortices are not merely a remnant architype of the primordial forebrain but varied and independent regions. PMID:26407299

Concentrators Enhance Solar Power Systems

NASA Technical Reports Server (NTRS)

2013-01-01

"Right now, solar electric propulsion is being looked at very seriously," says Michael Piszczor, chief of the photovoltaic and power technologies branch at Glen Research Center. The reason, he explains, originates with a unique NASA mission from the late 1990s. In 1998, the Deep Space 1 spacecraft launched from Kennedy Space Center to test a dozen different space technologies, including SCARLET, or the Solar Concentrator Array with Refractive Linear Element Technology. As a solar array that focused sunlight on a smaller solar cell to generate electric power, SCARLET not only powered Deep Space 1 s instruments but also powered its ion engine, which propelled the spacecraft throughout its journey. Deep Space 1 was the first spacecraft powered by a refractive concentrator design like SCARLET, and also utilized multi-junction solar cells, or cells made of multiple layers of different materials. For the duration of its 38-month mission, SCARLET performed flawlessly, even as Deep Space 1 flew by Comet Borrelly and Asteroid Braille. "Everyone remembers the ion engine on Deep Space 1, but they tend to forget that the SCARLET array powered it," says Piszczor. "Not only did both technologies work as designed, but the synergy between the two, solar power and propulsion together, is really the important aspect of this technology demonstration mission. It was the first successful use of solar electric propulsion for primary propulsion." More than a decade later, NASA is keenly interested in using solar electric propulsion (SEP) for future space missions. A key issue is cost, and SEP has the potential to substantially reduce cost compared to conventional chemical propulsion technology. "SEP allows you to use spacecraft that are smaller, lighter, and less costly," says Piszczor. "Even though it might take longer to get somewhere using SEP, if you are willing to trade time for cost and smaller vehicles, it s a good trade." Potentially, SEP could be used on future science missions in orbit around the Earth or Moon, to planets or asteroids, on deep space science missions, and even on exploration missions. In fact, electric propulsion is already being used on Earth-orbiting satellites for positioning.

A data-driven multi-model methodology with deep feature selection for short-term wind forecasting

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

Feng, Cong; Cui, Mingjian; Hodge, Bri-Mathias

With the growing wind penetration into the power system worldwide, improving wind power forecasting accuracy is becoming increasingly important to ensure continued economic and reliable power system operations. In this paper, a data-driven multi-model wind forecasting methodology is developed with a two-layer ensemble machine learning technique. The first layer is composed of multiple machine learning models that generate individual forecasts. A deep feature selection framework is developed to determine the most suitable inputs to the first layer machine learning models. Then, a blending algorithm is applied in the second layer to create an ensemble of the forecasts produced by firstmore » layer models and generate both deterministic and probabilistic forecasts. This two-layer model seeks to utilize the statistically different characteristics of each machine learning algorithm. A number of machine learning algorithms are selected and compared in both layers. This developed multi-model wind forecasting methodology is compared to several benchmarks. The effectiveness of the proposed methodology is evaluated to provide 1-hour-ahead wind speed forecasting at seven locations of the Surface Radiation network. Numerical results show that comparing to the single-algorithm models, the developed multi-model framework with deep feature selection procedure has improved the forecasting accuracy by up to 30%.« less

RETINAL DEEP CAPILLARY ISCHEMIA ASSOCIATED WITH AN OCCLUDED CONGENITAL RETINAL MACROVESSEL.

PubMed

Hasegawa, Taiji; Ogata, Nahoko

2017-01-01

To report the case of a patient with an occluded congenital retinal macrovessel accompanied by retinal deep capillary ischemia. A 38-year-old woman presented with a 2-day history of a paracentral scotoma of her right eye. Fundus photograph showed a dilated congenital retinal macrovessel with arteriovenous anastomosis, an intravascular white region indicating the thrombus at arteriovenous anastomotic region, and an area of retinal whitening temporal to the fovea. The spectral domain optical coherence tomography images through the area of retinal whitening showed a thickening and highly reflectivity at the level of the inner nuclear layer, which is likely due to the deep capillary ischemia. After 6 weeks, spectral domain optical coherence tomography images through the same area demonstrated a thinning and atrophy of only the inner nuclear layer, and the patient's paracentral scotoma persisted. Acute capillary hemodynamic changes caused deep capillary ischemia. The spectral domain optical coherence tomography showed a highly reflective lesion at the level of the inner nuclear layer in the acute phase.

Influences of drizzle on stratocumulus cloudiness and organization [Influences of drizzle on cloudiness and stratocumulus organization

DOE PAGES

Zhou, Xiaoli; Heus, Thijs; Kollias, Pavlos

2017-06-06

Large-eddy simulations are used to study the influence of drizzle on stratocumulus organization, based on measurements made as part of the Second Dynamics and Chemistry of the Marine Stratocumulus field study-II. Cloud droplet number concentration ( N c) is prescribed and considered as the proxy for different aerosol loadings. Our study shows that the amount of cloudiness does not decrease linearly with precipitation rate. An N c threshold is observed below which the removal of cloud water via precipitation efficiently reduces cloud depth, allowing evaporation to become efficient and quickly remove the remaining thin clouds, facilitating a fast transition frommore » closed cells to open cells. Using Fourier analysis, stratocumulus length scales are found to increase with drizzle rates. Raindrop evaporation below 300 m lowers the cloud bases and amplifies moisture variances in the subcloud layer, while it does not alter the horizontal scales in the cloud layer, suggesting that moist cold pool dynamic forcings are not essential for mesoscale organization of stratocumulus. Furthermore, the cloud scales are greatly increased when the boundary layer is too deep to maintain well mixed.« less

Influences of drizzle on stratocumulus cloudiness and organization [Influences of drizzle on cloudiness and stratocumulus organization

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

Zhou, Xiaoli; Heus, Thijs; Kollias, Pavlos

Large-eddy simulations are used to study the influence of drizzle on stratocumulus organization, based on measurements made as part of the Second Dynamics and Chemistry of the Marine Stratocumulus field study-II. Cloud droplet number concentration ( N c) is prescribed and considered as the proxy for different aerosol loadings. Our study shows that the amount of cloudiness does not decrease linearly with precipitation rate. An N c threshold is observed below which the removal of cloud water via precipitation efficiently reduces cloud depth, allowing evaporation to become efficient and quickly remove the remaining thin clouds, facilitating a fast transition frommore » closed cells to open cells. Using Fourier analysis, stratocumulus length scales are found to increase with drizzle rates. Raindrop evaporation below 300 m lowers the cloud bases and amplifies moisture variances in the subcloud layer, while it does not alter the horizontal scales in the cloud layer, suggesting that moist cold pool dynamic forcings are not essential for mesoscale organization of stratocumulus. Furthermore, the cloud scales are greatly increased when the boundary layer is too deep to maintain well mixed.« less

Can shallow-layer measurements at a single location be used to predict deep soil water storage at the slope scale?

NASA Astrophysics Data System (ADS)

Gao, Lei; Lv, Yujuan; Wang, Dongdong; Tahir, Muhammad; Peng, Xinhua

2015-12-01

Knowing the amount of soil water storage (SWS) in agricultural soil profiles is important for understanding physical, chemical, and biological soil processes. However, measuring the SWS in deep soil layers is more expensive and time consuming than in shallower layers. Whether deep SWS can be predicted from shallow-layer measurements through temporal stability analysis (TSA) remains unclear. To address this issue, the soil water content was measured at depths of 0-1.6 m (0.2-m depth intervals) at 79 locations along an agricultural slope on 28 occasions between July 2013 and October 2014. SWSs values were then calculated for the 0-0.4, 0.4-0.8, 0.8-1.2, 1.2-1.6, and 0-1.6 m soil layers. The SWS exhibited strong temporal stability, with mean Spearman's ranking coefficients (rs) of 0.83, 0.92, 0.83, and 0.79 in the 0-0.4, 0.4-0.8, 0.8-1.2, and 1.2-1.6 m soil layers, respectively. As expected, the most temporally stable location (MTSL1) accurately predicted the average SWS of the corresponding soil layer, and the values of absolute bias relative to mean (ARB) were lower than 3% for all of the investigated soil layers. Using TSA, deep-layer SWS information could be predicted using a single-location measurement in the 0-0.4 m soil layer. The mean ARB values between the observed and predicted mean SWS values were 2.9%, 4.3%, 3.9%, and 2.7% in the 0.4-0.8, 0.8-1.2, 1.2-1.6, and 0-1.6 m soil layers, respectively. The prediction accuracy of the spatial distribution generally decreased with increasing depth, with linear determination coefficients (R2) of 0.93, 0.79, 0.72, and 0.84 for the four soil layers, respectively. The proposed method could further expand the application of the temporal stability technique in the estimation of SWS.

Archive of bacterial community in anhydrite crystals from a deep-sea basin provides evidence of past oil-spilling in a benthic environment in the Red Sea

NASA Astrophysics Data System (ADS)

Wang, Yong; Li, Tie Gang; Wang, Meng Ying; Lai, Qi Liang; Li, Jiang Tao; Gao, Zhao Ming; Shao, Zong Ze; Qian, Pei-Yuan

2016-11-01

In deep-sea sediment, the microbes present in anhydrite crystals are potential markers of the past environment. In the Atlantis II Deep, anhydrite veins were produced by mild mixture of calcium-rich hydrothermal solutions and sulfate in the bottom water, which had probably preserved microbial inhabitants in the past seafloor of the Red Sea. In this study, this hypothesis was tested by analyzing the metagenome of an anhydrite crystal sample from the Atlantis II Deep. The estimated age of the anhydrite layer was between 750 and 770 years, which might span the event of hydrothermal eruption into the benthic floor. The 16S/18S rRNA genes in the metagenome were assigned to bacteria, archaea, fungi and even invertebrate species. The dominant species in the crystals was an oil-degrading Alcanivorax borkumensis bacterium, which was not detected in the adjacent sediment layer. Fluorescence microscopy using 16S rRNA and marker gene probes revealed intact cells of the Alcanivorax bacterium in the crystals. A draft genome of A. borkumensis was binned from the metagenome. It contained all functional genes for alkane utilization and the reduction of nitrogen oxides. Moreover, the metagenomes of the anhydrites and control sediment contained aromatic degradation pathways, which were mostly derived from Ochrobactrum sp. Altogether, these results indicate an oxic, oil-spilling benthic environment in the Atlantis II basin of the Red Sea in approximately the 14th century. The original microbial inhabitants probably underwent a dramatic selection process via drastic environmental changes following the formation of an overlying anoxic brine pool in the basin due to hydrothermal activities.

Minority Carrier Electron Traps in CZTSSe Solar Cells Characterized by DLTS and DLOS

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

Kheraj, V.; Lund, E. A.; Caruso, A. E.

2016-11-21

We report observations of minority carrier interactions with deep levels in 6-8% efficient Cu2ZnSn(S, Se)4 (CZTSSe) devices using conventional and minority deep level transient spectroscopy (DLTS) and deep level optical spectroscopy (DLOS). Directly observing defect interactions with minority carriers is critical to understanding the recombination impact of deep levels. In devices with Cu2ZnSn(S, Se)4 nanoparticle ink absorber layers we identify a mid-gap state capturing and emitting minority electrons. It is 590+/-50 meV from the conduction band mobility edge, has a concentration near 1015/cm3, and has an apparent electron capture cross section ~10-14 cm2. We conclude that, while energetically positioned nearly-ideallymore » to be a recombination center, these defects instead act as electron traps because of a smaller hole cross-section. In CZTSe devices produced using coevaporation, we used minority carrier DLTS on traditional samples as well as ones with transparent Ohmic back contacts. These experiments demonstrate methods for unambiguously probing minority carrier/defect interactions in solar cells in order to establish direct links between defect energy level observations and minority carrier lifetimes. Furthermore, we demonstrate the use of steady-state device simulation to aid in the interpretation of DLTS results e.g. to put bounds on the complimentary carrier cross section even in the absence its direct measurement. This combined experimental and theoretical approach establishes rigorous bounds on the impact on carrier lifetime and Voc of defects observed with DLTS as opposed to, for example, assuming that all deep states act as strong recombination centers.« less

Microscopic medical image classification framework via deep learning and shearlet transform.

PubMed

Rezaeilouyeh, Hadi; Mollahosseini, Ali; Mahoor, Mohammad H

2016-10-01

Cancer is the second leading cause of death in US after cardiovascular disease. Image-based computer-aided diagnosis can assist physicians to efficiently diagnose cancers in early stages. Existing computer-aided algorithms use hand-crafted features such as wavelet coefficients, co-occurrence matrix features, and recently, histogram of shearlet coefficients for classification of cancerous tissues and cells in images. These hand-crafted features often lack generalizability since every cancerous tissue and cell has a specific texture, structure, and shape. An alternative approach is to use convolutional neural networks (CNNs) to learn the most appropriate feature abstractions directly from the data and handle the limitations of hand-crafted features. A framework for breast cancer detection and prostate Gleason grading using CNN trained on images along with the magnitude and phase of shearlet coefficients is presented. Particularly, we apply shearlet transform on images and extract the magnitude and phase of shearlet coefficients. Then we feed shearlet features along with the original images to our CNN consisting of multiple layers of convolution, max pooling, and fully connected layers. Our experiments show that using the magnitude and phase of shearlet coefficients as extra information to the network can improve the accuracy of detection and generalize better compared to the state-of-the-art methods that rely on hand-crafted features. This study expands the application of deep neural networks into the field of medical image analysis, which is a difficult domain considering the limited medical data available for such analysis.

Time-response of cultured deep-sea benthic foraminifera to different algal diets

NASA Astrophysics Data System (ADS)

Heinz, P.; Hemleben, Ch; Kitazato, H.

2002-03-01

The vertical distribution of benthic foraminifera in the surface sediment is influenced by environmental factors, mainly by food and oxygen supply. An experiment of three different time series was performed to investigate the response of deep-sea benthic foraminifera to simulated phytodetritus pulses under stable oxygen concentrations. Each series was fed constantly with one distinct algal species in equivalent amounts. The temporal reactions of the benthic foraminifera with regard to the vertical distribution in the sediment, the total number, and the species composition were observed and compared within the three series. Additionally, oxygen contents and bacterial cell numbers were measured to ensure that these factors were invariable and did not influence foraminiferal communities. The addition of algae leads to higher population densities 21 days after food was added. Higher numbers of individuals were probably caused by higher organic levels, which in turn induced reproduction. A stronger response is found after feeding with Amphiprora sp. and Pyramimonas sp., compared to Dunaliella tertiolecta. At a constant high oxygen supply, no migration to upper layers was observed after food addition, and more individuals were found in deeper layers. The laboratory results thus agree with the predictions of the TROX-model. An epifaunal microhabitat preference was shown for Adercotryma glomerata. Hippocrepina sp. was spread over the entire sediment depth with a shallow infaunal maximum. Melonis barleeanum preferred a deeper infaunal habitat. Bacterial cell concentrations were stable during the laboratory experiments and showed no significant response to higher organic fluxes.

Siphonophores and the Deep Scattering Layer.

PubMed

Barham, E G

1963-05-17

Bathyscaphe dives in the San Diego Trough have revealed a close spatial relation between siphonophores and the deep scattering layer as recorded by precision depth recording echo-sounders. Measurements of gas bubbles within the flotation structures of Nanomia bijuga captured in a closing net in an ascended scattering layer indicate that these are very close to the resonant size for 12-kcy/sec sound. Because such organisms are capable of making prolonged vertical migrations, and are widespread geographically, they are very probably the major cause of stratified zones of scattering throughout the oceans of the world.

The Tlx gene regulates the timing of neurogenesis in the cortex.

PubMed

Roy, Kristine; Kuznicki, Kathleen; Wu, Qiang; Sun, Zhuoxin; Bock, Dagmar; Schutz, Gunther; Vranich, Nancy; Monaghan, A Paula

2004-09-22

The tailless (tlx) gene is a forebrain-restricted transcription factor. Tlx mutant animals exhibit a reduction in the size of the cerebral hemispheres and associated structures (Monaghan et al., 1997). Superficial cortical layers are specifically reduced, whereas deep layers are relatively unaltered (Land and Monaghan, 2003). To determine whether the adult laminar phenotype has a developmental etiology and whether it is associated with a change in proliferation/differentiation decisions, we examined the cell cycle and neurogenesis in the embryonic cortex. We found that there is a temporal and regional requirement for the Tlx protein in progenitor cells (PCs). Neurons prematurely differentiate at all rostrocaudal levels up to mid-neurogenesis in mutant animals. Heterozygote animals have an intermediate phenotype indicating there is a threshold requirement for Tlx in early cortical neurogenesis. Our studies indicate that PCs in the ventricular zone are sensitive to loss of Tlx in caudal regions only; however, PCs in the subventricular zone are altered at all rostrocaudal levels in tlx-deficient animals. Furthermore, we found that the cell cycle is shorter from embryonic day 9.5 in tlx-/- embryos. At mid-neurogenesis, the PC population becomes depleted, and late PCs have a longer cell cycle in tlx-deficient animals. Consequently, later generated structures, such as upper cortical layers, the dentate gyrus, and the olfactory bulbs, are severely reduced. These studies indicate that tlx is an essential intrinsic regulator in the decision to proliferate or differentiate in the developing forebrain.

The Tlx Gene Regulates the Timing of Neurogenesis in the Cortex

PubMed Central

Roy, Kristine; Kuznicki, Kathleen; Wu, Qiang; Sun, Zhuoxin; Bock, Dagmar; Schutz, Gunther; Vranich, Nancy; Monaghan, A. Paula

2009-01-01

The tailless (tlx) gene is a forebrain-restricted transcription factor. Tlx mutant animals exhibit a reduction in the size of the cerebral hemispheres and associated structures (Monaghan et al., 1997). Superficial cortical layers are specifically reduced, whereas deep layers are relatively unaltered (Land and Monaghan, 2003). To determine whether the adult laminar phenotype has a developmental etiology and whether it is associated with a change in proliferation/differentiation decisions, we examined the cell cycle and neurogenesis in the embryonic cortex. We found that there is a temporal and regional requirement for the Tlx protein in progenitor cells (PCs). Neurons prematurely differentiate at all rostrocaudal levels up to mid-neurogenesis in mutant animals. Heterozygote animals have an intermediate phenotype indicating there is a threshold requirement for Tlx in early cortical neurogenesis. Our studies indicate that PCs in the ventricular zone are sensitive to loss of Tlx in caudal regions only; however, PCs in the subventricular zone are altered at all rostrocaudal levels in tlx-deficient animals. Furthermore, we found that the cell cycle is shorter from embryonic day 9.5 in tlx−/− embryos. At mid-neurogenesis, the PC population becomes depleted, and late PCs have a longer cell cycle in tlx-deficient animals. Consequently, later generated structures, such as upper cortical layers, the dentate gyrus, and the olfactory bulbs, are severely reduced. These studies indicate that tlx is an essential intrinsic regulator in the decision to proliferate or differentiate in the developing forebrain. PMID:15385616

Controlled electrodeposition of Cu-Ga from a deep eutectic solvent for low cost fabrication of CuGaSe2 thin film solar cells.

PubMed

Steichen, Marc; Thomassey, Matthieu; Siebentritt, Susanne; Dale, Phillip J

2011-03-14

The electrochemical deposition of Ga and Cu-Ga alloys from the deep eutectic solvent choline chloride/urea (Reline) is investigated to prepare CuGaSe(2) (CGS) semiconductors for their use in thin film solar cells. Ga electrodeposition is difficult from aqueous solution due to its low standard potential and the interfering hydrogen evolution reaction (HER). Ionic liquid electrolytes offer a better thermal stability and larger potential window and thus eliminate the interference of solvent breakdown reactions during Ga deposition. We demonstrate that metallic Ga can be electrodeposited from Reline without HER interference with high plating efficiency on Mo and Cu electrodes. A new low cost synthetic route for the preparation of CuGaSe(2) absorber thin films is presented and involves the one-step electrodeposition of Cu-Ga precursors from Reline followed by thermal annealing. Rotating disk electrode (RDE) cyclic voltammetry (CV) is used in combination with viscosity measurements to determine the diffusion coefficients of gallium and copper ions in Reline. The composition of the codeposited Cu-Ga precursor layers can be controlled to form Cu/Ga thin films with precise stoichiometry, which is important for achieving good optoelectronic properties of the final CuGaSe(2) absorbers. The morphology, the chemical composition and the crystal structure of the deposited thin films are analysed by scanning electron microscopy/energy dispersive X-ray spectroscopy (SEM/EDX) and X-ray diffraction (XRD). Annealing of the Cu-Ga films in a selenium atmosphere allowed the formation of high quality CuGaSe(2) absorber layers. Completed CGS solar cells achieved a 4.1% total area power conversion efficiency.

How was the deep scattering layers (DSLs) influenced by the Deepwater Horizon Spill? - Evidences from 10-year NTL oil/gas ADCP backscattering data collected at the spill site

NASA Astrophysics Data System (ADS)

Wang, Z.; DiMarco, S. F.; Socolofsky, S. A.

2016-02-01

There are suspicions that the 2010 DWH oil spill might have affected the biomass in the deep scattering layers (DSLs), at least during the period in which the spill was active and oil dispersants were used. The acoustic backscattering intensity (ABI) data from acoustic Doppler current profilers (ADCPs) have been shown to detect and monitor the spatial and temporal evolution of DSLs in many oceans. Since 2005 with the issue of a Notice of Lessees and Operators (NTL), namely, NTL No. 2005-G5, large amounts of continuous ADCP data have been collected by oil/gas companies in the Northern Gulf at more than 100 stations and made publically available via the National Data Buoyancy Center (NDBC) website. NTL ADCPs data have also been collected prior to, during and after the DWH spill at the spill site. The ADCP with station # 42872 was mounted on the DWH rig and collected ABI data from 2005 until the rig sank in April 2010. ADCPs with station # 42916 and 42868 were then moved into the spill region and collected ABI data during and after the spill. The deep scattering layers were well resolved by those 38 kHz with vertical range of 1000m. The SSL provides key food for many large sea-animals, including whales, dolphins, billfishes and giant tunas and therefore have important roles in the ecosystem of the deep Gulf. By carefully applying calibrations and corrections, the ABI data can be converted to biologically meaningful mean volume backscattering strength (MVBS) and areal backscattering strength (ABS). This is an effective and powerful way to study the pelagic communality dynamics in the deep scattering layers and to investigate greater details that were previously inaccessible. Utilizing the NTL data collected during the past 10 years around the DWH site, we investigate the spill influence on deep scattering layers by comparing the biomass pre- and post BP spill and comparing biomass variations in areas with and without oil contamination. Preliminary results have shown that there is a clear decrease trend of relative biomass in the deep scattering layer in 2010 after the spill. We also find extremely dense scattering patches at the depth of DSLs, which appear only during the spill and are likely formed by spill materials. Statistical analysis on the layer depth, intensity, and thickness and their variations over time are also investigated.

Fast convergence of learning requires plasticity between inferior olive and deep cerebellar nuclei in a manipulation task: a closed-loop robotic simulation

PubMed Central

Luque, Niceto R.; Garrido, Jesús A.; Carrillo, Richard R.; D'Angelo, Egidio; Ros, Eduardo

2014-01-01

The cerebellum is known to play a critical role in learning relevant patterns of activity for adaptive motor control, but the underlying network mechanisms are only partly understood. The classical long-term synaptic plasticity between parallel fibers (PFs) and Purkinje cells (PCs), which is driven by the inferior olive (IO), can only account for limited aspects of learning. Recently, the role of additional forms of plasticity in the granular layer, molecular layer and deep cerebellar nuclei (DCN) has been considered. In particular, learning at DCN synapses allows for generalization, but convergence to a stable state requires hundreds of repetitions. In this paper we have explored the putative role of the IO-DCN connection by endowing it with adaptable weights and exploring its implications in a closed-loop robotic manipulation task. Our results show that IO-DCN plasticity accelerates convergence of learning by up to two orders of magnitude without conflicting with the generalization properties conferred by DCN plasticity. Thus, this model suggests that multiple distributed learning mechanisms provide a key for explaining the complex properties of procedural learning and open up new experimental questions for synaptic plasticity in the cerebellar network. PMID:25177290

Robust hepatic vessel segmentation using multi deep convolution network

NASA Astrophysics Data System (ADS)

Kitrungrotsakul, Titinunt; Han, Xian-Hua; Iwamoto, Yutaro; Foruzan, Amir Hossein; Lin, Lanfen; Chen, Yen-Wei

2017-03-01

Extraction of blood vessels of the organ is a challenging task in the area of medical image processing. It is really difficult to get accurate vessel segmentation results even with manually labeling by human being. The difficulty of vessels segmentation is the complicated structure of blood vessels and its large variations that make them hard to recognize. In this paper, we present deep artificial neural network architecture to automatically segment the hepatic vessels from computed tomography (CT) image. We proposed novel deep neural network (DNN) architecture for vessel segmentation from a medical CT volume, which consists of three deep convolution neural networks to extract features from difference planes of CT data. The three networks have share features at the first convolution layer but will separately learn their own features in the second layer. All three networks will join again at the top layer. To validate effectiveness and efficiency of our proposed method, we conduct experiments on 12 CT volumes which training data are randomly generate from 5 CT volumes and 7 using for test. Our network can yield an average dice coefficient 0.830, while 3D deep convolution neural network can yield around 0.7 and multi-scale can yield only 0.6.

Deep-levels in gallium arsenide for device applications

NASA Astrophysics Data System (ADS)

McManis, Joseph Edward

Defects in semiconductors have been studied for over 40 years as a diagnostic of the quality of crystal growth. In this thesis, we investigate GaAs deep-levels specifically intended for devices. This thesis summarizes our efforts to characterize the near-infrared photoluminescence from deep-levels, study optical transitions via absorption, and fabricate and characterize deep-level light-emitting diodes (LEDs). This thesis also describes the first tunnel diodes which explicitly make use of GaAs deep-levels. Photoluminescence measurements of GaAs deep-levels showed a broad peak around a wavelength extending from 1.0--1.7 mum, which includes important wavelengths for fiber-optic communications (1.3--1.55 mum). Transmission measurements show the new result that very little of the radiative emission is self-absorbed. We measured the deep-level photoluminescence at several temperatures. We are also the first to report the internal quantum efficiency associated with the deep-level transitions. We have fabricated LEDs that, utilize the optical transitions of GaAs deep-levels. The electroluminescence spectra showed a broad peak from 1.0--1.7 mum at low currents, but the spectrum exhibited a blue-shift as the current was increased. To improve device performance, we designed an AlGaAs layer into the structure of the LEDs. The AlGaAs barrier layer acts as a resistive barrier so that the holes in the p-GaAs layer are swept away from underneath the gold p-contact. The AlGaAs layer also reduces the blue-shift by acting as a potential barrier so that only higher-energy holes are injected. We found that the LEDs with AlGaAs were brighter at long wavelengths, which was a significant improvement. Photoluminescence measurements show that the spectral blue-shift is not due to sample heating. We have developed a new physical model to explain the blue-shift: it is caused by Coloumb charging of the deep-centers. We have achieved the first tunnel diodes with which specifically utilize deep-levels in low-temperature-grown (LTG) GaAs. Our devices show the largest ever peak current density in a GaAs tunnel diode at room temperature. Our devices also show significant room-temperature peak-to-valley current ratios. The shape of the current-voltage characteristic and the properties of the optical emission enable us to determine the peak and valley transport mechanisms.

Structural organization of parallel information processing within the tectofugal visual system of the pigeon.

PubMed

Hellmann, B; Güntürkün, O

2001-01-01

Visual information processing within the ascending tectofugal pathway to the forebrain undergoes essential rearrangements between the mesencephalic tectum opticum and the diencephalic nucleus rotundus of birds. The outer tectal layers constitute a two-dimensional map of the visual surrounding, whereas nucleus rotundus is characterized by functional domains in which different visual features such as movement, color, or luminance are processed in parallel. Morphologic correlates of this reorganization were investigated by means of focal injections of the neuronal tracer choleratoxin subunit B into different regions of the nuclei rotundus and triangularis of the pigeon. Dependent on the thalamic injection site, variations in the retrograde labeling pattern of ascending tectal efferents were observed. All rotundal projecting neurons were located within the deep tectal layer 13. Five different cell populations were distinguished that could be differentiated according to their dendritic ramifications within different retinorecipient laminae and their axons projecting to different subcomponents of the nucleus rotundus. Because retinorecipient tectal layers differ in their input from distinct classes of retinal ganglion cells, each tectorotundal cell type probably processes different aspects of the visual surrounding. Therefore, the differential input/output connections of the five tectorotundal cell groups might constitute the structural basis for spatially segregated parallel information processing of different stimulus aspects within the tectofugal visual system. Because two of five rotundal projecting cell groups additionally exhibited quantitative shifts along the dorsoventral extension of the tectum, data also indicate visual field-dependent alterations in information processing for particular visual features. Copyright 2001 Wiley-Liss, Inc.

Chapter 7: Total internal reflection fluorescence microscopy.

PubMed

Axelrod, Daniel

2008-01-01

Total internal reflection fluorescence microscopy (TIRFM), also known as evanescent wave microscopy, is used in a wide range of applications, particularly to view single molecules attached to planar surfaces and to study the position and dynamics of molecules and organelles in living culture cells near the contact regions with the glass coverslip. TIRFM selectively illuminates fluorophores only in a very thin (less than 100 nm deep) layer near the substrate, thereby avoiding excitation of fluorophores outside this subresolution optical section. This chapter reviews the history, current applications in cell biology and biochemistry, basic optical theory, combinations with numerous other optical and spectroscopic approaches, and a range of setup methods, both commercial and custom.

Deep neural network convolution (NNC) for three-class classification of diffuse lung disease opacities in high-resolution CT (HRCT): consolidation, ground-glass opacity (GGO), and normal opacity

NASA Astrophysics Data System (ADS)

Hashimoto, Noriaki; Suzuki, Kenji; Liu, Junchi; Hirano, Yasushi; MacMahon, Heber; Kido, Shoji

2018-02-01

Consolidation and ground-glass opacity (GGO) are two major types of opacities associated with diffuse lung diseases. Accurate detection and classification of such opacities are crucially important in the diagnosis of lung diseases, but the process is subjective, and suffers from interobserver variability. Our study purpose was to develop a deep neural network convolution (NNC) system for distinguishing among consolidation, GGO, and normal lung tissue in high-resolution CT (HRCT). We developed ensemble of two deep NNC models, each of which was composed of neural network regression (NNR) with an input layer, a convolution layer, a fully-connected hidden layer, and a fully-connected output layer followed by a thresholding layer. The output layer of each NNC provided a map for the likelihood of being each corresponding lung opacity of interest. The two NNC models in the ensemble were connected in a class-selection layer. We trained our NNC ensemble with pairs of input 2D axial slices and "teaching" probability maps for the corresponding lung opacity, which were obtained by combining three radiologists' annotations. We randomly selected 10 and 40 slices from HRCT scans of 172 patients for each class as a training and test set, respectively. Our NNC ensemble achieved an area under the receiver-operating-characteristic (ROC) curve (AUC) of 0.981 and 0.958 in distinction of consolidation and GGO, respectively, from normal opacity, yielding a classification accuracy of 93.3% among 3 classes. Thus, our deep-NNC-based system for classifying diffuse lung diseases achieved high accuracies for classification of consolidation, GGO, and normal opacity.

Fronts and intrusions in the upper Deep Polar Water of the Eurasian and Makarov basins

NASA Astrophysics Data System (ADS)

Kuzmina, Natalia; Rudels, Bert; Zhurbas, Natalia; Lyzhkov, Dmitry

2013-04-01

CTD data obtained in the Arctic Basin are analyzed to describe structural features of intrusive layers and fronts encountered in the upper Deep Polar Water. This work is an extension of Arctic intrusions studies by Rudels et al. (1999) and Kuzmina et al. (2011). Numerous examples of fronts and intrusions observed in a deep layer (depth range of 600-1300 m) in the Eurasian and Makarov basins where salinity is increasing, and temperature is decreasing with depth (stable-stable thermohaline stratification), are described. The data are used to estimate hydrological parameters capable of determining different types of fronts and characterizing intrusive layers depending on the front structure. Coherence of intrusive layers is shown to get broken with the change of front structure. An evidence is found that enhanced turbulent mixing above local bottom elevations can prevent from intrusive layering. A linear stability model description of the observed intrusions is developed based on the Merryfield's (2000) assumption that interleaving is caused by differential mixing. Theoretical analysis is focused on prediction of the slopes of unstable modes at baroclinic and thermohaline fronts. Apparent vertical diffusivity due to turbulent mixing at baroclinic and thermohaline fronts is estimated on the basis of comparison of observed intrusion slopes with modeled slopes of the most unstable modes. Apparent lateral diffusivity is estimated too, based on Joyce (1980) approach. These estimates show that intrusive instability of fronts caused by differential mixing can result in sizable values of apparent lateral heat diffusivity in the deep Arctic layer that are quite comparable with those of the upper and intermediate Arctic layers (Walsh, Carmack, 2003; Kuzmina et al., 2011).

Microbial diversity in methane hydrate-bearing deep marine sediments core preserved in the original pressure.

NASA Astrophysics Data System (ADS)

Takahashi, Y.; Hata, T.; Nishida, H.

2017-12-01

In normal coring of deep marine sediments, the sampled cores are exposed to the pressure of the atmosphere, which results in dissociation of gas-hydrates and might change microbial diversity. In this study, we analyzed microbial composition in methane hydrate-bearing sediment core sampled and preserved by Hybrid-PCS (Pressure Coring System). We sliced core into three layers; (i) outside layer, which were most affected by drilling fluids, (ii) middle layer, and (iii) inner layer, which were expected to be most preserved as the original state. From each layer, we directly extracted DNA, and amplified V3-V4 region of 16S rRNA gene. We determined at least 5000 of nucleotide sequences of the partial 16S rDNA from each layer by Miseq (Illumina). In the all layers, facultative anaerobes, which can grow with or without oxygen because they can metabolize energy aerobically or anaerobically, were detected as majority. However, the genera which are often detected anaerobic environment is abundant in the inner layer compared to the outside layer, indicating that condition of drilling and preservation affect the microbial composition in the deep marine sediment core. This study was conducted as a part of the activity of the Research Consortium for Methane Hydrate Resources in Japan [MH21 consortium], and supported by JOGMEC (Japan Oil, Gas and Metals National Corporation). The sample was provided by AIST (National Institute of Advanced Industrial Science and Technology).

Alternative experiments using the geophysical fluid flow cell

NASA Technical Reports Server (NTRS)

Hart, J. E.

1984-01-01

This study addresses the possibility of doing large scale dynamics experiments using the Geophysical Fluid Flow Cell. In particular, cases where the forcing generates a statically stable stratification almost everywhere in the spherical shell are evaluated. This situation is typical of the Earth's atmosphere and oceans. By calculating the strongest meridional circulation expected in the spacelab experiments, and testing its stability using quasi-geostrophic stability theory, it is shown that strongly nonlinear baroclinic waves on a zonally symmetric modified thermal wind will not occur. The Geophysical Fluid Flow Cell does not have a deep enough fluid layer to permit useful studies of large scale planetary wave processes arising from instability. It is argued, however, that by introducing suitable meridional barriers, a significant contribution to the understanding of the oceanic thermocline problem could be made.

Convective transport over the central United States and its role in regional CO and ozone budgets

NASA Technical Reports Server (NTRS)

Thompson, Anne M.; Pickering, Kenneth E.; Dickerson, Russell R.; Ellis, William G., Jr.; Jacob, Daniel J.; Scala, John R.; Tao, Wei-Kuo; Mcnamara, Donna P.; Simpson, Joanne

1994-01-01

We have constructed a regional budget for boundary layer carbon monoxide over the central United States (32.5 deg - 50 deg N, 90 deg - 105 deg W), emphasizing a detailed evaluation of deep convective vertical fluxes appropriate for the month of June. Deep convective venting of the boundary layer (upward) dominates other components of the CO budget, e.g., downward convective transport, loss of CO by oxidation, anthropogenic emissions, and CO produced from oxidation of methane, isoprene, and anthropogenic nonmethane hydrocarbons (NMHCs). Calculations of deep convective venting are based on the method pf Pickering et al.(1992a) which uses a satellite-derived deep convective cloud climatology along with transport statistics from convective cloud model simulations of observed prototype squall line events. This study uses analyses of convective episodes in 1985 and 1989 and CO measurements taken during several midwestern field campaigns. Deep convective venting of the boundary layer over this moderately polluted region provides a net (upward minus downward) flux of 18.1 x 10(exp 8) kg CO/month to the free troposphere during early summer. Shallow cumulus and synoptic-scale weather systems together make a comparable contribution (total net flux 16.2 x 10(exp 8) kg CO/month). Boundary layer venting of CO with other O3 precursors leads to efficient free troposheric O3 formation. We estimate that deep convective transport of CO and other precursors over the central United States in early summer leads to a gross production of 0.66 - 1.1 Gmol O3/d in good agreement with estimates of O3 production from boundary layer venting in a continental-scale model (Jacob et al., 1993a, b). On this respect the central U.S. region acts as s `chimney' for the country, and presumably this O3 contributes to high background levels of O3 in the eastern United States and O3 export to the North Atlantic.

Biogeochemical and physical controls on the distribution of dissolved organic carbon in the deep Gulf of Mexico and basins of the Caribbean

NASA Astrophysics Data System (ADS)

Margolin, A. R.; Hansell, D. A.

2016-02-01

Over the past two decades, significant advances have been made in understanding dissolved organic carbon (DOC) distributions in the Atlantic and throughout the global ocean. Surprisingly, however, little is known about DOC distributions in the Atlantic's neighboring Gulf of Mexico (GoM) and Caribbean due to few observations, especially in their deep layers. To address the dearth of DOC data in the GoM and Caribbean, samples were collected during multiple cruises spanning the region, allowing comparisons between the deep layers of the basins. Additionally, complementary biogeochemical (oxygen, nutrients) and physical (temperature, salinity) measurements were made to aid in DOC interpretation, which show clear distinctions between the deep waters of the GoM, basins of the Caribbean and Atlantic. The unique characteristics of these deep layers result from exchanges being restricted to narrow passages that separate the basins, limiting the deep water renewal to periodic overflows of relatively dense water, capable of penetrating below the 2000 m sill depths. Furthermore, hydrocarbon seeps (in GoM) and hydrothermal activity (in Caribbean), along with the offshore oil industry have the potential to alter deep DOC concentrations regionally, which are considered here. Samples collected below 250 m show that concentrations decrease with depth, ranging from 40-50 µmol kg-1. Compared to the Atlantic, the GoM and Venezuelan Basin concentrations are lower, while they are similar to the Atlantic in the Yucatan Basin; responsible processes are inferred.

Deep-Layer Microvasculature Dropout by Optical Coherence Tomography Angiography and Microstructure of Parapapillary Atrophy.

PubMed

Suh, Min Hee; Zangwill, Linda M; Manalastas, Patricia Isabel C; Belghith, Akram; Yarmohammadi, Adeleh; Akagi, Tadamichi; Diniz-Filho, Alberto; Saunders, Luke; Weinreb, Robert N

2018-04-01

To investigate the association between the microstructure of β-zone parapapillary atrophy (βPPA) and parapapillary deep-layer microvasculature dropout assessed by optical coherence tomography angiography (OCT-A). Thirty-seven eyes with βPPA devoid of the Bruch's membrane (BM) (γPPA) ranging between completely absent and discontinuous BM were matched by severity of the visual field (VF) damage with 37 eyes with fully intact BM (βPPA+BM) based on the spectral-domain (SD) OCT imaging. Parapapillary deep-layer microvasculature dropout was defined as a dropout of the microvasculature within choroid or scleral flange in the βPPA on the OCT-A. The widths of βPPA, γPPA, and βPPA+BM were measured on six radial SD-OCT images. Prevalence of the dropout was compared between eyes with and without γPPA. Logistic regression was performed for evaluating association of the dropout with the width of βPPA, γPPA, and βPPA+BM, and the γPPA presence. Eyes with γPPA had significantly higher prevalence of the dropout than did those without γPPA (75.7% versus 40.8%; P = 0.004). In logistic regression, presence and longer width of the γPPA, worse VF mean deviation, and presence of focal lamina cribrosa defects were significantly associated with the dropout (P < 0.05), whereas width of the βPPA and βPPA+BM, axial length, and choroidal thickness were not (P > 0.10). Parapapillary deep-layer microvasculature dropout was associated with the presence and larger width of γPPA, but not with the βPPA+BM width. Presence and width of the exposed scleral flange, rather than the retinal pigmented epithelium atrophy, may be associated with deep-layer microvasculature dropout.

Deep-Layer Microvasculature Dropout by Optical Coherence Tomography Angiography and Microstructure of Parapapillary Atrophy

PubMed Central

Suh, Min Hee; Zangwill, Linda M.; Manalastas, Patricia Isabel C.; Belghith, Akram; Yarmohammadi, Adeleh; Akagi, Tadamichi; Diniz-Filho, Alberto; Saunders, Luke; Weinreb, Robert N.

2018-01-01

Purpose To investigate the association between the microstructure of β-zone parapapillary atrophy (βPPA) and parapapillary deep-layer microvasculature dropout assessed by optical coherence tomography angiography (OCT-A). Methods Thirty-seven eyes with βPPA devoid of the Bruch's membrane (BM) (γPPA) ranging between completely absent and discontinuous BM were matched by severity of the visual field (VF) damage with 37 eyes with fully intact BM (βPPA+BM) based on the spectral-domain (SD) OCT imaging. Parapapillary deep-layer microvasculature dropout was defined as a dropout of the microvasculature within choroid or scleral flange in the βPPA on the OCT-A. The widths of βPPA, γPPA, and βPPA+BM were measured on six radial SD-OCT images. Prevalence of the dropout was compared between eyes with and without γPPA. Logistic regression was performed for evaluating association of the dropout with the width of βPPA, γPPA, and βPPA+BM, and the γPPA presence. Results Eyes with γPPA had significantly higher prevalence of the dropout than did those without γPPA (75.7% versus 40.8%; P = 0.004). In logistic regression, presence and longer width of the γPPA, worse VF mean deviation, and presence of focal lamina cribrosa defects were significantly associated with the dropout (P < 0.05), whereas width of the βPPA and βPPA+BM, axial length, and choroidal thickness were not (P > 0.10). Conclusions Parapapillary deep-layer microvasculature dropout was associated with the presence and larger width of γPPA, but not with the βPPA+BM width. Presence and width of the exposed scleral flange, rather than the retinal pigmented epithelium atrophy, may be associated with deep-layer microvasculature dropout. PMID:29677362

A charge carrier transport model for donor-acceptor blend layers

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

Fischer, Janine, E-mail: janine.fischer@iapp.de; Widmer, Johannes; Koerner, Christian

2015-01-28

Highly efficient organic solar cells typically comprise donor-acceptor blend layers facilitating effective splitting of excitons. However, the charge carrier mobility in the blends can be substantially smaller than in neat materials, hampering the device performance. Currently, available mobility models do not describe the transport in blend layers entirely. Here, we investigate hole transport in a model blend system consisting of the small molecule donor zinc phthalocyanine (ZnPc) and the acceptor fullerene C{sub 60} in different mixing ratios. The blend layer is sandwiched between p-doped organic injection layers, which prevent minority charge carrier injection and enable exploiting diffusion currents for themore » characterization of exponential tail states from a thickness variation of the blend layer using numerical drift-diffusion simulations. Trap-assisted recombination must be considered to correctly model the conductivity behavior of the devices, which are influenced by local electron currents in the active layer, even though the active layer is sandwiched in between p-doped contacts. We find that the density of deep tail states is largest in the devices with 1:1 mixing ratio (E{sub t} = 0.14 eV, N{sub t} = 1.2 × 10{sup 18 }cm{sup −3}) directing towards lattice disorder as the transport limiting process. A combined field and charge carrier density dependent mobility model are developed for this blend layer.« less

Gyre-scale deep convection in the subpolar North Atlantic Ocean during winter 2014-2015

NASA Astrophysics Data System (ADS)

Piron, A.; Thierry, V.; Mercier, H.; Caniaux, G.

2017-02-01

Using Argo floats, we show that a major deep convective activity occurred simultaneously in the Labrador Sea (LAB), south of Cape Farewell (SCF), and the Irminger Sea (IRM) during winter 2014-2015. Convection was driven by exceptional heat loss to the atmosphere (up to 50% higher than the climatological mean). This is the first observation of deep convection over such a widespread area. Mixed layer depths exceptionally reached 1700 m in SCF and 1400 m in IRM. The deep thermocline density gradient limited the mixed layer deepening in the Labrador Sea to 1800 m. Potential densities of deep waters were similar in the three basins (27.73-27.74 kg m-3) but warmer by 0.3°C and saltier by 0.04 in IRM than in LAB and SCF, meaning that each basin formed locally its own deep water. The cold anomaly that developed recently in the North Atlantic Ocean favored and was enhanced by this exceptional convection.

Active semi-supervised learning method with hybrid deep belief networks.

PubMed

Zhou, Shusen; Chen, Qingcai; Wang, Xiaolong

2014-01-01

In this paper, we develop a novel semi-supervised learning algorithm called active hybrid deep belief networks (AHD), to address the semi-supervised sentiment classification problem with deep learning. First, we construct the previous several hidden layers using restricted Boltzmann machines (RBM), which can reduce the dimension and abstract the information of the reviews quickly. Second, we construct the following hidden layers using convolutional restricted Boltzmann machines (CRBM), which can abstract the information of reviews effectively. Third, the constructed deep architecture is fine-tuned by gradient-descent based supervised learning with an exponential loss function. Finally, active learning method is combined based on the proposed deep architecture. We did several experiments on five sentiment classification datasets, and show that AHD is competitive with previous semi-supervised learning algorithm. Experiments are also conducted to verify the effectiveness of our proposed method with different number of labeled reviews and unlabeled reviews respectively.

Spatial and temporal characterization of endometrial mesenchymal stem-like cells activity during the menstrual cycle

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

Shan, Xu; Chan, Rachel W.S., E-mail: rwschan@hku.hk; Centre of Reproduction, Development of Growth, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR

The human endometrium is a highly dynamic tissue with the ability to cyclically regenerate during the reproductive life. Endometrial mesenchymal stem-like cells (eMSCs) located throughout the endometrium have shown to functionally contribute to endometrial regeneration. In this study we examine whether the menstrual cycle stage and the location in the endometrial bilayer (superficial and deep portions of the endometrium) has an effect on stem cell activities of eMSCs (CD140b{sup +}CD146{sup +} cells). Here we show the percentage and clonogenic ability of eMSCs were constant in the various stages of the menstrual cycle (menstrual, proliferative and secretory). However, eMSCs from themore » menstrual endometrium underwent significantly more rounds of self-renewal and enabled a greater total cell output than those from the secretory phase. Significantly more eMSCs were detected in the deeper portion of the endometrium compared to the superficial layer but their clonogenic and self-renewal activities remained similar. Our findings suggest that eMSCs are activated in the menstrual phase for the cyclical regeneration of the endometrium. - Highlights: • The percentages of endometrial mesenchymal-like stem cells (eMSCs) were constant across the menstrual cycle. • Menstruation eMSCs display superior self-renewal and long-term proliferative activities. • More eMSCs reside in the deeper portion of the endometrium than the superficial layer.« less

Identification of the spatial location of deep trap states in AlGaN/GaN heterostructures by surface photovoltage spectroscopy

NASA Astrophysics Data System (ADS)

Jana, Dipankar; Porwal, S.; Sharma, T. K.

2017-12-01

Spatial and spectral origin of deep level defects in molecular beam epitaxy grown AlGaN/GaN heterostructures are investigated by using surface photovoltage spectroscopy (SPS) and pump-probe SPS techniques. A deep trap center ∼1 eV above the valence band is observed in SPS measurements which is correlated with the yellow luminescence feature in GaN. Capture of electrons and holes is resolved by performing temperature dependent SPS and pump-probe SPS measurements. It is found that the deep trap states are distributed throughout the sample while their dominance in SPS spectra depends on the density, occupation probability of deep trap states and the background electron density of GaN channel layer. Dynamics of deep trap states associated with GaN channel layer is investigated by performing frequency dependent photoluminescence (PL) and SPS measurements. A time constant of few millisecond is estimated for the deep defects which might limit the dynamic performance of AlGaN/GaN based devices.

Constraints on the properties of Pluto's nitrogen-ice rich layer from convection simulations

NASA Astrophysics Data System (ADS)

Wong, T.; McKinnon, W. B.; Schenk, P.

2016-12-01

Pluto's Sputnik Planum basin (informally named) displays regular cellular patterns strongly suggesting that solid-state convection is occurring in a several-kilometers-deep nitrogen-ice rich layer (McKinnon et al., Convection in a volatile nitrogen-ice-rich layer drives Pluto's geological vigour, Nature 534, 82-85, 2016). We investigate the behavior of thermal convection in 2-D that covers a range of parameters applicable to the nitrogen ice layer to constrain its properties such that these long-wavelength surface features can be explained. We perform a suite of numerical simulations of convection with basal heating and temperature-dependent viscosity in either exponential form or Arrhenius form. For a plausible range of Rayleigh numbers and viscosity contrasts for solid nitrogen, convection can occur in all possible regimes: sluggish lid, transitional, or stagnant lid, or the layer could be purely conducting. We suggest the range of depth and temperature difference across the layer for convection to occur. We observe that the plume dynamics can be widely different in terms of the aspect ratio of convecting cells, or the width and spacing of plumes, and also in the lateral movement of plumes. These differences depend on the regime of convection determined by the Rayleigh number and the actual viscosity contrast across the layer, but is not sensitive to whether the viscosity is in Arrhenius or exponential form. The variations in plume dynamics result in different types of dynamic topography, which can be compared with the observed horizontal and vertical scales of the cells in Sputnik Planum. Based on these simulations we suggest several different possibilities for the formation and evolution of Sputnik Planum, which may be a consequence of the time-dependent behavior of thermal convection.

Muscular innervation of the proximal duodenum of the guinea pig.

PubMed

Iino, S

2000-10-01

We investigated the muscular structure and innervation of the gastroduodenal junction in the guinea pig. In the gastroduodenal junction, the innermost layer of the circular muscle contained numerous nerve fibers and terminals. Since this nerve network continued onto the deep muscular plexus (DMP) of the duodenum, we surmised that the numerous nerve fibers in the gastroduodenal junction were specialized DMP in the most proximal part of the duodenum. The innermost layer containing many nerve fibers was about 1,000 microm in length and 100 microm in thickness in the proximal duodenum. This layer contained numerous connective tissue fibers composed of collagen and elastic fibers. Five to 30 smooth muscle cells lay in contact with each other and were surrounded by fine connective tissue. The nerve fibers in the proximal duodenum contained nerve terminals immunoreactive for choline acetyltransferase, dynorphin, enkephalin, galanin, gastrin-releasing peptide, nitric oxide synthase, substance P, and vasoactive intestinal polypeptide. Adrenergic fibers which contained tyrosine hydroxylase immunoreactivity were rare in the proximal duodenum. In the innermost layer of the proximal duodenum, there were numerous c-Kit immunopositive cells that were in contact with nerve terminals. This study allowed us to clarify the specific architecture of the most proximal portion of the duodenum. The functional significance of the proximal duodenum in relation to the electrical connection and neural cooperation of the musculature between the antrum and the duodenum is also discussed.

The deep-sea as a final global sink of semivolatile persistent organic pollutants? Part I: PCBs in surface and deep-sea dwelling fish of the north and south Atlantic and the Monterey Bay Canyon (California).

PubMed

Froescheis, O; Looser, R; Cailliet, G M; Jarman, W M; Ballschmiter, K

2000-03-01

The understanding of the global environmental multiphase distribution of persistent organic pollutants (POPs) as a result of the physico-chemical properties of the respective compounds is well established. We have analysed the results of a vertical transport of POPs from upper water layers (0-200 m) to the deepwater region (> 800 m) in terms of the contamination of the biophase in both water layers. The contents of persistent organochlorine compounds like polychlorinated biphenyls (PCBs) in fish living in the upper water layers of the North Atlantic and the South Atlantic, and at the continental shelf of California (Marine Sanctuary Monterey Bay and its deep-sea Canyon) are compared to the levels in deep-sea or bottom dwelling fish within the same geographic area. The deep-sea biota show significantly higher burdens as compared to surface-living species of the same region. There are also indications for recycling processes of POPs--in this case the PCBs--in the biophase of the abyss as well. It can be concluded that the bio- and geo phase of the deep-sea may act similarly as the upper horizons of forest and grasslands on the continents as an ultimate global sink for POPs in the marine environment.

Interactions between deep bedrock aquifers and surface water in function of recharge and topography: a numerical study

NASA Astrophysics Data System (ADS)

Goderniaux, P.; Davy, P.; Le Borgne, T.; Bresciani, E.; Jimenez-Martinez, J.

2011-12-01

In crystalline rock regions, such as Brittany (France), important reserves of groundwater into deep fractured aquifers are increasingly used and provide high quality water compared to shallow aquifers which can be subject to agricultural contamination. However, recharge processes of these deep aquifers and interactions with surface water are not yet fully understood. In some areas, intensive pumping is carried out without guarantee of the resource quantity and quality. Understanding these processes is crucial for sustainable management of the resource. In this study, we study how deep groundwater fluxes, pathways, ages, and river-aquifer interactions vary according to recharge. We assume that water flowing from the ground surface is distributed between shallow more permeable layers and deep layers. This repartition mostly depends on recharge rates. With high recharge, groundwater levels are high and subsurface streamlines are relatively short between recharge areas and existing draining rivers, which constitutes a very dense network. Therefore, most of the groundwater fluxes occur through the more permeable shallow layers. With low recharge, groundwater levels are lower, and river and shallow permeable levels are partly disconnected from each other. This induces a general increase of the groundwater streamlines length from the recharge areas to more sporadic discharge areas, and more fluxes occur through the deep layers. Recharge conditions and river-aquifer interactions have changed over the last thousands of years, due to change in precipitation, temperatures, existence of permafrost, etc. They have strongly influenced deep groundwater fluxes and can explain current groundwater age and flux distribution. To study these interactions, a regional-scale finite difference flow model was implemented. The model covers an area of 1400 km 2 , a depth of 1 km, and the topography is characteristic of Brittany. As rivers are mainly fed by groundwater drainage, seepages faces are used on the whole modelled area, so that the river network is not prescribed but dependent on simulated groundwater conditions. Different recharge conditions were tested (from 20 to 500 mm/yr). Results show that streamline lengths and groundwater ages have exponential distributions with characteristic lengths increasing with decreasing recharge. The total area of discharge zones decreases with recharge. Groundwater age is quite variable and increases with depth, but the variability is much more important in discharge areas than recharge areas. The proportion of groundwater discharge into the sea (compared to total recharge) increases when total recharge decreases. The model was also used to test the influence of heterogeneity or hydraulic conductivity contrast between shallow and deep layers on deep groundwater fluxes. In a completely homogeneous model, deep fluxes are correlated with recharge fluxes. Correlation decreases while contrast increases. If the permeability of the shallow weather zone is now 3 orders of magnitude larger than of deep aquifer, we observed that simulated deep groundwater fluxes increase locally, despite total recharge at the level of the ground surface decreases.

Water withdrawal in deep soil layers: a key strategy to cope with drought in tropical eucalypt plantations

NASA Astrophysics Data System (ADS)

Christina, M.; Laclau, J.; Nouvellon, Y.; Duursma, R. A.; Stape, J. L.; Lambais, G. R.; Le Maire, G.

2013-12-01

Little is known about the role of very deep roots to supply the water requirements of tropical forests. Clonal Eucalyptus plantations managed in short rotation on very deep Ferralsols are simple forest ecosystems (only 1 plant genotype growing on a relatively homogeneous soil) likely to provide an insight into tree water use strategies in tropical forests. Fine roots have been observed down to a depth of 6 m at age 1 year in Brazilian eucalypt plantations. However, the contribution of water stored in very deep soil layers to stand evapotranspiration over tree growth has been poorly quantified. An eco-physiological model, MAESPA, has been used to simulate half-hourly stand water balance over the first three years of growth in a clonal Eucalyptus grandis plantation in southern Brazil (Eucflux project, State of São Paulo). The water balance model in MAESPA is an equilibrium-type model between soil and leaf water potentials for individual trees aboveground, and at the stand scale belowground. The dynamics of the vertical fine root distribution have been taken into account empirically from linear interpolations between successive measurements. The simulations were compared to time series of soil water contents measured every meter down to 10m deep and to daily latent heat fluxes measured by eddy covariance. Simulations of volumetric soil water contents matched satisfactorily with measurements (RMSE = 0.01) over the three-year period. Good agreement was also observed between simulated and measured latent heat fluxes. In the rainy season, more than 75 % of tree transpiration was supplied by water withdrawn in the upper 1 m of soil, but water uptake progressed to deeper soil layers during dry periods, down to a depth of 6 m, 12 m and 15 m the first, second and third year after planting, respectively. During the second growing season, 15% of water was withdrawn below a depth of 6 m, and 5% below 10m. Most of the soil down to 12m deep was dried out the second year after planting and deep drainage was negligible after 2 years. As a consequence, during the third year after planting only 4% of water was taken up below 6m. However, during the dry season, this deep water still supplied 50% of water requirements. Our results show that deep fine roots of E. grandis play a major role in supplying tree water requirements during extended dry periods. Large amounts of water are stored in the whole soil profile after clear cutting and the fast exploration of deep soil layers by roots make it available for tree growth. After canopy closure, precipitation becomes the key limitation for the productivity of these plantations grown in deep sandy soils. Our results suggest that a territorial strategy leading to a fast exploration of very deep soil layers might provide a strong competitive advantage in regions prone to drought.

Dense deconvolution net: Multi path fusion and dense deconvolution for high resolution skin lesion segmentation.

PubMed

He, Xinzi; Yu, Zhen; Wang, Tianfu; Lei, Baiying; Shi, Yiyan

2018-01-01

Dermoscopy imaging has been a routine examination approach for skin lesion diagnosis. Accurate segmentation is the first step for automatic dermoscopy image assessment. The main challenges for skin lesion segmentation are numerous variations in viewpoint and scale of skin lesion region. To handle these challenges, we propose a novel skin lesion segmentation network via a very deep dense deconvolution network based on dermoscopic images. Specifically, the deep dense layer and generic multi-path Deep RefineNet are combined to improve the segmentation performance. The deep representation of all available layers is aggregated to form the global feature maps using skip connection. Also, the dense deconvolution layer is leveraged to capture diverse appearance features via the contextual information. Finally, we apply the dense deconvolution layer to smooth segmentation maps and obtain final high-resolution output. Our proposed method shows the superiority over the state-of-the-art approaches based on the public available 2016 and 2017 skin lesion challenge dataset and achieves the accuracy of 96.0% and 93.9%, which obtained a 6.0% and 1.2% increase over the traditional method, respectively. By utilizing Dense Deconvolution Net, the average time for processing one testing images with our proposed framework was 0.253 s.

Frequency and morphology of tropical tropopause layer cirrus from CALIPSO observations: Are isolated cirrus different from those connected to deep convection?

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

Riihimaki, Laura D.; McFarlane, Sally A.

2010-09-16

Tropical Tropopause Layer cirrus (TTLC) profiles identified from CALIPSO LIDAR measurements are grouped into cloud objects and classified according to whether or not they are connected to deep convection. TTLC objects connected to deep convection are optically and physically thicker than isolated objects, consistent with what would be expected if connected objects were formed from convective detrainment and isolated objects formed in situ. In the tropics (±20 Latitude), 36% of TTLC profiles are classified as connected to deep convection, 43% as isolated, and the remaining 21% are part of lower, thicker cirrus clouds. Regions with higher occurence of deep convectionmore » also have higher occurrence of TTLC, and a greater percentage of those TTLC are connected to deep convection. Cloud top heights of both isolated and connected clouds are distributed similarly with respect to the height of the cold point tropopause. No difference in thickness or optical depth was found between TTLC above deep convection or above clear sky, though both cloud base and top heights are higher over deep convection than over clear sky.« less

A model of traffic signs recognition with convolutional neural network

NASA Astrophysics Data System (ADS)

Hu, Haihe; Li, Yujian; Zhang, Ting; Huo, Yi; Kuang, Wenqing

2016-10-01

In real traffic scenes, the quality of captured images are generally low due to some factors such as lighting conditions, and occlusion on. All of these factors are challengeable for automated recognition algorithms of traffic signs. Deep learning has provided a new way to solve this kind of problems recently. The deep network can automatically learn features from a large number of data samples and obtain an excellent recognition performance. We therefore approach this task of recognition of traffic signs as a general vision problem, with few assumptions related to road signs. We propose a model of Convolutional Neural Network (CNN) and apply the model to the task of traffic signs recognition. The proposed model adopts deep CNN as the supervised learning model, directly takes the collected traffic signs image as the input, alternates the convolutional layer and subsampling layer, and automatically extracts the features for the recognition of the traffic signs images. The proposed model includes an input layer, three convolutional layers, three subsampling layers, a fully-connected layer, and an output layer. To validate the proposed model, the experiments are implemented using the public dataset of China competition of fuzzy image processing. Experimental results show that the proposed model produces a recognition accuracy of 99.01 % on the training dataset, and yield a record of 92% on the preliminary contest within the fourth best.

Argo float observations of basin-scale deep convection in the Irminger Sea during winter 2011-2012

NASA Astrophysics Data System (ADS)

Thierry, V.; Piron, A.; Mercier, H.; Caniaux, G.

2016-02-01

An analysis of Argo data during the 2011-2012 winter revealed the presence of an exceptionally large number of profiles over the Irminger Basin with mixed layer depths (MLD) exceeding 700 m, which was deep enough to reach the pool of the intermediate Labrador Sea Water located in the Irminger Sea. Among them, 4 profiles exhibited an MLD of 1000 m, which was the maximum value observed this winter. Owing to the exceptional Argo sampling in the Irminger Sea during that winter the different phases of the mixed layer deepening down to 1000 m and their spatial extents were observed for the first time in the Irminger Sea. Two intense convective periods occurred in late January south of Cape Farewell and in late February-early March east of Greenland. A final deepening period was observed in mid-March during which the deepest mixed layers were observed. This long deepening period occurred in large regional areas and was followed by a rapid restratification phase. A mixed layer heat budget along the trajectories of the 4 floats that sampled the deepest mixed layers showed that heat loss at the air-sea interface was mainly responsible for heat content variations in the mixed layer. Greenland Tip Jets were of primary importance for the development of deep convection in the Irminger Sea in the 2011-2012 winter. They enhanced the winter heat loss and two long (more than 24 hours), intense and close in time late events boosted the mixed layer deepening down to 1000m. Net air-sea fluxes, the number of Greenland Tip Jets, the stratification of the water column, the NAO index and Ekman-induced heat flux are pertinent indicators to assess the favorable conditions for the development of deep convection in the Irminger Sea. When considering each of those indicators, we concluded that the 2011-2012 event was not significantly different compared to the three other documented occurrences of deep convection in the Irminger Sea.This work is a contribution to the NAOS project.

The synaptic pharmacology underlying sensory processing in the superior colliculus.

PubMed

Binns, K E

1999-10-01

The superior colliculus (SC) is one of the most ancient regions of the vertebrate central sensory system. In this hub afferents from several sensory pathways converge, and an extensive range of neural circuits enable primary sensory processing, multi-sensory integration and the generation of motor commands for orientation behaviours. The SC has a laminar structure and is usually considered in two parts; the superficial visual layers and the deep multi-modal/motor layers. Neurones in the superficial layers integrate visual information from the retina, cortex and other sources, while the deep layers draw together data from many cortical and sub-cortical sensory areas, including the superficial layers, to generate motor commands. Functional studies in anaesthetized subjects and in slice preparations have used pharmacological tools to probe some of the SC's interacting circuits. The studies reviewed here reveal important roles for ionotropic glutamate receptors in the mediation of sensory inputs to the SC and in transmission between the superficial and deep layers. N-methyl-D-aspartate receptors appear to have special responsibility for the temporal matching of retinal and cortical activity in the superficial layers and for the integration of multiple sensory data-streams in the deep layers. Sensory responses are shaped by intrinsic inhibitory mechanisms mediated by GABA(A) and GABA(B) receptors and influenced by nicotinic acetylcholine receptors. These sensory and motor-command activities of SC neurones are modulated by levels of arousal through extrinsic connections containing GABA, serotonin and other transmitters. It is possible to naturally stimulate many of the SC's sensory and non-sensory inputs either independently or simultaneously and this brain area is an ideal location in which to study: (a) interactions between inputs from the same sensory system; (b) the integration of inputs from several sensory systems; and (c) the influence of non-sensory systems on sensory processing.

Deep Correlated Holistic Metric Learning for Sketch-Based 3D Shape Retrieval.

PubMed

Dai, Guoxian; Xie, Jin; Fang, Yi

2018-07-01

How to effectively retrieve desired 3D models with simple queries is a long-standing problem in computer vision community. The model-based approach is quite straightforward but nontrivial, since people could not always have the desired 3D query model available by side. Recently, large amounts of wide-screen electronic devices are prevail in our daily lives, which makes the sketch-based 3D shape retrieval a promising candidate due to its simpleness and efficiency. The main challenge of sketch-based approach is the huge modality gap between sketch and 3D shape. In this paper, we proposed a novel deep correlated holistic metric learning (DCHML) method to mitigate the discrepancy between sketch and 3D shape domains. The proposed DCHML trains two distinct deep neural networks (one for each domain) jointly, which learns two deep nonlinear transformations to map features from both domains into a new feature space. The proposed loss, including discriminative loss and correlation loss, aims to increase the discrimination of features within each domain as well as the correlation between different domains. In the new feature space, the discriminative loss minimizes the intra-class distance of the deep transformed features and maximizes the inter-class distance of the deep transformed features to a large margin within each domain, while the correlation loss focused on mitigating the distribution discrepancy across different domains. Different from existing deep metric learning methods only with loss at the output layer, our proposed DCHML is trained with loss at both hidden layer and output layer to further improve the performance by encouraging features in the hidden layer also with desired properties. Our proposed method is evaluated on three benchmarks, including 3D Shape Retrieval Contest 2013, 2014, and 2016 benchmarks, and the experimental results demonstrate the superiority of our proposed method over the state-of-the-art methods.

Differentiated epidermal outgrowths in the planarian Dugesia gonocephala: a model for studying cell renewal and patterning in single-layered epithelial tissue.

PubMed

Chandebois, R

1985-01-01

Large deep wounds on the ventral side of a flatworm (Planaria) will not heal. Instead, the damage to the parenchyma in the wound's roof will result in a differentiated swelling in the dorsal epidermis, above the wound which will eventually disappear with the disintegration of the underlying damaged tissue and a ventrodorsal hole appears in place of the wound. The dorsal epidermal outgrowth is formed by a number of excrescences, the development of which involves four successive stages. Their analysis suggests that epidermal cells are continuously produced by their own stem cells which remain unnoticed because their nuclei are hardly stainable. The daughter cells differentiate without information from either the underlying tissues or the basal epithelial membrane. During the first stage of this differentiation the cells become ciliated and motile, with some embryonic features. They then produce rhabdites and take up a columnar shape as they may become attached to the basal membrane. After wound setting the production of epidermal cells increases and the overcrowding of the basal membrane results in (1) detachment of stem cells and motile ciliated cells from the basal tissues, i.e. outgrowths; (2) stretching of columnar cells at the base of the outgrowths. When in the process of tissue disintegration the basal membrane of the epithelium also disappears, the cells remain in a single-layered epithelial configuration and retain their original polarity. These results are at variance with the generally accepted hypothesis that, in planarians, epidermal cells originate from the parenchyma and the epidermis is not an autonomous tissue.

[Progress of midfacial fat compartments and related clinical applications].

PubMed

Wen, Lihong; Wang, Jinhuang; Li, Yang; Liu, Dalie

2018-02-01

To review the research progress of midfacial fat compartments, and to thoroughly understand its current state of the anatomy and the aging morphologic characters of midfacial fat compartments, as well as the current status of clinical applications. The recent literature concerning the midfacial fat compartments and related clinical applications were extensively reviewed and analyzed. Midfacial fat layer has been considered as a fusion and a continuous layer, experiencing a global atrophy when aging. As more anatomical researches have done, recent studies have shown that midfacial fat layer is broadly divided into superficial and deep layers, which are both divided into different fat compartments by fascia, ligaments, or muscles. Midfacial fat compartments tend to atrophy with age, specifically in the deep fat compartments while hypertrophy in the superficial fat compartments. Clinical applications show that fat volumetric restoration with deep medial cheek fat and Ristow's space can restore the appearance of midface effectively. In recent years, the researches of midfacial fat compartments have achieved obvious progress, which will provide new ideas and basis for fat volumetric restoration. Corresponding treatments are selected based on different sites and different layers with different aging changes, reshaping a more youthful midface.

Cytokeratin expression in pseudoepitheliomatous hyperplasia of oral paracoccidioidomycosis.

PubMed

Kaminagakura, E; Bonan, P R F; Lopes, M A; Almeida, O P; Scully, C

2006-08-01

Paracoccidioidomycosis (Pmycosis) is one the most prevalent deep systemic mycoses in Latin America. It is characterized by granulomatous inflammation and pseudoepitheliomatous hyperplasia. Cytokeratins (CKs) are a group of intermediate filaments of epithelial cells and their expression varies according to the epithelium type, differentiation and pathological processes. This study describes cytokeratin expression as examined by immunohistochemistry, in 28 cases of oral Pmycosis involving the buccal mucosa, lip, gingiva and hard palate. Expression of CKs in the basal layer of the epithelium in pseudoepitheliomatous hyperplasia of Pmycosis was similar to that in normal oral mucosa (NOM), but in Pmycosis CK1 and CK10 were not expressed in the spinous and superficial layers of the lip, gingiva or hard palate, and, in the spinous and superficial layers of the lip and buccal mucosa, CK14 was positive in contrast to NOM where it was negative. In Pmycosis, CK6 was more frequently expressed in the spinous layer of the lip, gingiva and hard palate, but nevertheless CK16 expression was decreased in the spinous and superficial layers of the gingiva and hard palate. We conclude that pseudoepitheliomatous hyperplasia in oral Pmycosis shows a different pattern of CK expression, particularly CKs 1, 10 and 14, compared with NOM.

Single-step fabrication of polydimethylsiloxane microwell arrays with long-lasting hydrophilic inner surfaces

NASA Astrophysics Data System (ADS)

Gowa Oyama, Tomoko; Barba, Bin Jeremiah Duenas; Hosaka, Yuji; Taguchi, Mitsumasa

2018-05-01

We propose a single-step fabrication method for polydimethylsiloxane (PDMS) cell-adhesive microwell arrays with long-lasting (>10 months in aqueous medium) hydrophilic inner surfaces without the need for any chemical treatment such as development. Irradiation of a PDMS film with a low-energy electron beam (55 kV) in air generated a ˜40-μm-thick hydrophilic silica-like layer on the PDMS surface, which was the key to the prolonged hydrophilicity. Moreover, the concomitant compaction of the irradiated area produced dozens-of-micrometers-deep concave wells. The hydrophilic microwells generated on the hydrophobic non-irradiated PDMS surface easily trapped nano-/picoliter droplets and cells/single-cells. In addition, the surfaces of the microwells offered stable and favorable cell-adherent environments. The method presented here can realize stable and reliable lab-on-chips and cater to the expanding demand in biological and medical applications.

Ultrastructure and Composition of the Nannochloropsis gaditana Cell Wall

PubMed Central

Scholz, Matthew J.; Weiss, Taylor L.; Jinkerson, Robert E.; Jing, Jia; Roth, Robyn; Goodenough, Ursula; Posewitz, Matthew C.

2014-01-01

Marine algae of the genus Nannochloropsis are promising producers of biofuel precursors and nutraceuticals and are also harvested commercially for aquaculture feed. We have used quick-freeze, deep-etch electron microscopy, Fourier transform infrared spectroscopy, and carbohydrate analyses to characterize the architecture of the Nannochloropsis gaditana (strain CCMP 526) cell wall, whose recalcitrance presents a significant barrier to biocommodity extraction. The data indicate a bilayer structure consisting of a cellulosic inner wall (∼75% of the mass balance) protected by an outer hydrophobic algaenan layer. Cellulase treatment of walls purified after cell lysis generates highly enriched algaenan preparations without using the harsh chemical treatments typically used in algaenan isolation and characterization. Nannochloropsis algaenan was determined to comprise long, straight-chain, saturated aliphatics with ether cross-links, which closely resembles the cutan of vascular plants. Chemical identification of >85% of the isolated cell wall mass is detailed, and genome analysis is used to identify candidate biosynthetic enzymes. PMID:25239976

Deep greedy learning under thermal variability in full diurnal cycles

NASA Astrophysics Data System (ADS)

Rauss, Patrick; Rosario, Dalton

2017-08-01

We study the generalization and scalability behavior of a deep belief network (DBN) applied to a challenging long-wave infrared hyperspectral dataset, consisting of radiance from several manmade and natural materials within a fixed site located 500 m from an observation tower. The collections cover multiple full diurnal cycles and include different atmospheric conditions. Using complementary priors, a DBN uses a greedy algorithm that can learn deep, directed belief networks one layer at a time and has two layers form to provide undirected associative memory. The greedy algorithm initializes a slower learning procedure, which fine-tunes the weights, using a contrastive version of the wake-sleep algorithm. After fine-tuning, a network with three hidden layers forms a very good generative model of the joint distribution of spectral data and their labels, despite significant data variability between and within classes due to environmental and temperature variation occurring within and between full diurnal cycles. We argue, however, that more questions than answers are raised regarding the generalization capacity of these deep nets through experiments aimed at investigating their training and augmented learning behavior.

Classification of Exacerbation Frequency in the COPDGene Cohort Using Deep Learning with Deep Belief Networks.

PubMed

Ying, Jun; Dutta, Joyita; Guo, Ning; Hu, Chenhui; Zhou, Dan; Sitek, Arkadiusz; Li, Quanzheng

2016-12-21

This study aims to develop an automatic classifier based on deep learning for exacerbation frequency in patients with chronic obstructive pulmonary disease (COPD). A threelayer deep belief network (DBN) with two hidden layers and one visible layer was employed to develop classification models and the models' robustness to exacerbation was analyzed. Subjects from the COPDGene cohort were labeled with exacerbation frequency, defined as the number of exacerbation events per year. 10,300 subjects with 361 features each were included in the analysis. After feature selection and parameter optimization, the proposed classification method achieved an accuracy of 91.99%, using a 10-fold cross validation experiment. The analysis of DBN weights showed that there was a good visual spatial relationship between the underlying critical features of different layers. Our findings show that the most sensitive features obtained from the DBN weights are consistent with the consensus showed by clinical rules and standards for COPD diagnostics. We thus demonstrate that DBN is a competitive tool for exacerbation risk assessment for patients suffering from COPD.

Very Deep Convolutional Neural Networks for Morphologic Classification of Erythrocytes.

PubMed

Durant, Thomas J S; Olson, Eben M; Schulz, Wade L; Torres, Richard

2017-12-01

Morphologic profiling of the erythrocyte population is a widely used and clinically valuable diagnostic modality, but one that relies on a slow manual process associated with significant labor cost and limited reproducibility. Automated profiling of erythrocytes from digital images by capable machine learning approaches would augment the throughput and value of morphologic analysis. To this end, we sought to evaluate the performance of leading implementation strategies for convolutional neural networks (CNNs) when applied to classification of erythrocytes based on morphology. Erythrocytes were manually classified into 1 of 10 classes using a custom-developed Web application. Using recent literature to guide architectural considerations for neural network design, we implemented a "very deep" CNN, consisting of >150 layers, with dense shortcut connections. The final database comprised 3737 labeled cells. Ensemble model predictions on unseen data demonstrated a harmonic mean of recall and precision metrics of 92.70% and 89.39%, respectively. Of the 748 cells in the test set, 23 misclassification errors were made, with a correct classification frequency of 90.60%, represented as a harmonic mean across the 10 morphologic classes. These findings indicate that erythrocyte morphology profiles could be measured with a high degree of accuracy with "very deep" CNNs. Further, these data support future efforts to expand classes and optimize practical performance in a clinical environment as a prelude to full implementation as a clinical tool. © 2017 American Association for Clinical Chemistry.

Depth profile composition studies of thin film CdS:Cu2S solar cells using XPS and AES

NASA Astrophysics Data System (ADS)

Bhide, V. G.; Salkalachen, S.; Rastogi, A. C.; Rao, C. N. R.; Hegde, M. S.

1981-09-01

Studies of the surface composition and depth profiles of thin film CdS:Cu2S solar cells based on the techniques of X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES) are reported. Specimens were fabricated by the thermal deposition of polycrystalline CdS films onto silver-backed electrodes predeposited on window glass substrates, followed by texturization in hot HCl and chemical plating in a hot CuCl(I) bath for a few seconds to achieve the topotaxial growth of CuS films. The XPS and AES studies indicate the junction to be fairly diffused in the as-prepared cell, with heat treatment in air at 210 C sharpening the junction, improving the stoichiometry of the Cu2S layer and thus improving cell performance. The top copper sulfide layer is found to contain impurities such as Cd, Cl, O and C, which may be removed by mild Ar(+) ion beam etching. The presence of copper deep in the junction is invariably detected, apparently in the grain boundary region in the form of CuS or Cu(2+) trapped in the lattice. It is also noted that the nominal valence state of copper changes abruptly from Cu(+) to Cu(2+) across the junction.

Enhanced Sb 2Se 3 solar cell performance through theory-guided defect control: Enhanced Sb 2Se 3 solar cell performance

DOE PAGES

Liu, Xinsheng; Xiao, Xun; Yang, Ye; ...

2017-05-30

Defects present in the absorber layer largely dictate photovoltaic device performance. Recently, a binary photovoltaic material, Sb 2Se 3, has drawn much attention due to its low-cost and nontoxic constituents and rapid performance promotion. So far, however, the intrinsic defects of Sb 2Se 3 remain elusive. Here in this work, through a combined theoretical and experimental investigation, we revealed that shallow acceptors, SeSb antisites, are the dominant defects in Sb 2Se 3 produced in an Se-rich environment, where deep donors, SbSe and VSe, dominate in Sb 2Se 3 produced in an Se-poor environment. We further constructed a superstrate CdS/Sb 2Semore » 3 thin-film solar cell achieving 5.76% efficiency through in situ Se compensation during Sb 2Se 3 evaporation and through careful optimization of absorber layer thickness. In conclusion, the understanding of intrinsic defects in Sb 2Se 3 film and the demonstrated success of in situ Se compensation strategy pave the way for further efficiency improvement of this very promising photovoltaic technology.« less

Morphology-controlled preparation of lead powders by electrodeposition from different PbO-containing choline chloride-urea deep eutectic solvent

NASA Astrophysics Data System (ADS)

Ru, Juanjian; Hua, Yixin; Xu, Cunying; Li, Jian; Li, Yan; Wang, Ding; Qi, Cancan; Jie, Yafei

2015-04-01

Lead powders with different morphologies, including corals, rods, wires, needles, ferns and dendritic forms, are prepared by electrodeposition onto a stainless steel substrate from different PbO-containing (10-60 mM) choline chloride-urea deep eutectic solvent at cell voltage 2.5 V and 343 K for 2 h. The electrochemical behavior of the PbO dissolved in this solvent is investigated with cyclic voltammetry. It is demonstrated that the increasing of PbO concentration makes the reduction potential EPb(II)/Pb shift positively and facilitates the electrodeposition of lead from PbO in the deep eutectic solvent. According to the analysis of the morphological and crystallographic characteristics of lead powders, the predominant origin of the growth layers is turned away from centre type towards the edge and corner types with the increase in PbO concentration. Due to the large number of growth centres at higher PbO concentration, fine and irregular grains are observed on the surface of formed particles which results in the development of primary and secondary branches in dendrites.

Gut barrier in health and disease: focus on childhood.

PubMed

Viggiano, D; Ianiro, G; Vanella, G; Bibbò, S; Bruno, G; Simeone, G; Mele, G

2015-01-01

The gut barrier is a functional unit, organized as a multi-layer system, made up of two main components: a physical barrier surface, which prevents bacterial adhesion and regulates paracellular diffusion to the host tissues, and a deep functional barrier, that is able to discriminate between pathogens and commensal microorganisms, organizing the immune tolerance and the immune response to pathogens. Other mechanisms, such as gastric juice and pancreatic enzymes (which both have antibacterial properties) participate in the luminal integrity of the gut barrier. From the outer layer to the inner layer, the physical barrier is composed of gut microbiota (that competes with pathogens to gain space and energy resources, processes the molecules necessary to mucosal integrity and modulates the immunological activity of deep barrier), mucus (which separates the intraluminal content from more internal layers and contains antimicrobial products and secretory IgA), epithelial cells (which form a physical and immunological barrier) and the innate and adaptive immune cells forming the gut-associated lymphoid tissue (which is responsible for antigen sampling and immune responses). Disruption of the gut barrier has been associated with many gastrointestinal diseases, but also with extra-intestinal pathological condition, such as type 1 diabetes mellitus, allergic diseases or autism spectrum disorders. The maintenance of a healthy intestinal barrier is therefore of paramount importance in children, for both health and economic reasons. Many drugs or compounds used in the treatment of gastrointestinal disorders act through the restoration of a normal intestinal permeability. Several studies have highlighted the role of probiotics in the modulation and reduction of intestinal permeability, considering the strong influence of gut microbiota in the modulation of the function and structure of gut barrier, but also on the immune response of the host. To date, available weapons for the maintenance and repair of gut barrier are however few, even if promising. Considerable efforts, including both a better understanding of the gut barrier features and mechanisms in health and disease, and the development of new pharmacological approaches for the modulation of gut barrier components, are needed for the prevention and treatment of gastrointestinal and extraintestinal diseases associated with gut barrier impairment.

Novel techniques with multiphoton microscopy: Deep-brain imaging with microprisms, neurometabolism of epilepsy, and counterfeit paper money detection

NASA Astrophysics Data System (ADS)

Chia, Thomas H.

Multiphoton microscopy is a laser-scanning fluorescence imaging method with extraordinary potential. We describe three innovative multiphoton microscopy techniques across various disciplines. Traditional in vivo fluorescence microscopy of the mammalian brain has a limited penetration depth (<400 microm). We present a method of imaging 1 mm deep into mouse neocortex by using a glass microprism to relay the excitation and emission light. This technique enables simultaneous imaging of multiple cortical layers, including layer V, at an angle typical of slice preparations. At high-magnification imaging using an objective with 1-mm of coverglass correction, resolution was sufficient to resolve dendritic spines on layer V GFP neurons. Functional imaging of blood flow at various neocortical depths is also presented, allowing for quantification of red blood cell flux and velocity. Multiphoton fluorescence lifetime imaging (FLIM) of NADH reveals information on neurometabolism. NADH, an intrinsic fluorescent molecule and ubiquitous metabolic coenzyme, has a lifetime dependent on enzymatic binding. A novel NADH FLIM algorithm is presented that produces images showing spatially distinct NADH fluorescence lifetimes in mammalian brain slices. This program provides advantages over traditional FLIM processing of multi-component lifetime data. We applied this technique to a GFP-GFAP pilocarpine mouse model of temporal lobe epilepsy. Results indicated significant changes in the neurometabolism of astrocytes and neuropil in the cell and dendritic layers of the hippocampus when compared to control tissue. Data obtained with NADH FLIM were subsequently interpreted based on the abnormal activity reported in epileptic tissue. Genuine U.S. Federal Reserve Notes have a consistent, two-component intrinsic fluorescence lifetime. This allows for detection of counterfeit paper money because of its significant differences in fluorescence lifetime when compared to genuine paper money. We used scanning multiphoton laser excitation to sample a ˜4 mm2 region from 54 genuine Reserve Notes. Three types of counterfeit samples were tested. Four out of the nine counterfeit samples fit to a one-component decay. Five out of nine counterfeit samples fit to a two-component model, but are identified as counterfeit due to significant deviations in the longer lifetime component compared to genuine bills.

Dermis, acellular dermal matrix, and fibroblasts from different layers of pig skin exhibit different profibrotic characteristics: evidence from in vivo study

PubMed Central

Zuo, Yanhai; Lu, Shuliang

2017-01-01

To explore the profibrotic characteristics of the autografted dermis, acellular dermal matrix, and dermal fibroblasts from superficial/deep layers of pig skin, 93 wounds were established on the dorsa of 7 pigs. 72 wounds autografted with the superficial/deep dermis and acellular dermal matrix served as the superficial/deep dermis and acellular dermal matrix group, respectively, and were sampled at 2, 4, and 8 weeks post-wounding. 21 wounds autografted with/without superficial/deep dermal fibroblasts served as the superficial/deep dermal fibroblast group and the control group, respectively, and were sampled at 2 weeks post-wounding. The hematoxylin and eosin staining showed that the wounded skin thicknesses in the deep dermis group (superficial acellular dermal matrix group) were significantly greater than those in the superficial dermis group (deep acellular dermal matrix group) at each time point, the thickness of the cutting plane in the deep dermal fibroblast group was significantly greater than that in the superficial dermal fibroblast group and the control group. The western blots showed that the α-smooth muscle actin expression in the deep dermis group (superficial acellular dermal matrix group) was significantly greater than that in the superficial dermis group (deep acellular dermal matrix group) at each time point. In summary, the deep dermis and dermal fibroblasts exhibited more profibrotic characteristics than the superficial ones, on the contrary, the deep acellular dermal matrix exhibited less profibrotic characteristics than the superficial one. PMID:28423561

Development of the human lateral geniculate nucleus: A morphometric and computerized 3D-reconstruction study.

PubMed

Yamaguchi, Katsuyuki

2018-04-04

The lateral geniculate nucleus (LGN) is the major relay center of the visual pathway in humans. There are few quantitative data on the morphology of LGN in prenatal infants. In this study, using serial brain sections, the author investigated the morphology of this nucleus during the second half of fetal period. Eleven human brains were obtained at routine autopsy from preterm infants aged 20-39 postmenstrual weeks. After fixation, the brain was embedded en bloc in celloidin and cut serially at 30 μm in the horizontal plane. The sections were stained at regular intervals using the Klüver-Barrera method. At 20-21 weeks, the long axis of LGN declined obliquely from the vertical to horizontal plane, while a deep groove was noted on the ventro-lateral surface of the superior half. At this time, an arcuate cell-sparse zone appeared in the dorso-medial region, indicating the beginning of lamination. From 25 weeks onwards, the magnocellular and parvocellular layers were distinguishable, and the characteristic six-layered structure was recognized. The magnocellular layer covered most of the dorsal surface, and parts of the medial, lateral, and inferior surfaces but not the ventral and superior surfaces. Nuclear volume increased exponentially with age during 20-39 weeks, while the mean neuronal profile area increased linearly during 25-39 weeks. Human LGN develops a deep groove on the ventro-lateral surface at around mid-gestation, when the initial lamination is recognized in the prospective magnocellular layer. Thereafter, the nuclear volume increases with age in an exponential function. Copyright © 2018 Elsevier B.V. All rights reserved.

Deep learning in the small sample size setting: cascaded feed forward neural networks for medical image segmentation

NASA Astrophysics Data System (ADS)

Gaonkar, Bilwaj; Hovda, David; Martin, Neil; Macyszyn, Luke

2016-03-01

Deep Learning, refers to large set of neural network based algorithms, have emerged as promising machine- learning tools in the general imaging and computer vision domains. Convolutional neural networks (CNNs), a specific class of deep learning algorithms, have been extremely effective in object recognition and localization in natural images. A characteristic feature of CNNs, is the use of a locally connected multi layer topology that is inspired by the animal visual cortex (the most powerful vision system in existence). While CNNs, perform admirably in object identification and localization tasks, typically require training on extremely large datasets. Unfortunately, in medical image analysis, large datasets are either unavailable or are extremely expensive to obtain. Further, the primary tasks in medical imaging are organ identification and segmentation from 3D scans, which are different from the standard computer vision tasks of object recognition. Thus, in order to translate the advantages of deep learning to medical image analysis, there is a need to develop deep network topologies and training methodologies, that are geared towards medical imaging related tasks and can work in a setting where dataset sizes are relatively small. In this paper, we present a technique for stacked supervised training of deep feed forward neural networks for segmenting organs from medical scans. Each `neural network layer' in the stack is trained to identify a sub region of the original image, that contains the organ of interest. By layering several such stacks together a very deep neural network is constructed. Such a network can be used to identify extremely small regions of interest in extremely large images, inspite of a lack of clear contrast in the signal or easily identifiable shape characteristics. What is even more intriguing is that the network stack achieves accurate segmentation even when it is trained on a single image with manually labelled ground truth. We validate this approach,using a publicly available head and neck CT dataset. We also show that a deep neural network of similar depth, if trained directly using backpropagation, cannot acheive the tasks achieved using our layer wise training paradigm.

Histopathology of motor cortex in an experimental focal ischemic stroke in mouse model.

PubMed

de Oliveira, Juçara Loli; Crispin, Pedro di Tárique Barreto; Duarte, Elisa Cristiana Winkelmann; Marloch, Gilberto Domingos; Gargioni, Rogério; Trentin, Andréa Gonçalves; Alvarez-Silva, Marcio

2014-05-01

Experimental ischemia results in cortical brain lesion followed by ischemic stroke. In this study, focal cerebral ischemia was induced in mice by occlusion of the middle cerebral artery. We studied cortical layers I, II/III, V and VI in the caudal forelimb area (CFA) and medial agranular cortex (AGm) from control and C57BL/6 mice induced with ischemic stroke. Based on our analysis of CFA and AGm motor cortex, significant differences were observed in the numbers of neurons, astrocytes and microglia in the superficial II/III and deep V cortical layers. Cellular changes were more prominent in layer V of the CFA with nuclear pyknosis, chromatin fragmentation, necrosis and degeneration, as well as, morphological evidence of apoptosis, mainly in neurons. As result, the CFA was more severely impaired than the AGm in this focal cerebral ischemic model, as evidenced by the proliferation of astrocytes, potentially resulting in neuroinflammation by microglia-like cells. Copyright © 2014 Elsevier B.V. All rights reserved.

Step-off, vertical electromagnetic responses of a deep resistivity layer buried in marine sediments

NASA Astrophysics Data System (ADS)

Jang, Hangilro; Jang, Hannuree; Lee, Ki Ha; Kim, Hee Joon

2013-04-01

A frequency-domain, marine controlled-source electromagnetic (CSEM) method has been applied successfully in deep water areas for detecting hydrocarbon (HC) reservoirs. However, a typical technique with horizontal transmitters and receivers requires large source-receiver separations with respect to the target depth. A time-domain EM system with vertical transmitters and receivers can be an alternative because vertical electric fields are sensitive to deep resistive layers. In this paper, a time-domain modelling code, with multiple source and receiver dipoles that are finite in length, has been written to investigate transient EM problems. With the use of this code, we calculate step-off responses for one-dimensional HC reservoir models. Although the vertical electric field has much smaller amplitude of signal than the horizontal field, vertical currents resulting from a vertical transmitter are sensitive to resistive layers. The modelling shows a significant difference between step-off responses of HC- and water-filled reservoirs, and the contrast can be recognized at late times at relatively short offsets. A maximum contrast occurs at more than 4 s, being delayed with the depth of the HC layer.

A Deep-Structured Conditional Random Field Model for Object Silhouette Tracking

PubMed Central

Shafiee, Mohammad Javad; Azimifar, Zohreh; Wong, Alexander

2015-01-01

In this work, we introduce a deep-structured conditional random field (DS-CRF) model for the purpose of state-based object silhouette tracking. The proposed DS-CRF model consists of a series of state layers, where each state layer spatially characterizes the object silhouette at a particular point in time. The interactions between adjacent state layers are established by inter-layer connectivity dynamically determined based on inter-frame optical flow. By incorporate both spatial and temporal context in a dynamic fashion within such a deep-structured probabilistic graphical model, the proposed DS-CRF model allows us to develop a framework that can accurately and efficiently track object silhouettes that can change greatly over time, as well as under different situations such as occlusion and multiple targets within the scene. Experiment results using video surveillance datasets containing different scenarios such as occlusion and multiple targets showed that the proposed DS-CRF approach provides strong object silhouette tracking performance when compared to baseline methods such as mean-shift tracking, as well as state-of-the-art methods such as context tracking and boosted particle filtering. PMID:26313943

GaN ultraviolet p-i-n photodetectors with enhanced deep ultraviolet quantum efficiency

NASA Astrophysics Data System (ADS)

Wang, Guosheng; Xie, Feng; Wang, Jun; Guo, Jin

2017-10-01

GaN ultraviolet (UV) p-i-n photodetectors (PDs) with a thin p-AlGaN/GaN contact layer are designed and fabricated. The PD exhibits a low dark current density of˜7 nA/cm2 under -5 V, and a zero-bias peak responsivity of ˜0.16 A/W at 360 nm, which corresponds to a maximum quantum efficiency of 55%. It is found that, in the wavelength range between 250 and 365 nm, the PD with thin p-AlGaN/GaN contact layer exhibits enhanced quantum efficiency especially in a deep-UV wavelength range, than that of the control PD with conventional thin p-GaN contact layer. The improved quantum efficiency of the PD with thin p-AlGaN/GaN contact layer in the deep-UV wavelength range is mainly attributed to minority carrier reflecting properties of thin p-AlGaN/GaN heterojunction which could reduce the surface recombination loss of photon-generated carriers and improve light current collection efficiency.

A new cytotoxic sesquiterpene quinone produced by Penicillium sp. F00120 isolated from a deep sea sediment sample.

PubMed

Lin, Xiuping; Zhou, Xuefeng; Wang, Fazuo; Liu, Kaisheng; Yang, Bin; Yang, Xianwen; Peng, Yan; Liu, Juan; Ren, Zhe; Liu, Yonghong

2012-01-01

A new fungal strain, displaying strong toxic activity against brine shrimp larvae, was isolated from a deep sea sediment sample collected at a depth of 1300 m. The strain, designated as F00120, was identified as a member of the genus Penicillium on the basis of morphology and ITS sequence analysis. One new sesquiterpene quinone, named penicilliumin A (1), along with two known compounds ergosterol (2) and ergosterol peroxide (3), were isolated and purified from the cultures of F00120 by silica gel column, Sephadex LH-20 column, and preparative thin layer chromatography. Their structures were elucidated by detailed nuclear magnetic resonance (NMR) and mass spectroscopic (MS) analysis as well as comparison with literature data. The new compound penicilliumin A inhibited in vitro proliferation of mouse melanoma (B16), human melanoma (A375), and human cervical carcinoma (Hela) cell lines moderately.

Onset of Tlx-3 expression in the chick cerebellar cortex correlates with the morphological development of fissures and delineates a posterior transverse boundary.

PubMed

Logan, Cairine; Millar, Cassie; Bharadia, Vinay; Rouleau, Katherine

2002-06-24

Recent studies have shown that the mammalian cerebellar cortex can be subdivided into a reproducible array of zones and stripes. In particular, discontinuous patterns of gene expression together with mutational analysis suggest that there are at least four distinct transverse zones along the rostrocaudal axis in mouse: the anterior zone (lobules I-V), the central zone (lobules VI and VII), the posterior zone (lobules VIII and IX), and the nodular zone (lobule X). Here we show that the divergent homeobox-containing transcription factor, Tlx- 3 (also known as Hox11L2 or Rnx) is transiently expressed in external granule cells in a distinct transverse domain of the developing chick cerebellar cortex. Expression is first detected at Hamburger and Hamilton (HH) stage 35. Interestingly, Tlx-3 mRNA expression is initially confined to, and coincident with, the morphological development of fissures. Slightly later, at HH stage 38, expression extends throughout the developing external granular layer (EGL) of lobules I-IXab. Notably, no Tlx-3 expression was detected in lobules IXc and X at any developmental time point examined. Expression is noticeably stronger in nonproliferating cells located in the deep layer of the EGL. Tlx-3 expression is downregulated as granule cells migrate inward to form the internal granule layer and is undetectable shortly after birth. These results suggest that Tlx-3 is expressed as granule cells become postmitotic and suggest that Tlx-3 may play a role in the differentiation of distinct neuronal populations in the cerebellum. Copyright 2002 Wiley-Liss, Inc.

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions

PubMed Central

Bukin, Sergei V.; Pavlova, Olga N.; Manakov, Andrei Y.; Kostyreva, Elena A.; Chernitsyna, Svetlana M.; Mamaeva, Elena V.; Pogodaeva, Tatyana V.; Zemskaya, Tamara I.

2016-01-01

The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids. PMID:27242716

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions.

PubMed

Bukin, Sergei V; Pavlova, Olga N; Manakov, Andrei Y; Kostyreva, Elena A; Chernitsyna, Svetlana M; Mamaeva, Elena V; Pogodaeva, Tatyana V; Zemskaya, Tamara I

2016-01-01

The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH4:H2:CO2. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH4 atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids.

Expression of the alpha and beta subunits of Ca2+/calmodulin kinase II in the cerebellum of jaundiced Gunn rats during development: a quantitative light microscopic analysis.

PubMed

Conlee, J W; Shapiro, S M; Churn, S B

2000-04-01

The homozygous (jj) jaundiced Gunn rat model for hyperbilirubinemia displays pronounced cerebellar hypoplasia. To examine the cellular mechanisms involved in bilirubin toxicity, this study focused on the effect of hyperbilirubinemia on calcium/calmodulin-dependent kinase II (CaM kinase II). CaM kinase II is a neuronally enriched enzyme which performs several important functions. Immunohistochemical analysis of alternating serial sections were performed using monoclonal antibodies for the alpha and beta subunits of CaM kinase II. Measurements were made of the total numbers of stained cells in each of the deep cerebellar nuclei and of Purkinje and granule cell densities in cerebellar lobules II, VI, and IX. The beta subunit was present in Purkinje cells and deep cerebellar nuclei of both groups at all ages, but only granule cells which had migrated through the Purkinje cell layer showed staining for beta subunit; external granule cells were completely negative. Many Purkinje cells had degenerated in the older animals, and the percent of granule cells stained for beta subunit was significantly reduced. The alpha subunit was found exclusively in Purkinje cells, although its appearance was delayed in the jaundiced animals. Sulfadimethoxine was administered to some jj rats 24 h or 15 days prior to sacrifice to increase brain bilirubin concentration. Results showed that bilirubin exposure modulated both alpha and beta CaM kinase II subunit expression in selective neuronal populations, but sulfadimethoxine had no acute effect on enzyme immunoreactivity. Thus, developmental expression of the alpha and beta subunits of CaM kinase II was affected by chronic bilirubin exposure during early postnatal development of jaundiced Gunn rats.

Ion beam evaluation of silicon carbide membrane structures intended for particle detectors

NASA Astrophysics Data System (ADS)

Pallon, J.; Syväjärvi, M.; Wang, Q.; Yakimova, R.; Iakimov, T.; Elfman, M.; Kristiansson, P.; Nilsson, E. J. C.; Ros, L.

2016-03-01

Thin ion transmission detectors can be used as a part of a telescope detector for mass and energy identification but also as a pre-cell detector in a microbeam system for studies of biological effects from single ion hits on individual living cells. We investigated a structure of graphene on silicon carbide (SiC) with the purpose to explore a thin transmission detector with a very low noise level and having mechanical strength to act as a vacuum window. In order to reach very deep cavities in the SiC wafers for the preparation of the membrane in the detector, we have studied the Inductive Coupled Plasma technique to etch deep circular cavities in 325 μm prototype samples. By a special high temperature process the outermost layers of the etched SiC wafers were converted into a highly conductive graphitic layer. The produced cavities were characterized by electron microscopy, optical microscopy and proton energy loss measurements. The average membrane thickness was found to be less than 40 μm, however, with a slightly curved profile. Small spots representing much thinner membrane were also observed and might have an origin in crystal defects or impurities. Proton energy loss measurement (also called Scanning Transmission Ion Microscopy, STIM) is a well suited technique for this thickness range. This work presents the first steps of fabricating a membrane structure of SiC and graphene which may be an attractive approach as a detector due to the combined properties of SiC and graphene in a monolithic materials structure.

A Circuit for Motor Cortical Modulation of Auditory Cortical Activity

PubMed Central

Nelson, Anders; Schneider, David M.; Takatoh, Jun; Sakurai, Katsuyasu; Wang, Fan

2013-01-01

Normal hearing depends on the ability to distinguish self-generated sounds from other sounds, and this ability is thought to involve neural circuits that convey copies of motor command signals to various levels of the auditory system. Although such interactions at the cortical level are believed to facilitate auditory comprehension during movements and drive auditory hallucinations in pathological states, the synaptic organization and function of circuitry linking the motor and auditory cortices remain unclear. Here we describe experiments in the mouse that characterize circuitry well suited to transmit motor-related signals to the auditory cortex. Using retrograde viral tracing, we established that neurons in superficial and deep layers of the medial agranular motor cortex (M2) project directly to the auditory cortex and that the axons of some of these deep-layer cells also target brainstem motor regions. Using in vitro whole-cell physiology, optogenetics, and pharmacology, we determined that M2 axons make excitatory synapses in the auditory cortex but exert a primarily suppressive effect on auditory cortical neuron activity mediated in part by feedforward inhibition involving parvalbumin-positive interneurons. Using in vivo intracellular physiology, optogenetics, and sound playback, we also found that directly activating M2 axon terminals in the auditory cortex suppresses spontaneous and stimulus-evoked synaptic activity in auditory cortical neurons and that this effect depends on the relative timing of motor cortical activity and auditory stimulation. These experiments delineate the structural and functional properties of a corticocortical circuit that could enable movement-related suppression of auditory cortical activity. PMID:24005287

Fast voltage-sensitive dye imaging of excitatory and inhibitory synaptic transmission in the rat granular retrosplenial cortex.

PubMed

Nixima, Ken'ichi; Okanoya, Kazuo; Ichinohe, Noritaka; Kurotani, Tohru

2017-09-01

Rodent granular retrosplenial cortex (GRS) has dense connections between the anterior thalamic nuclei (ATN) and hippocampal formation. GRS superficial pyramidal neurons exhibit distinctive late spiking (LS) firing property and form patchy clusters with prominent apical dendritic bundles. The aim of this study was to investigate spatiotemporal dynamics of signal transduction in the GRS induced by ATN afferent stimulation by using fast voltage-sensitive dye imaging in rat brain slices. In coronal slices, layer 1a stimulation, which presumably activated thalamic fibers, evoked propagation of excitatory synaptic signals from layers 2-4 to layers 5-6 in a direction perpendicular to the layer axis, followed by transverse signal propagation within each layer. In the presence of ionotropic glutamate receptor antagonists, inhibitory responses were observed in superficial layers, induced by direct activation of inhibitory interneurons in layer 1. In horizontal slices, excitatory signals in deep layers propagated transversely mainly from posterior to anterior via superficial layers. Cortical inhibitory responses upon layer 1a stimulation in horizontal slices were weaker than those in the coronal slices. Observed differences between coronal and horizontal planes suggest anisotropy of the intracortical circuitry. In conclusion, ATN inputs are processed differently in coronal and horizontal planes of the GRS and then conveyed to other cortical areas. In both planes, GRS superficial layers play an important role in signal propagation, which suggests that superficial neuronal cascade is crucial in the integration of multiple information sources. NEW & NOTEWORTHY Superficial neurons in the rat granular retrosplenial cortex (GRS) show distinctive late-spiking (LS) firing property. However, little is known about spatiotemporal dynamics of signal transduction in the GRS. We demonstrated LS neuron network relaying thalamic inputs to deep layers and anisotropic distribution of inhibition between coronal and horizontal planes. Since deep layers of the GRS receive inputs from the subiculum, GRS circuits may work as an integrator of multiple sources such as sensory and memory information. Copyright © 2017 the American Physiological Society.

[Effects of deep plowing and mulch in fallow period on soil water and yield of wheat in dryland].

PubMed

Deng, Yan; Gao, Zhi-Qiang; Sun, Min; Zhao, Wei-Feng; Zhao, Hong-Mei; Li, Qing

2014-01-01

A field test was carried out in Qiujialing Village, Wenxi, Shanxi from 2009 to 2011 to study the soil water movement of 0-300 cm layer, yield formation and water use efficiency (WUE) of wheat with deep plowing and mulching the whole ground immediately (no mulch as control) 15 days and 45 days after harvest. The results indicated that deep plowing and mulch in fallow period could improve soil water storage of the 100-180 cm layer before sowing, the soil water storage efficiency in fallow period, and soil water storage from pre-wintering stage to booting stage. Compared with deep plowing 15 days after wheat harvest, deep plowing 45 days after wheat harvest did better in improving soil water storage and water use efficiency, as well as ear number and yield, which was more conducive in the year with more precipitation. Generally, deep plowing and mulching after raining during fallow period could benefit the soil water storage and conservation, thus would be helpful to improve wheat yield in dryland.

Shakeout: A New Approach to Regularized Deep Neural Network Training.

PubMed

Kang, Guoliang; Li, Jun; Tao, Dacheng

2018-05-01

Recent years have witnessed the success of deep neural networks in dealing with a plenty of practical problems. Dropout has played an essential role in many successful deep neural networks, by inducing regularization in the model training. In this paper, we present a new regularized training approach: Shakeout. Instead of randomly discarding units as Dropout does at the training stage, Shakeout randomly chooses to enhance or reverse each unit's contribution to the next layer. This minor modification of Dropout has the statistical trait: the regularizer induced by Shakeout adaptively combines , and regularization terms. Our classification experiments with representative deep architectures on image datasets MNIST, CIFAR-10 and ImageNet show that Shakeout deals with over-fitting effectively and outperforms Dropout. We empirically demonstrate that Shakeout leads to sparser weights under both unsupervised and supervised settings. Shakeout also leads to the grouping effect of the input units in a layer. Considering the weights in reflecting the importance of connections, Shakeout is superior to Dropout, which is valuable for the deep model compression. Moreover, we demonstrate that Shakeout can effectively reduce the instability of the training process of the deep architecture.

Deep Unfolding for Topic Models.

PubMed

Chien, Jen-Tzung; Lee, Chao-Hsi

2018-02-01

Deep unfolding provides an approach to integrate the probabilistic generative models and the deterministic neural networks. Such an approach is benefited by deep representation, easy interpretation, flexible learning and stochastic modeling. This study develops the unsupervised and supervised learning of deep unfolded topic models for document representation and classification. Conventionally, the unsupervised and supervised topic models are inferred via the variational inference algorithm where the model parameters are estimated by maximizing the lower bound of logarithm of marginal likelihood using input documents without and with class labels, respectively. The representation capability or classification accuracy is constrained by the variational lower bound and the tied model parameters across inference procedure. This paper aims to relax these constraints by directly maximizing the end performance criterion and continuously untying the parameters in learning process via deep unfolding inference (DUI). The inference procedure is treated as the layer-wise learning in a deep neural network. The end performance is iteratively improved by using the estimated topic parameters according to the exponentiated updates. Deep learning of topic models is therefore implemented through a back-propagation procedure. Experimental results show the merits of DUI with increasing number of layers compared with variational inference in unsupervised as well as supervised topic models.

Comparative histometric analysis of the effects of high-intensity focused ultrasound and radiofrequency on skin.

PubMed

Suh, Dong Hye; Choi, Jeong Hwee; Lee, Sang Jun; Jeong, Ki-Heon; Song, Kye Yong; Shin, Min Kyung

2015-01-01

High-intensity focused ultrasound (HIFU) and radiofrequency (RF) are used for non-invasive skin tightening. Neocollagenesis and neoelastogenesis have been reported to have a mechanism of controlled thermal injury. To compare neocollagenesis and neoelastogenesis in each layer of the dermis after each session of HIFU and monopolar RF. We analyzed the area fraction of collagen and elastic fibers using the Masson's Trichrome and Victoria blue special stains, respectively, before and after 2 months of treatments. Histometric analyses were performed in each layer of the dermis, including the papillary dermis, and upper, mid, and deep reticular dermis. Monopolar RF led to neocollagenesis in the papillary dermis, and upper, mid, and deep reticular dermis, and neoelastogenesis in the papillary dermis, and upper and mid reticular dermis. HIFU led to neocollagenesis in the mid and deep reticular dermis and neoelastogenesis in the deep reticular dermis. Among these treatment methods, HIFU showed the highest level of neocollagenesis and neoelastogenesis in the deep reticular dermis. HIFU affects deep tissues and impacts focal regions. Monopolar RF also affects deep tissues, but impacts diffuse regions. We believe these data provide further insight into effective skin tightening.

Recognition of emotions using multimodal physiological signals and an ensemble deep learning model.

PubMed

Yin, Zhong; Zhao, Mengyuan; Wang, Yongxiong; Yang, Jingdong; Zhang, Jianhua

2017-03-01

Using deep-learning methodologies to analyze multimodal physiological signals becomes increasingly attractive for recognizing human emotions. However, the conventional deep emotion classifiers may suffer from the drawback of the lack of the expertise for determining model structure and the oversimplification of combining multimodal feature abstractions. In this study, a multiple-fusion-layer based ensemble classifier of stacked autoencoder (MESAE) is proposed for recognizing emotions, in which the deep structure is identified based on a physiological-data-driven approach. Each SAE consists of three hidden layers to filter the unwanted noise in the physiological features and derives the stable feature representations. An additional deep model is used to achieve the SAE ensembles. The physiological features are split into several subsets according to different feature extraction approaches with each subset separately encoded by a SAE. The derived SAE abstractions are combined according to the physiological modality to create six sets of encodings, which are then fed to a three-layer, adjacent-graph-based network for feature fusion. The fused features are used to recognize binary arousal or valence states. DEAP multimodal database was employed to validate the performance of the MESAE. By comparing with the best existing emotion classifier, the mean of classification rate and F-score improves by 5.26%. The superiority of the MESAE against the state-of-the-art shallow and deep emotion classifiers has been demonstrated under different sizes of the available physiological instances. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Decay of deep water convection in CMIP5 GCMs in the North Atlantic and Southern Ocean in the 21st century

NASA Astrophysics Data System (ADS)

Molodtsov, S.; Anis, A.; Marinov, I.; Cabre, A.

2016-12-01

Contemporary changes in the climate system due to anthropogenic activity have already resulted in unprecedented melting rates of the polar ice caps. This in turn may have a significant impact on the thermohaline circulation in the future. The freshening of the surface waters increases stable stratification in regions of deep water formation, eventually triggering a weakening and, ultimately, may bring to a cessation of deep convection in these regions. Here we present comparatively an analysis of the response of deep convective processes in the North Atlantic (NA) and Southern Ocean (SO) to anthropogenic forcing using output from the latest generation of Earth System Models (ESM), part of the CMIP5 intercomparison. Our findings indicate an attenuation of deep convection by the end of the 21st century from ESM simulations under representative concentration pathways (RCP) 8.5 scenario when compared to the years under historical scenario in both NA and SO. The average depth of the mixed layer in the regions studied during March/September, the months with maximum mixed layer depths in the NA/SO, respectively, was found to decrease dramatically by the end of the 21st century. Furthermore, the increase in stratification and decrease in mixed layer depths, resulting in the decay of deep convection, leads to accumulation of excess heat, previously released during the convection events, in the ocean interior in both regions.

deepNF: Deep network fusion for protein function prediction.

PubMed

Gligorijevic, Vladimir; Barot, Meet; Bonneau, Richard

2018-06-01

The prevalence of high-throughput experimental methods has resulted in an abundance of large-scale molecular and functional interaction networks. The connectivity of these networks provides a rich source of information for inferring functional annotations for genes and proteins. An important challenge has been to develop methods for combining these heterogeneous networks to extract useful protein feature representations for function prediction. Most of the existing approaches for network integration use shallow models that encounter difficulty in capturing complex and highly-nonlinear network structures. Thus, we propose deepNF, a network fusion method based on Multimodal Deep Autoencoders to extract high-level features of proteins from multiple heterogeneous interaction networks. We apply this method to combine STRING networks to construct a common low-dimensional representation containing high-level protein features. We use separate layers for different network types in the early stages of the multimodal autoencoder, later connecting all the layers into a single bottleneck layer from which we extract features to predict protein function. We compare the cross-validation and temporal holdout predictive performance of our method with state-of-the-art methods, including the recently proposed method Mashup. Our results show that our method outperforms previous methods for both human and yeast STRING networks. We also show substantial improvement in the performance of our method in predicting GO terms of varying type and specificity. deepNF is freely available at: https://github.com/VGligorijevic/deepNF. vgligorijevic@flatironinstitute.org, rb133@nyu.edu. Supplementary data are available at Bioinformatics online.

Ultra-diffuse hydrothermal venting supports Fe-oxidizing bacteria and massive umber deposition at 5000 m off Hawaii

PubMed Central

Edwards, Katrina J; Glazer, B T; Rouxel, O J; Bach, W; Emerson, D; Davis, R E; Toner, B M; Chan, C S; Tebo, B M; Staudigel, H; Moyer, C L

2011-01-01

A novel hydrothermal field has been discovered at the base of Lōihi Seamount, Hawaii, at 5000 mbsl. Geochemical analyses demonstrate that ‘FeMO Deep', while only 0.2 °C above ambient seawater temperature, derives from a distal, ultra-diffuse hydrothermal source. FeMO Deep is expressed as regional seafloor seepage of gelatinous iron- and silica-rich deposits, pooling between and over basalt pillows, in places over a meter thick. The system is capped by mm to cm thick hydrothermally derived iron-oxyhydroxide- and manganese-oxide-layered crusts. We use molecular analyses (16S rDNA-based) of extant communities combined with fluorescent in situ hybridizations to demonstrate that FeMO Deep deposits contain living iron-oxidizing Zetaproteobacteria related to the recently isolated strain Mariprofundus ferroxydans. Bioenergetic calculations, based on in-situ electrochemical measurements and cell counts, indicate that reactions between iron and oxygen are important in supporting chemosynthesis in the mats, which we infer forms a trophic base of the mat ecosystem. We suggest that the biogenic FeMO Deep hydrothermal deposit represents a modern analog for one class of geological iron deposits known as ‘umbers' (for example, Troodos ophilolites, Cyprus) because of striking similarities in size, setting and internal structures. PMID:21544100

Oxidation preventative capping layer for deep-ultra-violet and soft x-ray multilayers

DOEpatents

Prisbrey, Shon T.

2004-07-06

The invention uses iridium and iridium compounds as a protective capping layer on multilayers having reflectivity in the deep ultra-violet to soft x-ray regime. The iridium compounds can be formed in one of two ways: by direct deposition of the iridium compound from a prepared target or by depositing a thin layer (e.g., 5-50 angstroms) of iridium directly onto an element. The deposition energy of the incoming iridium is sufficient to activate the formation of the desired iridium compound. The compounds of most interest are iridium silicide (IrSi.sub.x) and iridium molybdenide (IrMo.sub.x).

Discrete model of the olivo-cerebellar system: structure and dynamics

NASA Astrophysics Data System (ADS)

Maslennikov, O. V.; Nekorkin, V. I.

2012-08-01

We propose a discrete model of the olivo-cerebellar system. The model consists of three layers of interacting elements, namely, inferior olive neurons, Purkinje cells, and deep cerebellar nuclear neurons combined into a structure by axonal connections. Each element of the structure is described by a two-dimensional map with an individual set of parameters for each type of neurons. Dynamic properties of different types of neurons are described and spontaneous and stimulusinduced dynamics of the system is explored. Unlike the previously proposed models, this study takes into account the axonal interaction of neurons of different layers, as well as the interaction of the inferior olive neurons through electrical synapses with the property of plasticity. It is shown that the inclusion of these factors plays a significant role in the formation of spatio-temporal activity of the inferior olive neurons.

Polydimethylsiloxane Droplets Exhibit Extraordinarily High Antioxidative Effects in Deep-Frying.

PubMed

Totani, Nagao; Yazaki, Naoko; Yawata, Miho

2017-04-03

The addition of more than about 1 ppm polydimethylsiloxane (PDMS) into oil results in PDMS forming both a layer at the oil-air interface and droplets suspended in the oil. It is widely accepted that the extraordinarily strong and stable antioxidative effects of PDMS are due to the PDMS layer. However, the PDMS layer showed no antioxidative effects when canola oil did not contain droplets but rather was covered with a layer of PDMS, then subjected to heating under high agitation to mimic deep-frying. Furthermore, no antioxidative effect was exhibited by oil-soluble methylphenylsiloxane (PMPS) in canola oil or by PDMS in PDMS-soluble canola oil fatty acid ester during heating, suggesting that PDMS must be insoluble and droplets in oil in order for PDMS to exhibit an antioxidative effect during deep-frying. The zeta potential of PDMS droplets suspended in canola oil was very high and thus the negatively charged PDMS droplets should attract nearby low molecular weight compounds. It was suggested that this attraction disturbed the motion of oxygen molecules and prevented their attack against unsaturated fatty acid moiety. This would be the reason in the deep-frying why PDMS suppressed the oxidation reaction of oil. PDMS droplets also attracted volatile compounds (molecular weight below 125 Da) generated by heating canola oil. Thus, adding PDMS to oil after heating the oil resulted in the heated oil smelling less than heated oil without PDMS.

How Diffusivity, Thermocline and Incident Light Intensity Modulate the Dynamics of Deep Chlorophyll Maximum in Tyrrhenian Sea

PubMed Central

Valenti, Davide; Denaro, Giovanni; Spagnolo, Bernardo; Conversano, Fabio; Brunet, Christophe

2015-01-01

During the last few years theoretical works have shed new light and proposed new hypotheses on the mechanisms which regulate the spatio-temporal behaviour of phytoplankton communities in marine pelagic ecosystems. Despite this, relevant physical and biological issues, such as effects of the time-dependent mixing in the upper layer, competition between groups, and dynamics of non-stationary deep chlorophyll maxima, are still open questions. In this work, we analyze the spatio-temporal behaviour of five phytoplankton populations in a real marine ecosystem by using a one-dimensional reaction-diffusion-taxis model. The study is performed, taking into account the seasonal variations of environmental variables, such as light intensity, thickness of upper mixed layer and profiles of vertical turbulent diffusivity, obtained starting from experimental findings. Theoretical distributions of phytoplankton cell concentration was converted in chlorophyll concentration, and compared with the experimental profiles measured in a site of the Tyrrhenian Sea at four different times (seasons) of the year, during four different oceanographic cruises. As a result we find a good agreement between theoretical and experimental distributions of chlorophyll concentration. In particular, theoretical results reveal that the seasonal changes of environmental variables play a key role in the phytoplankton distribution and determine the properties of the deep chlorophyll maximum. This study could be extended to other marine ecosystems to predict future changes in the phytoplankton biomass due to global warming, in view of devising strategies to prevent the decline of the primary production and the consequent decrease of fish species. PMID:25629963

Development of a functionalized UV-emitting nanocomposite for the treatment of cancer using indirect photodynamic therapy.

PubMed

Sengar, Prakhar; Juárez, Patricia; Verdugo-Meza, Andrea; Arellano, Danna L; Jain, Akhil; Chauhan, Kanchan; Hirata, Gustavo A; Fournier, Pierrick G J

2018-02-27

Photodynamic therapy is a promising cancer therapy modality but its application for deep-seated tumor is mainly hindered by the shallow penetration of visible light. X-ray-mediated photodynamic therapy (PDT) has gained a major attention owing to the limitless penetration of X-rays. However, substantial outcomes have still not been achieved due to the low luminescence efficiency of scintillating nanoparticles and weak energy transfer to the photosensitizer. The present work describes the development of Y 2.99 Pr 0.01 Al 5 O 12 -based (YP) mesoporous silica coated nanoparticles, multifunctionalized with protoporphyrin IX (PpIX) and folic acid (YPMS@PpIX@FA) for potential application in targeted deep PDT. A YP nanophosphor core was synthesized using the sol-gel method to be used as X-ray energy transducer and was then covered with a mesoporous silica layer. The luminescence analysis indicated a good spectral overlap between the PpIX and nanoscintillator at the Soret as well as Q-band region. The comparison of the emission spectra with or without PpIX showed signs of energy transfer, a prerequisite for deep PDT. In vitro studies showed the preferential uptake of the nanocomposite in cancer cells expressing the folate receptorFolr1, validating the targeting efficiency. Direct activation of conjugated PpIX with UVA in vitro induced ROS production causing breast and prostate cancer cell death indicating that the PpIX retained its activity after conjugation to the nanocomposite. The in vivo toxicity analysis showed the good biocompatibility and non-immunogenic response of YPMS@PpIX@FA. Our results indicate that YPMS@PpIX@FA nanocomposites are promising candidates for X-ray-mediated PDT of deep-seated tumors. The design of these nanoparticles allows the functionalization with exchangeable targeting ligands thus offering versatility, in order to target various cancer cells, expressing different molecular targets on their surface.

Global assessment of benthic nepheloid layers and linkage with upper ocean dynamics

NASA Astrophysics Data System (ADS)

Gardner, Wilford D.; Richardson, Mary Jo; Mishonov, Alexey V.

2018-01-01

Global maps of the maximum bottom concentration, thickness, and integrated particle mass in benthic nepheloid layers are published here to support collaborations to understand deep ocean sediment dynamics, linkage with upper ocean dynamics, and assessing the potential for scavenging of adsorption-prone elements near the deep ocean seafloor. Mapping the intensity of benthic particle concentrations from natural oceanic processes also provides a baseline that will aid in quantifying the industrial impact of current and future deep-sea mining. Benthic nepheloid layers have been mapped using 6,392 full-depth profiles made during 64 cruises using our transmissometers mounted on CTDs in multiple national/international programs including WOCE, SAVE, JGOFS, CLIVAR-Repeat Hydrography, and GO-SHIP during the last four decades. Intense benthic nepheloid layers are found in areas where eddy kinetic energy in overlying waters, mean kinetic energy 50 m above bottom (mab), and energy dissipation in the bottom boundary layer are near the highest values in the ocean. Areas of intense benthic nepheloid layers include the Western North Atlantic, Argentine Basin in the South Atlantic, parts of the Southern Ocean and areas around South Africa. Benthic nepheloid layers are weak or absent in most of the Pacific, Indian, and Atlantic basins away from continental margins. High surface eddy kinetic energy is associated with the Kuroshio Current east of Japan. Data south of the Kuroshio show weak nepheloid layers, but no transmissometer data exist beneath the Kuroshio, a deficiency that should be remedied to increase understanding of eddy dynamics in un-sampled and under-sampled oceanic areas.

[Effects of land use change on soil active organic carbon in deep soils in Hilly Loess Plateau region of Northwest China].

PubMed

Zhang, Shuai; Xu, Ming-Xiang; Zhang, Ya-Feng; Wang, Chao-Hua; Chen, Gai

2015-02-01

Response of soil active organic carbon to land-use change has become a hot topic in current soil carbon and nutrient cycling study. Soil active organic carbon distribution characteristics in soil profile under four land-use types were investigated in Ziwuling forest zone of the Hilly Loess Plateau region. The four types of land-use changes included natural woodland converted into artificial woodland, natural woodland converted into cropland, natural shrubland converted into cropland and natural shrubland converted into revegetated grassland. Effects of land-use changes on soil active organic carbon in deep soil layers (60-200 cm) were explored by comparison with the shallow soil layers (0-60 cm). The results showed that: (1) The labile organic carbon ( LOC) and microbial carbon (MBC) content were mainly concentrated in the shallow 0-60 cm soil, which accounted for 49%-66% and 71%-84% of soil active organic carbon in the profile (0-200 cm) under different land-use types. Soil active organic carbon content in shallow soil was significantly varied for the land-use changes types, while no obvious difference was observed in soil active organic carbon in deep soil layer. (2) Land-use changes exerted significant influence on soil active organic carbon, the active organic carbon in shallow soil was more sensitive than that in deep soil. The four types of land-use changes, including natural woodland to planted woodland, natural woodland to cropland, natural shrubland to revegetated grassland and natural shrubland to cropland, LOC in shallow soil was reduced by 10%, 60%, 29%, 40% and LOC in the deep layer was decreased by 9%, 21%, 12%, 1%, respectively. MBC in the shallow soil was reduced by 24% 73%, 23%, 56%, and that in the deep layer was decreased by 25%, 18%, 8% and 11%, respectively. (Land-use changes altered the distribution ratio of active organic carbon in soil profile. The ratio between LOC and SOC in shallow soil increased when natural woodland and shrubland were converted into farmland, but no obvious difference was observed in deep soil. The ratio of MBC/SOC in shallow soil decreased when natural shrubland was converted into farmland, also, no significant difference was detected in the ratio of MBC/SOC for other land-use change types. The results suggested that land-use change exerted significant influence on soil active organic carbon content and distribution proportion in soil profile. Soil organic carbon in deep soil was more stable than that in shallow soil.

Breast cancer molecular subtype classification using deep features: preliminary results

NASA Astrophysics Data System (ADS)

Zhu, Zhe; Albadawy, Ehab; Saha, Ashirbani; Zhang, Jun; Harowicz, Michael R.; Mazurowski, Maciej A.

2018-02-01

Radiogenomics is a field of investigation that attempts to examine the relationship between imaging characteris- tics of cancerous lesions and their genomic composition. This could offer a noninvasive alternative to establishing genomic characteristics of tumors and aid cancer treatment planning. While deep learning has shown its supe- riority in many detection and classification tasks, breast cancer radiogenomic data suffers from a very limited number of training examples, which renders the training of the neural network for this problem directly and with no pretraining a very difficult task. In this study, we investigated an alternative deep learning approach referred to as deep features or off-the-shelf network approach to classify breast cancer molecular subtypes using breast dynamic contrast enhanced MRIs. We used the feature maps of different convolution layers and fully connected layers as features and trained support vector machines using these features for prediction. For the feature maps that have multiple layers, max-pooling was performed along each channel. We focused on distinguishing the Luminal A subtype from other subtypes. To evaluate the models, 10 fold cross-validation was performed and the final AUC was obtained by averaging the performance of all the folds. The highest average AUC obtained was 0.64 (0.95 CI: 0.57-0.71), using the feature maps of the last fully connected layer. This indicates the promise of using this approach to predict the breast cancer molecular subtypes. Since the best performance appears in the last fully connected layer, it also implies that breast cancer molecular subtypes may relate to high level image features

Stratospheric mountain wave attenuation in positive and negative ambient wind shear

NASA Astrophysics Data System (ADS)

Kruse, C. G.; Smith, R. B.

2016-12-01

Recently, much has been learned about the vertical propagation and attenuation of mountain waves launched by the Southern Alps of New Zealand (NZ) from the Deep Propagating Gravity Wave Experiment (DEEPWAVE) field campaign. Over NZ, approximately half of mountain wave events are strongly attenuated in a lower-stratospheric "valve layer," defined as a layer of reduced wind with no critical levels. Within a valve layer, negative wind shear causes mountain waves steepen and attenuate, with the amount of transmitted momentum flux controlled by the minimum wind speed within the layer. The other half of wave events are deep (propagating to 35+ km), usually with positive wind shear. Within these deep events, increasing amplitude with decreasing density causes mountain waves to attenuate gradually (after spatial/temporal averaging). Global reanalyses indicate that this valve layer is a climatological feature in the wintertime mid-latitudes above the subtropical jet, while deep events and gradual attenuation occur over higher latitudes below the polar stratospheric jet. The local physics of mountain wave attenuation in positive and negative ambient wind shear are investigated using realistic winter-long (JJA) 6-km resolution Weather Research and Forecasting (WRF) model simulations over the Andes. Attention is given to the spatiotemporal variability of wave attenuation and the various factors driving this variability (e.g. variability in wave generation, ambient conditions at attenuation level, inherent wave-induced instabilities). Mesoscale potential vorticity generation is used as an indicator of wave attenuation. Additionally, regionally integrated wave momentum flux and gravity wave drag (GWD) within WRF are quantified and compared with parameterized quantities in the MERRA1 and 2 reanalyses.

First data release of the Hyper Suprime-Cam Subaru Strategic Program

NASA Astrophysics Data System (ADS)

Aihara, Hiroaki; Armstrong, Robert; Bickerton, Steven; Bosch, James; Coupon, Jean; Furusawa, Hisanori; Hayashi, Yusuke; Ikeda, Hiroyuki; Kamata, Yukiko; Karoji, Hiroshi; Kawanomoto, Satoshi; Koike, Michitaro; Komiyama, Yutaka; Lang, Dustin; Lupton, Robert H.; Mineo, Sogo; Miyatake, Hironao; Miyazaki, Satoshi; Morokuma, Tomoki; Obuchi, Yoshiyuki; Oishi, Yukie; Okura, Yuki; Price, Paul A.; Takata, Tadafumi; Tanaka, Manobu M.; Tanaka, Masayuki; Tanaka, Yoko; Uchida, Tomohisa; Uraguchi, Fumihiro; Utsumi, Yousuke; Wang, Shiang-Yu; Yamada, Yoshihiko; Yamanoi, Hitomi; Yasuda, Naoki; Arimoto, Nobuo; Chiba, Masashi; Finet, Francois; Fujimori, Hiroki; Fujimoto, Seiji; Furusawa, Junko; Goto, Tomotsugu; Goulding, Andy; Gunn, James E.; Harikane, Yuichi; Hattori, Takashi; Hayashi, Masao; Hełminiak, Krzysztof G.; Higuchi, Ryo; Hikage, Chiaki; Ho, Paul T. P.; Hsieh, Bau-Ching; Huang, Kuiyun; Huang, Song; Imanishi, Masatoshi; Iwata, Ikuru; Jaelani, Anton T.; Jian, Hung-Yu; Kashikawa, Nobunari; Katayama, Nobuhiko; Kojima, Takashi; Konno, Akira; Koshida, Shintaro; Kusakabe, Haruka; Leauthaud, Alexie; Lee, Chien-Hsiu; Lin, Lihwai; Lin, Yen-Ting; Mandelbaum, Rachel; Matsuoka, Yoshiki; Medezinski, Elinor; Miyama, Shoken; Momose, Rieko; More, Anupreeta; More, Surhud; Mukae, Shiro; Murata, Ryoma; Murayama, Hitoshi; Nagao, Tohru; Nakata, Fumiaki; Niida, Mana; Niikura, Hiroko; Nishizawa, Atsushi J.; Oguri, Masamune; Okabe, Nobuhiro; Ono, Yoshiaki; Onodera, Masato; Onoue, Masafusa; Ouchi, Masami; Pyo, Tae-Soo; Shibuya, Takatoshi; Shimasaku, Kazuhiro; Simet, Melanie; Speagle, Joshua; Spergel, David N.; Strauss, Michael A.; Sugahara, Yuma; Sugiyama, Naoshi; Suto, Yasushi; Suzuki, Nao; Tait, Philip J.; Takada, Masahiro; Terai, Tsuyoshi; Toba, Yoshiki; Turner, Edwin L.; Uchiyama, Hisakazu; Umetsu, Keiichi; Urata, Yuji; Usuda, Tomonori; Yeh, Sherry; Yuma, Suraphong

2018-01-01

The Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP) is a three-layered imaging survey aimed at addressing some of the most important outstanding questions in astronomy today, including the nature of dark matter and dark energy. The survey has been awarded 300 nights of observing time at the Subaru Telescope, and it started in 2014 March. This paper presents the first public data release of HSC-SSP. This release includes data taken in the first 1.7 yr of observations (61.5 nights), and each of the Wide, Deep, and UltraDeep layers covers about 108, 26, and 4 square degrees down to depths of i ˜ 26.4, ˜26.5, and ˜27.0 mag, respectively (5 σ for point sources). All the layers are observed in five broad bands (grizy), and the Deep and UltraDeep layers are observed in narrow bands as well. We achieve an impressive image quality of 0{^''.}6 in the i band in the Wide layer. We show that we achieve 1%-2% point spread function (PSF) photometry (root mean square) both internally and externally (against Pan-STARRS1), and ˜10 mas and 40 mas internal and external astrometric accuracy, respectively. Both the calibrated images and catalogs are made available to the community through dedicated user interfaces and database servers. In addition to the pipeline products, we also provide value-added products such as photometric redshifts and a collection of public spectroscopic redshifts. Detailed descriptions of all the data can be found online. The data release website is https://hsc-release.mtk.nao.ac.jp.

Water-rich planets: How habitable is a water layer deeper than on Earth?

NASA Astrophysics Data System (ADS)

Noack, L.; Höning, D.; Rivoldini, A.; Heistracher, C.; Zimov, N.; Journaux, B.; Lammer, H.; Van Hoolst, T.; Bredehöft, J. H.

2016-10-01

Water is necessary for the origin and survival of life as we know it. In the search for life-friendly worlds, water-rich planets therefore are obvious candidates and have attracted increasing attention in recent years. The surface H2O layer on such planets (containing a liquid water ocean and possibly high-pressure ice below a specific depth) could potentially be hundreds of kilometres deep depending on the water content and the evolution of the proto-atmosphere. We study possible constraints for the habitability of deep water layers and introduce a new habitability classification relevant for water-rich planets (from Mars-size to super-Earth-size planets). A new ocean model has been developed that is coupled to a thermal evolution model of the mantle and core. Our interior structure model takes into account depth-dependent thermodynamic properties and the possible formation of high-pressure ice. We find that heat flowing out of the silicate mantle can melt an ice layer from below (in some cases episodically), depending mainly on the thickness of the ocean-ice shell, the mass of the planet, the surface temperature and the interior parameters (e.g. radioactive mantle heat sources). The high pressure at the bottom of deep water-ice layers could also impede volcanism at the water-mantle boundary for both stagnant lid and plate tectonics silicate shells. We conclude that water-rich planets with a deep ocean, a large planet mass, a high average density or a low surface temperature are likely less habitable than planets with an Earth-like ocean.

Assessment of Southern Ocean water mass circulation and characteristics in CMIP5 models: Historical bias and forcing response

NASA Astrophysics Data System (ADS)

Sallée, J.-B.; Shuckburgh, E.; Bruneau, N.; Meijers, A. J. S.; Bracegirdle, T. J.; Wang, Z.; Roy, T.

2013-04-01

The ability of the models contributing to the fifth Coupled Models Intercomparison Project (CMIP5) to represent the Southern Ocean hydrological properties and its overturning is investigated in a water mass framework. Models have a consistent warm and light bias spread over the entire water column. The greatest bias occurs in the ventilated layers, which are volumetrically dominated by mode and intermediate layers. The ventilated layers have been observed to have a strong fingerprint of climate change and to impact climate by sequestrating a significant amount of heat and carbon dioxide. The mode water layer is poorly represented in the models and both mode and intermediate water have a significant fresh bias. Under increased radiative forcing, models simulate a warming and lightening of the entire water column, which is again greatest in the ventilated layers, highlighting the importance of these layers for propagating the climate signal into the deep ocean. While the intensity of the water mass overturning is relatively consistent between models, when compared to observation-based reconstructions, they exhibit a slightly larger rate of overturning at shallow to intermediate depths, and a slower rate of overturning deeper in the water column. Under increased radiative forcing, atmospheric fluxes increase the rate of simulated upper cell overturning, but this increase is counterbalanced by diapycnal fluxes, including mixed-layer horizontal mixing, and mostly vanishes.

Distributed Cerebellar Motor Learning: A Spike-Timing-Dependent Plasticity Model

PubMed Central

Luque, Niceto R.; Garrido, Jesús A.; Naveros, Francisco; Carrillo, Richard R.; D'Angelo, Egidio; Ros, Eduardo

2016-01-01

Deep cerebellar nuclei neurons receive both inhibitory (GABAergic) synaptic currents from Purkinje cells (within the cerebellar cortex) and excitatory (glutamatergic) synaptic currents from mossy fibers. Those two deep cerebellar nucleus inputs are thought to be also adaptive, embedding interesting properties in the framework of accurate movements. We show that distributed spike-timing-dependent plasticity mechanisms (STDP) located at different cerebellar sites (parallel fibers to Purkinje cells, mossy fibers to deep cerebellar nucleus cells, and Purkinje cells to deep cerebellar nucleus cells) in close-loop simulations provide an explanation for the complex learning properties of the cerebellum in motor learning. Concretely, we propose a new mechanistic cerebellar spiking model. In this new model, deep cerebellar nuclei embed a dual functionality: deep cerebellar nuclei acting as a gain adaptation mechanism and as a facilitator for the slow memory consolidation at mossy fibers to deep cerebellar nucleus synapses. Equipping the cerebellum with excitatory (e-STDP) and inhibitory (i-STDP) mechanisms at deep cerebellar nuclei afferents allows the accommodation of synaptic memories that were formed at parallel fibers to Purkinje cells synapses and then transferred to mossy fibers to deep cerebellar nucleus synapses. These adaptive mechanisms also contribute to modulate the deep-cerebellar-nucleus-output firing rate (output gain modulation toward optimizing its working range). PMID:26973504

Enhancing the Durability and Carrier Selectivity of Perovskite Solar Cells Using a Blend Interlayer.

PubMed

Sin, Dong Hun; Jo, Sae Byeok; Lee, Seung Goo; Ko, Hyomin; Kim, Min; Lee, Hansol; Cho, Kilwon

2017-05-31

A mechanically and thermally stable and electron-selective ZnO/CH 3 NH 3 PbI 3 interface is created via hybridization of a polar insulating polymer, poly(ethylene glycol) (PEG), into ZnO nanoparticles (NPs). PEG successfully passivates the oxygen defects on ZnO and prevents direct contact between CH 3 NH 3 PbI 3 and defects on ZnO. A uniform CH 3 NH 3 PbI 3 film is formed on a soft ZnO:PEG layer after dispersion of the residual stress from the volume expansion during CH 3 NH 3 PbI 3 conversion. PEG also increases the work of adhesion of the CH 3 NH 3 PbI 3 film on the ZnO:PEG layer and holds the CH 3 NH 3 PbI 3 film with hydrogen bonding. Furthermore, PEG tailors the interfacial electronic structure of ZnO, reducing the electron affinity of ZnO. As a result, a selective electron-collection cathode is formed with a reduced electron affinity and a deep-lying valence band of ZnO, which significantly enhances the carrier lifetime (473 μs) and photovoltaic performance (15.5%). The mechanically and electrically durable ZnO:PEG/CH 3 NH 3 PbI 3 interface maintains the sustainable performance of the solar cells over 1 year. A soft and durable cathodic interface via PEG hybridization in a ZnO layer is an effective strategy toward flexible electronics and commercialization of the perovskite solar cells.

Transformation of soil organic matter in leached chernozems under minimized treatment in the forest-steppe of West Siberia

NASA Astrophysics Data System (ADS)

Sharkov, I. N.; Samokhvalova, L. M.; Mishina, P. V.

2016-07-01

Changes in the contents of total organic carbon and the carbon of easily mineralizable fractions of organic matter (labile humus, detritus, and mortmass) in the layers of 0-10, 10-25, and 0-25 cm were studied in leached chernozems ((Luvic Chernozems (Loamic, Aric)) subjected to deep plowing and surface tillage for nine years. In the layer of 0-25 cm, the content of Corg did not show significant difference between these two treatments and comprised 3.68-3.92% in the case of deep plowing and 3.63-4.08% in the case of surface tillage. Tillage practices greatly affected the distribution of easily mineralizable fractions of organic matter in the layers of 0-10 and 10-25 cm, though the difference between two treatments for the entire layer (0-25 cm) was insignificant. Surface tillage resulted in the increase in the contents of mortmass (by 59%), detritus (by 32%), and labile humus (by 8%) in the layer of 0-10 cm in comparison with deep plowing. At the same time, the contents of these fractions in the layer of 10-25 cm in the surface tillage treatment decreased by 67, 46, and 3%, respectively. The estimate of the nitrogen-mineralizing capacity made according to the data on the uptake of soil nitrogen by oat plants in a special greenhouse experiment confirmed the observed regularities of the redistribution of easily mineralizable organic matter fractions by the soil layers. In case of surface tillage, it increased by 23% in the layer of 0-10 cm; for the layer of 0-25 cm, no significant differences in the uptake of nitrogen by oat plants were found for the two studied treatments.

Ultrastructure of the embryonic snake skin and putative role of histidine in the differentiation of the shedding complex.

PubMed

Alibardi, Lorenzo

2002-02-01

The morphogenesis and ultrastructure of the epidermis of snake embryos were studied at progressive stages of development through hatching to determine the time and modality of differentiation of the shedding complex. Scales form as symmetric epidermal bumps that become slanted and eventually very overlapped. During the asymmetrization of the bumps, the basal cells of the forming outer surface of the scale become columnar, as in an epidermal placode, and accumulate glycogen. Small dermal condensations are sometimes seen and probably represent primordia of the axial dense dermis of the growing tip of scales. Deep, dense, and superficial loose dermal regions are formed when the epidermis is bilayered (periderm and basal epidermis) and undifferentiated. Glycogen and lipids decrease from basal cells to differentiating suprabasal cells. On the outer scale surface, beneath the peridermis, a layer containing dense granules and sparse 25-30-nm thick coarse filaments is formed. The underlying clear layer does not contain keratohyalin-like granules but has a rich cytoskeleton of intermediate filaments. Small denticles are formed and they interdigitate with the oberhautchen spinulae formed underneath. On the inner scale surface the clear layer contains dense granules, coarse filaments, and does not form denticles with the aspinulated oberhautchen. On the inner side surface the oberhautchen only forms occasional spinulae. The sloughing of the periderm and embryonic epidermis takes place in ovo 5-6 days before hatching. There follow beta-, mesos-, and alpha-layers, not yet mature before hatching. No resting period is present but a new generation is immediately produced so that at 6-10 h posthatching an inner generation and a new shedding complex are forming beneath the outer generation. The first shedding complex differentiates 10-11 days before hatching. In hatchlings 6-10 h old, tritiated histidine is taken up in the epidermis 4 h after injection and is found mainly in the shedding complex, especially in the apposed membranes of the clear layer and oberhautchen cells. This indicates that a histidine-rich protein is produced in preparation for shedding, as previously seen in lizard epidermis. The second shedding (first posthatching) takes place at 7-9 days posthatching. It is suggested that the shedding complex in lepidosaurian reptiles has evolved after the production of a histidine-rich protein and of a beta-keratin layer beneath the former alpha-layer. Copyright 2002 Wiley-Liss, Inc.

Dro1, a major QTL involved in deep rooting of rice under upland field conditions.

PubMed

Uga, Yusaku; Okuno, Kazutoshi; Yano, Masahiro

2011-05-01

Developing a deep root system is an important strategy for avoiding drought stress in rice. Using the 'basket' method, the ratio of deep rooting (RDR; the proportion of total roots that elongated through the basket bottom) was calculated to evaluate deep rooting. A new major quantitative trait locus (QTL) controlling RDR was detected on chromosome 9 by using 117 recombinant inbred lines (RILs) derived from a cross between the lowland cultivar IR64, with shallow rooting, and the upland cultivar Kinandang Patong (KP), with deep rooting. This QTL explained 66.6% of the total phenotypic variance in RDR in the RILs. A BC(2)F(3) line homozygous for the KP allele of the QTL had an RDR of 40.4%, compared with 2.6% for the homozygous IR64 allele. Fine mapping of this QTL was undertaken using eight BC(2)F(3) recombinant lines. The RDR QTL Dro1 (Deeper rooting 1) was mapped between the markers RM24393 and RM7424, which delimit a 608.4 kb interval in the reference cultivar Nipponbare. To clarify the influence of Dro1 in an upland field, the root distribution in different soil layers was quantified by means of core sampling. A line homozygous for the KP allele of Dro1 (Dro1-KP) and IR64 did not differ in root dry weight in the shallow soil layers (0-25 cm), but root dry weight of Dro1-KP in deep soil layers (25-50 cm) was significantly greater than that of IR64, suggesting that Dro1 plays a crucial role in increased deep rooting under upland field conditions.

Structure-Property-Environmental Relations in Glass and Glass-Ceramics.

DTIC Science & Technology

1980-03-01

dense Al203 result in a deep surface layer of preferred orientation detection by RKS methods. ii: C Mv CL.ASSIFICAIC S . e .. fa " " p h D e TABLE OF...distribution and decreases the isoelectric point of the powders. Variations in processing of dense Al 203 result in a deep surface layer of preferred...by their surfaces, it is essential that we learn how to predict the surface chemistry of these materials in order to optimize their performance. The

Role of Deep Convection in Establishing the Isotopic Composition of Water Vapor in the Tropical Transition Layer

NASA Technical Reports Server (NTRS)

Smith, Jamison A.; Ackerman, Andrew S.; Jensen, Eric J.; Toon, Owen B.

2006-01-01

The transport of H2O and HDO within deep convection is investigated with 3-D large eddy simulations (LES) using bin microphysics. The lofting and sublimation of HDO-rich ice invalidate the Rayleigh fractionation model of isotopologue distribution within deep convection. Bootstrapping the correlation of the ratio of HDO to H2O (deltaD) to water vapor mixing ratio (q(sub v)) through a sequence of convective events produced non-Rayleigh correlations resembling observations. These results support two mechanisms for stratospheric entry. Deep convection can inject air with water vapor of stratospheric character directly into the tropical transition layer (TTL). Alternatively, moister air detraining from convection may be dehydrated via cirrus formation n the TTL to produce stratospheric water vapor. Significant production of subsaturated air in the TTL via convective dehydration is not observed in these simulations, nor is it necessary to resolve the stratospheric isotope paradox.

Deep learning of support vector machines with class probability output networks.

PubMed

Kim, Sangwook; Yu, Zhibin; Kil, Rhee Man; Lee, Minho

2015-04-01

Deep learning methods endeavor to learn features automatically at multiple levels and allow systems to learn complex functions mapping from the input space to the output space for the given data. The ability to learn powerful features automatically is increasingly important as the volume of data and range of applications of machine learning methods continues to grow. This paper proposes a new deep architecture that uses support vector machines (SVMs) with class probability output networks (CPONs) to provide better generalization power for pattern classification problems. As a result, deep features are extracted without additional feature engineering steps, using multiple layers of the SVM classifiers with CPONs. The proposed structure closely approaches the ideal Bayes classifier as the number of layers increases. Using a simulation of classification problems, the effectiveness of the proposed method is demonstrated. Copyright © 2014 Elsevier Ltd. All rights reserved.

Deep tissue massage: What are we talking about?

PubMed

Koren, Yogev; Kalichman, Leonid

2018-04-01

Massage is a common treatment in complementary and integrative medicine. Deep tissue massage, a form of therapeutic massage, has become more and more popular in recent years. Hence, the use of massage generally and deep tissue massage specifically, should be evaluated as any other modality of therapy to establish its efficacy and safety. To determine the definitions used for deep tissue massage in the scientific literature and to review the current scientific evidence for its efficacy and safety. Narrative review. There is no commonly accepted definition of deep tissue massage in the literature. The definition most frequently used is the intention of the therapist. We suggest separating the definitions of deep massage and deep tissue massage as follows: deep massage should be used to describe the intention of the therapist to treat deep tissue by using any form of massage and deep tissue massage should be used to describe a specific and independent method of massage therapy, utilizing the specific set of principles and techniques as defined by Riggs: "The understanding of the layers of the body, and the ability to work with tissue in these layers to relax, lengthen, and release holding patterns in the most effective and energy efficient way possible within the client's parameters of comfort". Heterogeneity of techniques and protocols used in published studies have made it difficult to draw any clear conclusions. Favorable outcomes may result from deep tissue massage in pain populations and patients with decreased range of motion. In addition, several rare serious adverse events were found related to deep tissue massage, probably as a result of the forceful application of massage therapy. Future research of deep tissue massage should be based on a common definition, classification system and the use of common comparators as controls. Copyright © 2017 Elsevier Ltd. All rights reserved.

Three dimensional amorphous silicon/microcrystalline silicon solar cells

DOEpatents

Kaschmitter, James L.

1996-01-01

Three dimensional deep contact amorphous silicon/microcrystalline silicon (a-Si/.mu.c-Si) solar cells which use deep (high aspect ratio) p and n contacts to create high electric fields within the carrier collection volume material of the cell. The deep contacts are fabricated using repetitive pulsed laser doping so as to create the high aspect p and n contacts. By the provision of the deep contacts which penetrate the electric field deep into the material where the high strength of the field can collect many of the carriers, thereby resulting in a high efficiency solar cell.

Three dimensional amorphous silicon/microcrystalline silicon solar cells

DOEpatents

Kaschmitter, J.L.

1996-07-23

Three dimensional deep contact amorphous silicon/microcrystalline silicon (a-Si/{micro}c-Si) solar cells are disclosed which use deep (high aspect ratio) p and n contacts to create high electric fields within the carrier collection volume material of the cell. The deep contacts are fabricated using repetitive pulsed laser doping so as to create the high aspect p and n contacts. By the provision of the deep contacts which penetrate the electric field deep into the material where the high strength of the field can collect many of the carriers, thereby resulting in a high efficiency solar cell. 4 figs.

Structure of the screening layer near a plane isolated body in the deep vacuum. Part 2. Monoenergetic isotropic flow

NASA Astrophysics Data System (ADS)

Gunko, Yuri F.; Gunko, Natalia A.

2018-05-01

In this paper we consider the problem of determining the structure of the electric field near the surface of a flat insulated body under conditions of a deep vacuum. It is assumed that the emitted particles are electrons leaving the body surface under the influence of ionizing radiation whose velocities distribution near the surface is isotropic. It is estimated the thickness of the screening layer under conditions of stationary emission from a flat surface. The solutio of the problem of determining a stationary self-consistent electric field near the surface is found in a simple analytical form. The thickness of the screening layer is calculated from this formula.

Optimization of solar cells for air mass zero operation and a study of solar cells at high temperatures

NASA Technical Reports Server (NTRS)

Hovel, H. J.; Vernon, S. M.

1982-01-01

The power to weight ratio of GaAs cells can be reduced by fabricating devices using thin GaAs films on low density substrate materials (silicon, glass, plastics). A graphoepitaxy technique was developed which uses fine geometric patterns in the substrate to affect growth. Initial substrates were processed by etching 25 microns deep grooves into 100 oriented wafers; fine-grained polycrystalline GaAs layers 25-50 microns thick were then deposited on these and recrystallization was performed, heating the substrates to above the GaAs melting point in ASH3 atmosphere, resulting in large grain regrowth oriented along the groove dimensions. Experiments with smaller groove depths and spacings were initially encouraging; single large GaAs grains would totally cover one and often two groove fields of 14 groove each spanning several hundred microns. Dielectric coatings on the grooved substrates were also used to modify the growth.

Patterns and Drivers of Vertical Distribution of the Ciliate Community from the Surface to the Abyssopelagic Zone in the Western Pacific Ocean.

PubMed

Zhao, Feng; Filker, Sabine; Xu, Kuidong; Huang, Pingping; Zheng, Shan

2017-01-01

The deep sea is one of the largest but least understood ecosystems on earth. Knowledge about the diversity and distribution patterns as well as drivers of microbial eukaryote (including ciliates) along the water column, particularly below the photic zone, is scarce. In this study, we investigated the diversity of pelagic ciliates, the main group of marine microeukaryotes, their vertical distribution from the surface to the abyssopelagic zone, as well as their horizontal distribution over a distance of 1,300 km in the Western Pacific Ocean, using high-throughput DNA and cDNA (complementary DNA) sequencing. No distance-decay relationship could be detected along the horizontal scale; instead, a distinct vertical distribution within the ciliate communities was revealed. The alpha diversity of the ciliate communities in the deep chlorophyll maximum (DCM) and the 200 m layer turned out to be significantly higher compared with the other water layers. The ciliate communities in the 200 m water layer appeared to be more similar to those in deeper layers from 1,000 m to about 5,000 m than to the surface and DCM ciliate communities. Dominant species in the bathypelagic and abyssopelagic zone, particularly some parasites, were also detected in the 200 m layer, but were almost absent in the surface layer. The 200 m layer, therefore, seems to be an important "species bank" for deep ocean layers. Statistical analyses further revealed significant effects of temperature and chlorophyll a on the partitioning of ciliate diversity, indicating that environmental factors are a stronger force in shaping marine pelagic ciliate communities than the geographic distance.

[3T magnetic resonance T2 mapping for evaluation of cartilage repair after matrix-associated autologous chondrocyte transplantation].

PubMed

Zhang, Jun; Xu, Xian; Li, Xue; Chen, Min; Dong, Tian-Ming; Zuo, Pan-Li; An, Ning-Yu

2015-01-01

To assess the value of magnetic resonance imaging (MRI) T2 mapping in quantitative evaluation of cartilage repair following matrix-associated autologous chondrocyte transplantation (MACT). Six patients (with 9 plug cartilages) following MACT underwent MRI on a 3.0 Tesla MR scan system at 3, 6 and 12 months after the surgery. The full-thickness and zonal areas (deep and superficial layers) T2 values were calculated for the repaired cartilage and control cartilage. The mean T2 values of the repaired cartilage after MACT were significantly higher than that of the control cartilages at 3 and 6 months (P<0.05), but not at 12 months (P=0.063). At 6 and 12 months, the T2 values of the superficial layers were significantly higher than those of the deep layers in the repaired cartilages (P<0.05). The zonal (deep and superficial layers) T2 values of the repaired cartilages decreased significantly over time at 6 and 12 months as compared to those at 3 months after the surgery (P<0.05). MRI T2 mapping can serve as an important modality for assessing the repair of the articular cartilage following MACT.

Photoinduced current transient spectroscopy of deep levels and transport mechanisms in iron-doped GaN thin films grown by low pressure-metalorganic vapor phase epitaxy

NASA Astrophysics Data System (ADS)

Muret, P.; Pernot, J.; Azize, M.; Bougrioua, Z.

2007-09-01

Electrical transport and deep levels are investigated in GaN:Fe layers epitaxially grown on sapphire by low pressure metalorganic vapor phase epitaxy. Photoinduced current transient spectroscopy and current detected deep level spectroscopy are performed between 200 and 650 K on three Fe-doped samples and an undoped sample. A detailed study of the detected deep levels assigns dominant centers to a deep donor 1.39 eV below the conduction band edge EC and to a deep acceptor 0.75 eV above the valence band edge EV at low electric field. A strong Poole-Frenkel effect is evidenced for the donor. Schottky diodes characteristics and transport properties in the bulk GaN:Fe layer containing a homogenous concentration of 1019 Fe/cm3 are typical of a compensated semiconductor. They both indicate that the bulk Fermi level is located typically 1.4 eV below EC, in agreement with the neutrality equation and dominance of the deep donor concentration. This set of results demonstrates unambiguously that electrical transport in GaN:Fe is governed by both types, either donor or acceptor, of the iron impurity, either substitutional in gallium sites or associated with other defects.

Physically-based distributed hydrologic modeling of tropical catchments: Hypothesis testing on model formation and runoff generation

NASA Astrophysics Data System (ADS)

Abebe, N. A.; Ogden, F. L.

2011-12-01

Watersheds vary in their nature based on their geographic location, altitude, climate, geology, soils, and land use/land cover. These variations lead to differences in the conceptualization and formulation of hydrological models intended to represent the expected hydrological processes in a given catchment. Watersheds in the tropics are characterized by intensive and persistent biological activity and a large amount of rainfall. Our study focuses on the Agua Salud project catchments located in the Panama Canal Watershed, Panama, which have steep rolling topography, deep soils derived from weathered bedrock, and limited exposed bedrock. These catchments are also highly affected by soil cracks, decayed tree roots and animal burrows that form a network of preferential flow paths. One hypothesis is that these macropores conduct interflow during heavy rainfall, when a transient perched water table forms at a depth where the vertical hydraulic conductivity is significantly reduced near the bottom of the bioturbation layer. We have developed a physics-based, spatially distributed, multi-layered hydrologic model to simulate the dominant flow processes, including overland flow, channel flow, vertical matrix and non-Richards film flow, lateral downslope saturated matrix and non-Darcian pipe flow in the bioturbation layer and deep saturated groundwater flow. In our model formulation, we use the model to examine a variety of hydrological processes which we anticipate may occur. Emphasis is given to the modeling of the soil moisture dynamics in the bioturbation layer, development of lateral preferential flow and activation of the macropores and exchange of water at the interface between a bioturbation layer and a second layer below it. We consider interactions between surface water, ground water, channel water and perched water in the riparian zone cells with the aim of understanding likely runoff generation mechanisms. Results show that inclusion of as many different flow processes as possible during conceptualization and during model development helps to reject infeasible scenarios/hypotheses, and suggests further watershed-scale studies to improve our understanding of the hydrologic behavior of these poorly understood catchments.

Optical characterization of an eddy-induced diatom bloom west of the island of Hawaii

NASA Astrophysics Data System (ADS)

Nencioli, F.; Chang, G.; Twardowski, M.; Dickey, T. D.

2009-08-01

Optical properties are used to characterize the biogeochemistry of cyclonic eddy Opal in the lee of Hawaii. The eddy featured an intense diatom bloom. Our results show that the ratio of chlorophyll concentration to particulate beam attenuation coefficient, [chl]/cp, is not a good indicator of the changes in particle composition through the water column. The ratio is controlled primarily by the variation in chlorophyll concentration per cell with depth (photoadaptation), so that its values increase throughout the Deep Chlorophyll Maximum Layer (DCML). Below the DCML, high values of [chl]/cp suggest that remineralization might be another important controlling factor. On the other hand, the backscattering ratio (particle backscattering to particle scattering ratio, b~bp) clearly indicates a shift from a small phytoplankton to a diatom dominated community. Below an upper layer characterized by constant values, the b~bp ratio showed a rapid decrease to a broad minimum within the DCML. The higher values below the DCML are consistent with enhanced remineralization below the eddy-induced bloom. The DCML was characterized by a layer of "healthy" diatoms underlying a layer of "senescent" diatoms. These two layers are characterized by similar optical properties, indicating some possible limitations in using optical measurements to fully characterize the composition of suspended material in the water column. An inverse relationship between b~bp and [chl]/cp, also reported by others, is observed as deep as the DCML. There, [chl]/cp increases whereas b~bp remains similar to values found in the empty frustule layer. This is a further indication that [chl]/cp might not be a good alternative to the backscattering ratio for investigating changes in particle composition with depth in Case I waters.