Deep two-photon microscopic imaging through brain tissue using the second singlet state from fluorescent agent chlorophyll α in spinach leaf

NASA Astrophysics Data System (ADS)

Shi, Lingyan; Rodríguez-Contreras, Adrián; Budansky, Yury; Pu, Yang; An Nguyen, Thien; Alfano, Robert R.

2014-06-01

Two-photon (2P) excitation of the second singlet (S) state was studied to achieve deep optical microscopic imaging in brain tissue when both the excitation (800 nm) and emission (685 nm) wavelengths lie in the "tissue optical window" (650 to 950 nm). S2 state technique was used to investigate chlorophyll α (Chl α) fluorescence inside a spinach leaf under a thick layer of freshly sliced rat brain tissue in combination with 2P microscopic imaging. Strong emission at the peak wavelength of 685 nm under the 2P S state of Chl α enabled the imaging depth up to 450 μm through rat brain tissue.

Deep two-photon microscopic imaging through brain tissue using the second singlet state from fluorescent agent chlorophyll α in spinach leaf.

PubMed

Shi, Lingyan; Rodríguez-Contreras, Adrián; Budansky, Yury; Pu, Yang; Nguyen, Thien An; Alfano, Robert R

2014-06-01

Two-photon (2P) excitation of the second singlet (S₂) state was studied to achieve deep optical microscopic imaging in brain tissue when both the excitation (800 nm) and emission (685 nm) wavelengths lie in the "tissue optical window" (650 to 950 nm). S₂ state technique was used to investigate chlorophyll α (Chl α) fluorescence inside a spinach leaf under a thick layer of freshly sliced rat brain tissue in combination with 2P microscopic imaging. Strong emission at the peak wavelength of 685 nm under the 2P S₂ state of Chl α enabled the imaging depth up to 450 μm through rat brain tissue.

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.

Hemodynamic monitoring in different cortical layers with a single fiber optical system

NASA Astrophysics Data System (ADS)

Yu, Linhui; Noor, M. Sohail; Kiss, Zelma H. T.; Murari, Kartikeya

2018-02-01

Functional monitoring of highly-localized deep brain structures is of great interest. However, due to light scattering, optical methods have limited depth penetration or can only measure from a large volume. In this research, we demonstrate continuous measurement of hemodynamics in different cortical layers in response to thalamic deep brain stimulation (DBS) using a single fiber optical system. A 200-μm-core-diameter multimode fiber is used to deliver and collect light from tissue. The fiber probe can be stereotaxically implanted into the brain region of interest at any depth to measure the di use reflectance spectra from a tissue volume of 0.02-0.03 mm3 near the fiber tip. Oxygenation is then extracted from the reflectance spectra using an algorithm based on Monte Carlo simulations. Measurements were performed on the surface (cortical layer I) and at 1.5 mm depth (cortical layer VI) of the motor cortex in anesthetized rats with thalamic DBS. Preliminary results revealed the oxygenation changes in response to DBS. Moreover, the baseline as well as the stimulus-evoked change in oxygenation were different at the two depths of cortex.

Photoacoustic diagnosis of burns in rats: two-dimensional photo-acoustic imaging of burned tissue

NASA Astrophysics Data System (ADS)

Yamazaki, Mutsuo; Sato, Shunichi; Saito, Daizo; Okada, Yoshiaki; Kurita, Akira; Kikuchi, Makoto; Ashida, Hiroshi; Obara, Minoru

2003-06-01

We previously reported that for rat burn models, deep dermal burns and deep burns can be well differentiated by measuring the propagation time of the photoacoustic signals originated from the blood in the healthy skin tissue under the damaged tissue layer. However, the diagnosis was based on point measurement in the wound, and therefore site-dependent information on the injuries was not obtained; such information is very important for diagnosis of extended burns. In the present study, we scanned a photoacoustic detector on the wound and constructed two-dimensional (2-D) images of the blood-originated photoacoustic signals for superficial dermal burns (SDB), deep dermal burns (DDB), deep burns (DB), and healthy skins (control) in rats. For each burn model, site-dependent variation of the signal was observed; the variation probably reflects the distribution of blood vessels in the skin tissue. In spite of the variation, clear differentiation was obtained between SDB, DDB, and DB from the 2D images. The images were constructed as a function of post burn time. Temporal signal variation will be also presented.

A Deep Learning Approach to Digitally Stain Optical Coherence Tomography Images of the Optic Nerve Head.

PubMed

Devalla, Sripad Krishna; Chin, Khai Sing; Mari, Jean-Martial; Tun, Tin A; Strouthidis, Nicholas G; Aung, Tin; Thiéry, Alexandre H; Girard, Michaël J A

2018-01-01

To develop a deep learning approach to digitally stain optical coherence tomography (OCT) images of the optic nerve head (ONH). A horizontal B-scan was acquired through the center of the ONH using OCT (Spectralis) for one eye of each of 100 subjects (40 healthy and 60 glaucoma). All images were enhanced using adaptive compensation. A custom deep learning network was then designed and trained with the compensated images to digitally stain (i.e., highlight) six tissue layers of the ONH. The accuracy of our algorithm was assessed (against manual segmentations) using the dice coefficient, sensitivity, specificity, intersection over union (IU), and accuracy. We studied the effect of compensation, number of training images, and performance comparison between glaucoma and healthy subjects. For images it had not yet assessed, our algorithm was able to digitally stain the retinal nerve fiber layer + prelamina, the RPE, all other retinal layers, the choroid, and the peripapillary sclera and lamina cribrosa. For all tissues, the dice coefficient, sensitivity, specificity, IU, and accuracy (mean) were 0.84 ± 0.03, 0.92 ± 0.03, 0.99 ± 0.00, 0.89 ± 0.03, and 0.94 ± 0.02, respectively. Our algorithm performed significantly better when compensated images were used for training (P < 0.001). Besides offering a good reliability, digital staining also performed well on OCT images of both glaucoma and healthy individuals. Our deep learning algorithm can simultaneously stain the neural and connective tissues of the ONH, offering a framework to automatically measure multiple key structural parameters of the ONH that may be critical to improve glaucoma management.

Investigation in clinical potential of polarization sensitive optical coherence tomography in laryngeal tumor model study

NASA Astrophysics Data System (ADS)

Zhou, Xin; Oak, Chulho; Ahn, Yeh-Chan; Kim, Sung Won; Tang, Shuo

2018-02-01

Polarization-sensitive optical coherence tomography (PS-OCT) is capable of measuring tissue birefringence. It has been widely applied to access the birefringence in tissues such as skin and cartilage. The vocal cord tissue consists of three anatomical layers from the surface to deep inside, the epithelium that contains almost no collagen, the lamina propria that is composed with abundant collagen, and the vocalis muscle layer. Due to the variation in the organization of collagen fibers, the different tissue layers show different tissue birefringence, which can be evaluated by PS-OCT phase retardation measurement. Furthermore, collagen fibers in healthy connective tissues are usually well organized, which provides relatively high birefringence. When the collagen organization is destroyed by diseases such as tumor, the birefringence of the tissue will decrease. In this study, a rabbit laryngeal tumor model with different stages of tumor progression is investigated ex-vivo by PS-OCT. The PS-OCT images show a gradual decrease in birefringence from normal tissue to severe tumor tissue. A phase retardation slope-based analysis is conducted to distinguish the epithelium, lamina propria, and muscle layers, respectively. The phase retardation slope quantifies the birefringence in different layers. The quantitative study provides a more detailed comparison among different stages of the rabbit laryngeal tumor model. The PS-OCT result is validated by the corresponding histology images of the same samples.

Cannula Versus Sharp Needle for Placement of Soft Tissue Fillers: An Observational Cadaver Study.

PubMed

van Loghem, Jani A J; Humzah, Dalvi; Kerscher, Martina

2017-12-13

Soft-tissue fillers have become important products for facial rejuvenation. Deep fat compartments and facial bones lose volume during the natural aging process. For the most natural-looking results, deep volumetric injections at strategic sites are therefore preferred. Supraperiosteal placement is performed with a sharp needle or a non-traumatic cannula. The primary objective was to determine whether there is a difference in precision between supraperiosteal placement with a sharp needle compared with a non-traumatic cannula in cadaver specimens. A secondary objective was to analyze the safety profiles of both injection techniques. Cadaver heads were injected with dye material and soft-tissue fillers at multiple aesthetic facial sites on the supraperiosteum and subsequently dissected for observation of dye and filler placement. The non-traumatic cannula technique resulted in product being confined to the deep anatomic layers. In contrast, with the sharp needle technique, material was placed in multiple anatomic layers, from the periosteum to more superficial skin layers. For both techniques results were consistent for all facial sites. Although direct extrapolation from cadavers to the in vivo situation cannot be made, cannulae showed more precision in placement of product. With the sharp needle, the material was injected on the periosteum, and then migrated in a retrograde direction along the trajectory of the needle path, ending up in multiple anatomic layers. The sharp needle technique also showed a higher complication risk with intra-arterial injection occurring, even though the needle tip was positioned on the periosteum and the product was injected with the needle in constant contact with the periosteum. © 2016 The American Society for Aesthetic Plastic Surgery, Inc. Reprints and permission: journals.permissions@oup.com

The muscular force transmission system: role of the intramuscular connective tissue.

PubMed

Turrina, Andrea; Martínez-González, Miguel Antonio; Stecco, Carla

2013-01-01

The objective of this review is to analyze in detail the microscopic structure and relations among muscular fibers, endomysium, perimysium, epimysium and deep fasciae. In particular, the multilayer organization and the collagen fiber orientation of these elements are reported. The endomysium, perimysium, epimysium and deep fasciae have not just a role of containment, limiting the expansion of the muscle with the disposition in concentric layers of the collagen tissue, but are fundamental elements for the transmission of muscular force, each one with a specific role. From this review it appears that the muscular fibers should not be studied as isolated elements, but as a complex inseparable from their fibrous components. The force expressed by a muscle depends not only on its anatomical structure, but also the angle at which its fibers are attached to the intramuscular connective tissue and the relation with the epimysium and deep fasciae. Copyright © 2012 Elsevier Ltd. All rights reserved.

Robust estimation of cerebral hemodynamics in neonates using multilayered diffusion model for normal and oblique incidences

NASA Astrophysics Data System (ADS)

Steinberg, Idan; Harbater, Osnat; Gannot, Israel

2014-07-01

The diffusion approximation is useful for many optical diagnostics modalities, such as near-infrared spectroscopy. However, the simple normal incidence, semi-infinite layer model may prove lacking in estimation of deep-tissue optical properties such as required for monitoring cerebral hemodynamics, especially in neonates. To answer this need, we present an analytical multilayered, oblique incidence diffusion model. Initially, the model equations are derived in vector-matrix form to facilitate fast and simple computation. Then, the spatiotemporal reflectance predicted by the model for a complex neonate head is compared with time-resolved Monte Carlo (TRMC) simulations under a wide range of physiologically feasible parameters. The high accuracy of the multilayer model is demonstrated in that the deviation from TRMC simulations is only a few percent even under the toughest conditions. We then turn to solve the inverse problem and estimate the oxygen saturation of deep brain tissues based on the temporal and spatial behaviors of the reflectance. Results indicate that temporal features of the reflectance are more sensitive to deep-layer optical parameters. The accuracy of estimation is shown to be more accurate and robust than the commonly used single-layer diffusion model. Finally, the limitations of such approaches are discussed thoroughly.

Stable microwave radiometry system for long term monitoring of deep tissue temperature

NASA Astrophysics Data System (ADS)

Stauffer, Paul R.; Rodriques, Dario B.; Salahi, Sara; Topsakal, Erdem; Oliveira, Tiago R.; Prakash, Aniruddh; D'Isidoro, Fabio; Reudink, Douglas; Snow, Brent W.; Maccarini, Paolo F.

2013-02-01

Background: There are numerous clinical applications for non-invasive monitoring of deep tissue temperature. We present the design and experimental performance of a miniature radiometric thermometry system for measuring volume average temperature of tissue regions located up to 5cm deep in the body. Methods: We constructed a miniature sensor consisting of EMI-shielded log spiral microstrip antenna with high gain onaxis and integrated high-sensitivity 1.35GHz total power radiometer with 500 MHz bandwidth. We tested performance of the radiometry system in both simulated and experimental multilayer phantom models of several intended clinical measurement sites: i) brown adipose tissue (BAT) depots within 2cm of the skin surface, ii) 3-5cm deep kidney, and iii) human brain underlying intact scalp and skull. The physical models included layers of circulating tissue-mimicking liquids controlled at different temperatures to characterize our ability to quantify small changes in target temperature at depth under normothermic surface tissues. Results: We report SAR patterns that characterize the sense region of a 2.6cm diameter receive antenna, and radiometric power measurements as a function of deep tissue temperature that quantify radiometer sensitivity. The data demonstrate: i) our ability to accurately track temperature rise in realistic tissue targets such as urine refluxed from prewarmed bladder into kidney, and 10°C drop in brain temperature underlying normothermic scalp and skull, and ii) long term accuracy and stability of +0.4°C over 4.5 hours as needed for monitoring core body temperature over extended surgery or monitoring effects of brown fat metabolism over an extended sleep/wake cycle. Conclusions: A non-invasive sensor consisting of 2.6cm diameter receive antenna and integral 1.35GHz total power radiometer has demonstrated sufficient sensitivity to track clinically significant changes in temperature of deep tissue targets underlying normothermic surface tissues for clinical applications like the detection of vesicoureteral reflux, and long term monitoring of brown fat metabolism or brain core temperature during extended surgery.

Stable Microwave Radiometry System for Long Term Monitoring of Deep Tissue Temperature.

PubMed

Stauffer, Paul R; Rodriques, Dario B; Salahi, Sara; Topsakal, Erdem; Oliveira, Tiago R; Prakash, Aniruddh; D'Isidoro, Fabio; Reudink, Douglas; Snow, Brent W; Maccarini, Paolo F

2013-02-26

There are numerous clinical applications for non-invasive monitoring of deep tissue temperature. We present the design and experimental performance of a miniature radiometric thermometry system for measuring volume average temperature of tissue regions located up to 5cm deep in the body. We constructed a miniature sensor consisting of EMI-shielded log spiral microstrip antenna with high gain on-axis and integrated high-sensitivity 1.35GHz total power radiometer with 500 MHz bandwidth. We tested performance of the radiometry system in both simulated and experimental multilayer phantom models of several intended clinical measurement sites: i) brown adipose tissue (BAT) depots within 2cm of the skin surface, ii) 3-5cm deep kidney, and iii) human brain underlying intact scalp and skull. The physical models included layers of circulating tissue-mimicking liquids controlled at different temperatures to characterize our ability to quantify small changes in target temperature at depth under normothermic surface tissues. We report SAR patterns that characterize the sense region of a 2.6cm diameter receive antenna, and radiometric power measurements as a function of deep tissue temperature that quantify radiometer sensitivity. The data demonstrate: i) our ability to accurately track temperature rise in realistic tissue targets such as urine refluxed from prewarmed bladder into kidney, and 10°C drop in brain temperature underlying normothermic scalp and skull, and ii) long term accuracy and stability of ∓0.4°C over 4.5 hours as needed for monitoring core body temperature over extended surgery or monitoring effects of brown fat metabolism over an extended sleep/wake cycle. A non-invasive sensor consisting of 2.6cm diameter receive antenna and integral 1.35GHz total power radiometer has demonstrated sufficient sensitivity to track clinically significant changes in temperature of deep tissue targets underlying normothermic surface tissues for clinical applications like the detection of vesicoureteral reflux, and long term monitoring of brown fat metabolism or brain core temperature during extended surgery.

Computerized Cuff Pressure Algometry as Guidance for Circumferential Tissue Compression for Wearable Soft Robotic Applications: A Systematic Review.

PubMed

Kermavnar, Tjaša; Power, Valerie; de Eyto, Adam; O'Sullivan, Leonard W

2018-02-01

In this article, we review the literature on quantitative sensory testing of deep somatic pain by means of computerized cuff pressure algometry (CPA) in search of pressure-related safety guidelines for wearable soft exoskeleton and robotics design. Most pressure-related safety thresholds to date are based on interface pressures and skin perfusion, although clinical research suggests the deep somatic tissues to be the most sensitive to excessive loading. With CPA, pain is induced in deeper layers of soft tissue at the limbs. The results indicate that circumferential compression leads to discomfort at ∼16-34 kPa, becomes painful at ∼20-27 kPa, and can become unbearable even below 40 kPa.

Dynamic viscosity of implantable autologous materials into the vocal fold.

PubMed

Wiikmann, Christian; da Silva, Marcelo Alves; Arêas, Elizabeth Pinheiro Gomes; Tsuji, Domingos Hiroshi; Sennes, Luiz Ubirajara

2012-07-01

To compare the dynamic viscosity (DV) of superficial layer of temporalis fascia (SLTF) with that of other biological tissues traditionally used for vocal fold implants to treat vocal fold rigidity. Experimental. Measurement of DV of samples of SLTF, deep layer of temporalis fascia (DLTF), and abdominal fat of 12 cadavers. DV values of the different samples were presented in the following increasing order: SLTF, DLTF, and abdominal fat. There was statistical difference between the samples. DV of SLTF is lower than of other tissues tested. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

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.

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.

Deconvolution improves the accuracy and depth sensitivity of time-resolved measurements

NASA Astrophysics Data System (ADS)

Diop, Mamadou; St. Lawrence, Keith

2013-03-01

Time-resolved (TR) techniques have the potential to distinguish early- from late-arriving photons. Since light travelling through superficial tissue is detected earlier than photons that penetrate the deeper layers, time-windowing can in principle be used to improve the depth sensitivity of TR measurements. However, TR measurements also contain instrument contributions - referred to as the instrument-response-function (IRF) - which cause temporal broadening of the measured temporal-point-spread-function (TPSF). In this report, we investigate the influence of the IRF on pathlength-resolved absorption changes (Δμa) retrieved from TR measurements using the microscopic Beer-Lambert law (MBLL). TPSFs were acquired on homogeneous and two-layer tissue-mimicking phantoms with varying optical properties. The measured IRF and TPSFs were deconvolved to recover the distribution of time-of-flights (DTOFs) of the detected photons. The microscopic Beer-Lambert law was applied to early and late time-windows of the TPSFs and DTOFs to access the effects of the IRF on pathlength-resolved Δμa. The analysis showed that the late part of the TPSFs contains substantial contributions from early-arriving photons, due to the smearing effects of the IRF, which reduced its sensitivity to absorption changes occurring in deep layers. We also demonstrated that the effects of the IRF can be efficiently eliminated by applying a robust deconvolution technique, thereby improving the accuracy and sensitivity of TR measurements to deep-tissue absorption changes.

Linear-array based full-view high-resolution photoacoustic computed tomography of whole mouse brain functions in vivo

NASA Astrophysics Data System (ADS)

Li, Lei; Zhang, Pengfei; Wang, Lihong V.

2018-02-01

Photoacoustic computed tomography (PACT) is a non-invasive imaging technique offering high contrast, high resolution, and deep penetration in biological tissues. We report a photoacoustic computed tomography (PACT) system equipped with a high frequency linear array for anatomical and functional imaging of the mouse whole brain. The linear array was rotationally scanned in the coronal plane to achieve the full-view coverage. We investigated spontaneous neural activities in the deep brain by monitoring the hemodynamics and observed strong interhemispherical correlations between contralateral regions, both in the cortical layer and in the deep regions.

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.

Necrotizing fasciitis in nephritic syndrome: a case report

NASA Astrophysics Data System (ADS)

Junaedi, I.; Pasaribu, A. P.

2018-03-01

Necrotizing fasciitis is an infection of any layer of tissue compartment; it can be in the dermis, subcutaneous tissue, superficial fascia, deep fascia, or even muscle. Usually, necrotizing fasciitis is associated with necrotizing process caused by the single bacterial organism. The most common pathogen is group A Streptococcus. Delayed in the diagnosis and surgical treatment of necrotizing fasciitis will lead to increased tissue loss and high mortality risk. Here we report a case of necrotizing fasciitis which has a great outcome since the surgical exploration of tissue and debridement was done as soon as the patient is suspected of necrotizing fasciitis.

Enhanced nutrient transport improves the depth-dependent properties of tri-layered engineered cartilage constructs with zonal co-culture of chondrocytes and MSCs.

PubMed

Kim, Minwook; Farrell, Megan J; Steinberg, David R; Burdick, Jason A; Mauck, Robert L

2017-08-01

Biomimetic design in cartilage tissue engineering is a challenge given the complexity of the native tissue. While numerous studies have generated constructs with near-native bulk properties, recapitulating the depth-dependent features of native tissue remains a challenge. Furthermore, limitations in nutrient transport and matrix accumulation in engineered constructs hinders maturation within the central core of large constructs. To overcome these limitations, we fabricated tri-layered constructs that recapitulate the depth-dependent cellular organization and functional properties of native tissue using zonally derived chondrocytes co-cultured with MSCs. We also introduced porous hollow fibers (HFs) and HFs/cotton threads to enhance nutrient transport. Our results showed that tri-layered constructs with depth-dependent organization and properties could be fabricated. The addition of HFs or HFs/threads improved matrix accumulation in the central core region. With HF/threads, the local modulus in the deep region of tri-layered constructs nearly matched that of native tissue, though the properties in the central regions remained lower. These constructs reproduced the zonal organization and depth-dependent properties of native tissue, and demonstrate that a layer-by-layer fabrication scheme holds promise for the biomimetic repair of focal cartilage defects. Articular cartilage is a highly organized tissue driven by zonal heterogeneity of cells, extracellular matrix proteins and fibril orientations, resulting in depth-dependent mechanical properties. Therefore, the recapitulation of the functional properties of native cartilage in a tissue engineered construct requires such a biomimetic design of the morphological organization, and this has remained a challenge in cartilage tissue engineering. This study demonstrates that a layer-by-layer fabrication scheme, including co-cultures of zone-specific articular CHs and MSCs, can reproduce the depth-dependent characteristics and mechanical properties of native cartilage while minimizing the need for large numbers of chondrocytes. In addition, introduction of a porous hollow fiber (combined with a cotton thread) enhanced nutrient transport and depth-dependent properties of the tri-layered construct. Such a tri-layered construct may provide critical advantages for focal cartilage repair. These constructs hold promise for restoring native tissue structure and function, and may be beneficial in terms of zone-to-zone integration with adjacent host tissue and providing more appropriate strain transfer after implantation. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Neck and Occipital Pain Caused by Deep Cervical Intramuscular Lipoma: A Surgical Case.

PubMed

Kogure, Kazunari; Yamazaki, Michio; Tamaki, Tomonori; Node, Yoji; Morita, Akio

2017-01-01

A lipoma is a slow-growing, benign tumor and is usually asymptomatic; hence, surgical intervention can often be avoided in patients with these tumors in the cervical and cranial area. Lipomas arise most commonly in the subcutaneous fat, but occasionally in muscle tissue. Intramuscular lipomas in the cervico-cranial area have rarely been reported. We describe here a patient with a large intramuscular lipoma in the deep cervical tissue. The patient experienced troublesome pain in the neck and occipital area, and surgical treatment was therefore suggested. Particularly in the cervical area, intramuscular lipomas sometimes invade the surrounding muscles and tissue layers and develop into an irregular mass, despite being benign. In addition, the cervical area has one of the most complex muscle structures. Nevertheless, surgical management of intramuscular lipoma in the cervical and cranial area is sometimes indicated, for example, in patients with clinical symptoms or masses with a tendency to grow large.

Optical property measurement from layered biological media

NASA Astrophysics Data System (ADS)

Muller, Matthew R.

1998-12-01

Near infrared (NIR) photon reflectance spectroscopy is applied to measurement of blood concentration and its oxygen saturation within biological tissue. The measurement relies upon the changes in photon absorption of hemoglobin in the tissue as changes occur in the hemoglobin concentration and oxygen content. In the present study, NIR light is introduced at the skin surface and the optical properties (absorption and scattering) within the underlying tissue are determined from the resulting surface reflectance. Typically the tissue is modeled as a homogeneous mixture of bloodless tissue and blood, and the model incorporates the physical relationship between the surface reflectance and the optical properties of the tissue. The skin and underlying tissue, although heterogeneous, have a characteristic layered structure. These layers can be differentiated optically. The modeling and the inverse problem of measuring the optical properties in each of the tissue layers from the surface reflectance have been the subject of much attention by a number of investigators. Nonetheless, quantification of the relationship between surface reflectance and the optical properties of layered tissue has not been well understood nor well described. In the forward problem, tissue optical properties yield surface reflectance profiles (SRPs). Surface reflectance profiles, or SRPs, from diffusive media consisting of two layers are calculated using numerical solutions to the Boltzmann equation. Experimental SRPs are also measured in vitro from a test medium and in vivo from the calf of human subjects. This study provides a new approach to solving the inverse problem of determining optical properties from SRPs. To solve the inverse problem, an effective diffusion constant (Ke) is determined for the layered media. The Ke is the diffusion constant of an equivalent homogeneous medium which best fits the SRP of the layered medium. The departure from Ke of the SRP for a layered media is captured concisely, and Ke becomes a tool in describing the layered optical properties. This approach is applied clinically to measure changes in the blood concentration and oxygenation measured in vivo from normals and patients with peripheral vascular disease. A significant finding from the modeling was to identify the functional relationship of Ke to the top and lower layer diffusion constants, and the top layer thickness. When applied to in vitro measurements from media containing homogeneous layers with known optical properties, this functional relationship predicted Ke within the 95% confidence interval of the measured Ke. For the in vivo measurements, changes in K e with exercise are consistent with expected exercise physiology. With the incorporation of the known optical absorbance of hemoglobin in the presence of oxygen, the SRPs provide a means to measure the oxygen saturation of a deep tissue layer from the surface light reflectance.

Propionibacterium acnes in shoulder surgery: is loss of hair protective for infection?

PubMed

Hudek, Robert; Sommer, Frank; Abdelkawi, Ayman F; Kerwat, Martina; Müller, Hans-Helge; Gohlke, Frank

2016-06-01

Propionibacterium acnes (P acnes) has been linked to chronic infections in shoulder surgery. It was recently observed during first-time shoulder surgery in healthy patients at a rate between 36% and 56%. Male gender and the anterolateral approach were reported risk factors. Because the skin biology greatly differs, we aimed to correlate skin complaints with P acnes-positive intraoperative cultures from different tissue layer samples in patients undergoing shoulder surgery for the first time. Intraoperative samples (1 skin, 1 superficial, 1 deep tissue, and 1 control sample) from 112 patients (70 men, 42 women; aged 59.2 years) were cultured. The association between the presence of P acnes in the deep or superficial tissue, or both, and 10 items of a validated preoperative questionnaire for skin pathology was explored. The cultures were positive for P acnes in 38.4% (n = 43) of the cases. Skin samples were positive for P acnes in 8% (n = 9), superficial samples were positive in 23% (n = 26), and deep samples were positive in 30% (n = 34). Self-reported "loss of hair" was significantly negatively associated with the presence of P acnes in the superficial or deep tissue sample (P = .00028). Patients who report having "loss of hair" show fewer P acnes-positive cultures in intraoperative tissue samples taken during open shoulder surgery. Whether this subgroup is at a lesser risk for P acnes infections remains to be substantiated. Basic Science Study; Microbiology. Copyright © 2016 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

[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.

Sex- and Age-Dependence of Region- and Layer-Specific Knee Cartilage Composition (Spin-Spin-Relaxation Time) in Healthy Reference Subjects

PubMed Central

Wirth, Wolfgang; Maschek, Susanne; Eckstein, Felix

2016-01-01

SUMMARY Compositional measures of articular cartilage are accessible in vivo by magnetic resonance imaging (MRI) based relaxometry and cartilage spin-spin transverse relaxation time (T2) has been related to tissue hydration, collagen content and orientation, and mechanical (functional) properties of articular cartilage. The objective of the current study was therefore to evaluate subregional variation, and sex- and age-differences, in laminar (deep and superficial) femorotibial cartilage T2 relaxation time in healthy adults. To this end, we studied the right knees of 92 healthy subjects from the Osteoarthritis Initiative reference cohort (55 women, 37 men; age range 45–78 years; BMI 24.4±3.1) without knee pain, radiographic signs, or risk factors of knee osteoarthritis in either knee. T2 of the deep and superficial femorotibial cartilages was determined in 16 femorotibial subregions, using a multi-echo spin-echo (MESE) MRI sequence. Significant subregional variation in femorotibial cartilage T2 was observed for the superficial and for the deep (both p<0.001) cartilage layer (Friedman test). Yet, layer- and region-specific femorotibial T2 did not differ between men and women, or between healthy adults below and above the median age (54y). In conclusion, this first study to report subregional (layer-specific) compositional variation of femorotibial cartilage T2 in healthy adults identifies significant differences in both superficial and deep cartilage T2 between femorotibial subregions. However, no relevant sex- or age-dependence of cartilage T2 was observed between age 45–78y. The findings suggest that a common, non-sex-specific set of layer-and region-specific T2 reference values can be used to identify compositional pathology in joint disease for this age group. PMID:27836800

Molecular structure of human aortic valve by μSR- FTIR microscopy

NASA Astrophysics Data System (ADS)

Borkowska, Anna M.; Nowakowski, Michał; Lis, Grzegorz J.; Wehbe, Katia; Cinque, Gianfelice; Kwiatek, Wojciech M.

2017-11-01

Aortic valve is a part of the heart most frequently affected by pathological processes in humans what constitute a very serious health problem. Therefore, studies of morphology and molecular microstructure of the AV are needed. μSR- FTIR spectroscopy and microscopy represent unique tools to study chemical composition of the tissue and to identify spectroscopic markers characteristic for structural and functional features. Normal AV reveals a multi-layered structure and the compositional and structural changes within particular layers may trigger degenerative processes within the valve. Thus, deep insight into the structure of the valve to understand pathological processes occurring in AV is needed. In order to identify differences between three layers of human AV, tissue sections of macroscopically normal AV were studied using μSR- FTIR spectroscopy in combination with histological and histochemical stainings. Tissue sections deposited onto CaF2 substrates were mapped and representative set of IR spectra collected from fibrosa, spongiosa and ventricularis were analysed by Principal Component Analysis (PCA) in the spectral range between 1850-1000 cm-1 and 3050-2750 cm-1. PCA revealed a layered molecular structure of the valve and it was possible to identify IR bands associated to different tissue parts. Spongiosa layer was well differentiated from other two layers mainly based on IR bands characteristic for the distribution of glycosaminoglycans (GAGs) in the tissue - like 1170 cm-1 (υas(C-O-S)) and 1380 cm-1 (acetyl amino group). Additionally, it was distinguished from fibrosa and ventricularis based on 1085 cm-1 and 1240 cm-1 bands characteristic for GAGs and for carbohydrates- ν(C-O) and ν(C-O-C) respectively and nucleic acids -νsym(PO2-) and νasym(PO2-) respectively, which were less specific for this layer. The use of μSR- FTIR spectroscopy demonstrated co-localization of GAGs and lipids in spongiosa layer what may indicate their contribution in the very early phase of aortic valve calcific degeneration.

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.

Segmenting Brain Tissues from Chinese Visible Human Dataset by Deep-Learned Features with Stacked Autoencoder

PubMed Central

Zhao, Guangjun; Wang, Xuchu; Niu, Yanmin; Tan, Liwen; Zhang, Shao-Xiang

2016-01-01

Cryosection brain images in Chinese Visible Human (CVH) dataset contain rich anatomical structure information of tissues because of its high resolution (e.g., 0.167 mm per pixel). Fast and accurate segmentation of these images into white matter, gray matter, and cerebrospinal fluid plays a critical role in analyzing and measuring the anatomical structures of human brain. However, most existing automated segmentation methods are designed for computed tomography or magnetic resonance imaging data, and they may not be applicable for cryosection images due to the imaging difference. In this paper, we propose a supervised learning-based CVH brain tissues segmentation method that uses stacked autoencoder (SAE) to automatically learn the deep feature representations. Specifically, our model includes two successive parts where two three-layer SAEs take image patches as input to learn the complex anatomical feature representation, and then these features are sent to Softmax classifier for inferring the labels. Experimental results validated the effectiveness of our method and showed that it outperformed four other classical brain tissue detection strategies. Furthermore, we reconstructed three-dimensional surfaces of these tissues, which show their potential in exploring the high-resolution anatomical structures of human brain. PMID:27057543

Segmenting Brain Tissues from Chinese Visible Human Dataset by Deep-Learned Features with Stacked Autoencoder.

PubMed

Zhao, Guangjun; Wang, Xuchu; Niu, Yanmin; Tan, Liwen; Zhang, Shao-Xiang

2016-01-01

Cryosection brain images in Chinese Visible Human (CVH) dataset contain rich anatomical structure information of tissues because of its high resolution (e.g., 0.167 mm per pixel). Fast and accurate segmentation of these images into white matter, gray matter, and cerebrospinal fluid plays a critical role in analyzing and measuring the anatomical structures of human brain. However, most existing automated segmentation methods are designed for computed tomography or magnetic resonance imaging data, and they may not be applicable for cryosection images due to the imaging difference. In this paper, we propose a supervised learning-based CVH brain tissues segmentation method that uses stacked autoencoder (SAE) to automatically learn the deep feature representations. Specifically, our model includes two successive parts where two three-layer SAEs take image patches as input to learn the complex anatomical feature representation, and then these features are sent to Softmax classifier for inferring the labels. Experimental results validated the effectiveness of our method and showed that it outperformed four other classical brain tissue detection strategies. Furthermore, we reconstructed three-dimensional surfaces of these tissues, which show their potential in exploring the high-resolution anatomical structures of human brain.

Seeking: Accurate Measurement Techniques for Deep-Bone Density and Structure

NASA Technical Reports Server (NTRS)

Sibonga, Jean

2009-01-01

We are seeking a clinically-useful technology with enough sensitivity to assess the microstructure of "spongy" bone that is found in the marrow cavities of whole bones. However, this technology must be for skeletal sites surrounded by layers of soft tissues, such as the spine and the hip. Soft tissue interferes with conventional imaging and using a more accessible area -- for example, the wrist or the ankle of limbs-- as a proxy for the less accessible skeletal regions, will not be accurate. A non-radioactive technology is strongly preferred.

Do Skeletal Density Changes Within the Tissue Layer of Corals Affect Paleoclimate Reconstructions?

NASA Astrophysics Data System (ADS)

Griffiths, J. S.; DeLong, K. L.; Quinn, T.; Taylor, F. W.; Kilbourne, K. H.; Wagner, A. J.

2016-02-01

Sea surface temperature (SST) reconstructions from coral geochemistry provide information on past climate variability; however, not all coral studies agree on a common calibration slope. Therefore, understanding the impacts of coral skeletal growth on strontium-to-calcium ratios (Sr/Ca) and oxygen isotopic ratios (δ18O) is necessary to ensure accurate calibrations. The study of Gagan et al. (2012) suggests that for the Pacific coral genera Porites, SST calibrations for coral Sr/Ca and δ18O need to be adjusted to account for skeletal density changes in the tissue layer, which may attenuate the seasonal cycle in coral geochemistry. We attempt to duplicate those results and density patterns in several Porites lutea colonies from two locations, yet our results do not show an increase in density in the tissue layer. Another study with Montastraea faveolata reveals reduced seasonality in coral Sr/Ca compared to slower-growing Siderastrea siderea in close proximity and same water depth, suggesting the faster growing M. faveolata geochemistry may be attenuated. By measuring skeletal density changes by micromilling a standard volume throughout the tissue layer and immediately below, we find no pattern of skeletal accumulation in the tissue layer of multiple colonies of M. faveolata and S. siderea from different locations. We conclude that these species lay down all of their skeletal material at the skeleton surface, thus skeletal density changes in the tissue layer do not account for reduced seasonality. We propose that time averaging occurs in M. faveolata as a result of the coral polyp's deep calyces mixing time intervals in the adjacent thecal wall in which micromilling for geochemical analysis produces a sample area that contains several growth increments. Our results show that skeletal density growth effects cannot be applied to all coral genera and paves the way for new research on calyx depth as an alternative explanation for differences in coral calibration slopes.

Layer-by-layer assembled fluorescent probes in the second near-infrared window for systemic delivery and detection of ovarian cancer

PubMed Central

Dang, Xiangnan; Gu, Li; Qi, Jifa; Correa, Santiago; Zhang, Geran; Belcher, Angela M.; Hammond, Paula T.

2016-01-01

Fluorescence imaging in the second near-infrared window (NIR-II, 1,000–1,700 nm) features deep tissue penetration, reduced tissue scattering, and diminishing tissue autofluorescence. Here, NIR-II fluorescent probes, including down-conversion nanoparticles, quantum dots, single-walled carbon nanotubes, and organic dyes, are constructed into biocompatible nanoparticles using the layer-by-layer (LbL) platform due to its modular and versatile nature. The LbL platform has previously been demonstrated to enable incorporation of diagnostic agents, drugs, and nucleic acids such as siRNA while providing enhanced blood plasma half-life and tumor targeting. This work carries out head-to-head comparisons of currently available NIR-II probes with identical LbL coatings with regard to their biodistribution, pharmacokinetics, and toxicities. Overall, rare-earth-based down-conversion nanoparticles demonstrate optimal biological and optical performance and are evaluated as a diagnostic probe for high-grade serous ovarian cancer, typically diagnosed at late stage. Successful detection of orthotopic ovarian tumors is achieved by in vivo NIR-II imaging and confirmed by ex vivo microscopic imaging. Collectively, these results indicate that LbL-based NIR-II probes can serve as a promising theranostic platform to effectively and noninvasively monitor the progression and treatment of serous ovarian cancer. PMID:27114520

A Digital Staining Algorithm for Optical Coherence Tomography Images of the Optic Nerve Head

PubMed Central

Mari, Jean-Martial; Aung, Tin; Cheng, Ching-Yu; Strouthidis, Nicholas G.; Girard, Michaël J. A.

2017-01-01

Purpose To digitally stain spectral-domain optical coherence tomography (OCT) images of the optic nerve head (ONH), and highlight either connective or neural tissues. Methods OCT volumes of the ONH were acquired from one eye of 10 healthy subjects. We processed all volumes with adaptive compensation to remove shadows and enhance deep tissue visibility. For each ONH, we identified the four most dissimilar pixel-intensity histograms, each of which was assumed to represent a tissue group. These four histograms formed a vector basis on which we ‘projected' each OCT volume in order to generate four digitally stained volumes P1 to P4. Digital staining was also verified using a digital phantom, and compared with k-means clustering for three and four clusters. Results Digital staining was able to isolate three regions of interest from the proposed phantom. For the ONH, the digitally stained images P1 highlighted mostly connective tissues, as demonstrated through an excellent contrast increase across the anterior lamina cribrosa boundary (3.6 ± 0.6 times). P2 highlighted the nerve fiber layer and the prelamina, P3 the remaining layers of the retina, and P4 the image background. Further, digital staining was able to separate ONH tissue layers that were not well separated by k-means clustering. Conclusion We have described an algorithm that can digitally stain connective and neural tissues in OCT images of the ONH. Translational Relevance Because connective and neural tissues are considerably altered in glaucoma, digital staining of the ONH tissues may be of interest in the clinical management of this pathology. PMID:28174676

Bessel light sheet structured illumination microscopy

NASA Astrophysics Data System (ADS)

Noshirvani Allahabadi, Golchehr

Biomedical study researchers using animals to model disease and treatment need fast, deep, noninvasive, and inexpensive multi-channel imaging methods. Traditional fluorescence microscopy meets those criteria to an extent. Specifically, two-photon and confocal microscopy, the two most commonly used methods, are limited in penetration depth, cost, resolution, and field of view. In addition, two-photon microscopy has limited ability in multi-channel imaging. Light sheet microscopy, a fast developing 3D fluorescence imaging method, offers attractive advantages over traditional two-photon and confocal microscopy. Light sheet microscopy is much more applicable for in vivo 3D time-lapsed imaging, owing to its selective illumination of tissue layer, superior speed, low light exposure, high penetration depth, and low levels of photobleaching. However, standard light sheet microscopy using Gaussian beam excitation has two main disadvantages: 1) the field of view (FOV) of light sheet microscopy is limited by the depth of focus of the Gaussian beam. 2) Light-sheet images can be degraded by scattering, which limits the penetration of the excitation beam and blurs emission images in deep tissue layers. While two-sided sheet illumination, which doubles the field of view by illuminating the sample from opposite sides, offers a potential solution, the technique adds complexity and cost to the imaging system. We investigate a new technique to address these limitations: Bessel light sheet microscopy in combination with incoherent nonlinear Structured Illumination Microscopy (SIM). Results demonstrate that, at visible wavelengths, Bessel excitation penetrates up to 250 microns deep in the scattering media with single-side illumination. Bessel light sheet microscope achieves confocal level resolution at a lateral resolution of 0.3 micron and an axial resolution of 1 micron. Incoherent nonlinear SIM further reduces the diffused background in Bessel light sheet images, resulting in confocal quality images in thick tissue. The technique was applied to live transgenic zebra fish tg(kdrl:GFP), and the sub-cellular structure of fish vasculature genetically labeled with GFP was captured in 3D. The superior speed of the microscope enables us to acquire signal from 200 layers of a thick sample in 4 minutes. The compact microscope uses exclusively off-the-shelf components and offers a low-cost imaging solution for studying small animal models or tissue samples.

New Details of the Human Corneal Limbus Revealed With Second Harmonic Generation Imaging.

PubMed

Park, Choul Yong; Lee, Jimmy K; Zhang, Cheng; Chuck, Roy S

2015-09-01

To report novel findings of the human corneal limbus by using second harmonic generation (SHG) imaging. Corneal limbus was imaged by using an inverted two-photon excitation fluorescence microscope. Laser (Ti:Sapphire) was tuned at 850 nm for two-photon excitation. Backscatter signals of SHG and autofluorescence (AF) were collected through a 425/30-nm emission filter and a 525/45-emission filter, respectively. Multiple, consecutive, and overlapping image stacks (z-stack) were acquired for the corneal limbal area. Two novel collagen structures were revealed by SHG imaging at the limbus: an anterior limbal cribriform layer and presumed anchoring fibers. Anterior limbal cribriform layer is an intertwined reticular collagen architecture just beneath the limbal epithelial niche and is located between the peripheral cornea and Tenon's/scleral tissue. Autofluorescence imaging revealed high vascularity in this structure. Central to the anterior limbal cribriform layer, radial strands of collagen were found to connect the peripheral cornea to the limbus. These presumed anchoring fibers have both collagen and elastin and were found more extensively in the superficial layers than deep layer and were absent in very deep limbus near Schlemm's canal. By using SHG imaging, new details of the collagen architecture of human corneal limbal area were elucidated. High resolution images with volumetric analysis revealed two novel collagen structures.

Propionibacterium acnes in shoulder surgery: true infection, contamination, or commensal of the deep tissue?

PubMed

Hudek, Robert; Sommer, Frank; Kerwat, Martina; Abdelkawi, Ayman F; Loos, Franziska; Gohlke, Frank

2014-12-01

Propionibacterium acnes has been linked to chronic infections in shoulder surgery. Whether the bacterium is a contaminant or commensal of the deep tissue is unclear. We aimed to assess P. acnes in intraoperative samples of different tissue layers in patients undergoing first-time shoulder surgery. In 118 consecutive patients (mean age, 59.2 years; 75 men, 43 women), intraoperative samples were correlated to preoperative subacromial injection, the type of surgical approach, and gender. One skin, one superficial, one deep tissue, and one test sample were cultured for each patient. The cultures were positive for P. acnes in 36.4% (n = 43) of cases. Subacromial injection was not associated with bacterial growth rates (P = .88 for P. acnes; P = .20 for bacteria other than P. acnes; P = .85 for the anterolateral approach; P = .92 for the deltopectoral approach; P = .56 for men; P = .51 for women). Skin samples were positive for P. acnes in 8.5% (n = 10), superficial samples were positive in 7.6% (n = 9), deep samples were positive in 13.6% (n = 16), and both samples (superficial and deep) were positive in 15.3% (n = 18) of cases (P < .0001). P. acnes was detected in the anterolateral approach in 27.1% (n = 32) of cases and in the deltopectoral approach in 9.3% (n = 11) of cases (P = .01; relative risk, 1.93; 95% confidence interval, 1.08-3.43). Thirty-five of the P. acnes-positive patients were men (81.4%), and 8 patients were women (18.6%; P = .001; relative risk, 2.51; 95% confidence interval, 1.28-4.90). P. acnes was detected in more than one third of patients undergoing first-time shoulder surgery. Preoperative subacromial injection was not associated with bacterial growth. P. acnes was observed more frequently in the deep tissues than in the superficial tissues. The relative risk for obtaining a positive P. acnes culture was 2-fold greater for the anterolateral approach than for the deltopectoral approach, and the risk was 2.5-fold greater for men. Copyright © 2014 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Optimal conditions for tissue perforation using high intensity focused ultrasound

NASA Astrophysics Data System (ADS)

Mochizuki, Takashi; Kihara, Taizo; Ogawa, Kouji; Tanabe, Ryoko; Yosizawa, Shin; Umemura, Shin-ichiro; Kakimoto, Takashi; Yamashita, Hiromasa; Chiba, Toshio

2012-10-01

To perforate tissue lying deep part in body, a large size transducer was assembled by combining four spherical-shaped transducers, and the optimal conditions for tissue perforation have studied using ventricle muscle of chicken as a target. The ex vivo experiments showed that ventricle muscle was successfully perforated both when it was exposed to High Intensity Focused Ultrasound (HIFU) directly and when it was exposed to HIFU through atrial muscle layer. Moreover, it was shown that calculated acoustic power distributions are well similar to the perforation patterns, and that the acoustic energy distributes very complexly near the focus. Lastly, perforation on the living rabbit bladder wall was demonstrated as a preliminary in vivo experiment.

The effect of Piriformospora indica on the root development of maize (Zea mays L.) and remediation of petroleum contaminated soil.

PubMed

Zamani, Javad; Hajabbasi, Mohammad Ali; Alaie, Ebrahim; Sepehri, Mozhgan; Leuchtmann, Adrian; Schulin, Rainer

2016-01-01

As the depth of soil petroleum contamination can vary substantially under field conditions, a rhizotron experiment was performed to investigate the influence of endophyte, P. indica, on maize growth and degradation of petroleum components in a shallow and a deep-reaching subsurface layer of a soil. For control, a treatment without soil contamination was also included. The degree in contamination and the depth to which it extended had a strong effect on the growth of the plant roots. Contaminated soil layers severely inhibited root growth thus many roots preferred to bypass the shallow contaminated layer and grow in the uncontaminated soil. While the length and branching pattern of these roots were similar to those of uncontaminated treatment. Inoculation of maize with P. indica could improve root distribution and root and shoot growth in all three contamination treatments. This inoculation also enhanced petroleum degradation in soil, especially in the treatment with deep-reaching contamination, consequently the accumulation of petroleum hydrocarbons (PAHs) in the plant tissues were increased.

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 Convolutional Neural Networks for Multi-Modality Isointense Infant Brain Image Segmentation

PubMed Central

Zhang, Wenlu; Li, Rongjian; Deng, Houtao; Wang, Li; Lin, Weili; Ji, Shuiwang; Shen, Dinggang

2015-01-01

The segmentation of infant brain tissue images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) plays an important role in studying early brain development in health and disease. In the isointense stage (approximately 6–8 months of age), WM and GM exhibit similar levels of intensity in both T1 and T2 MR images, making the tissue segmentation very challenging. Only a small number of existing methods have been designed for tissue segmentation in this isointense stage; however, they only used a single T1 or T2 images, or the combination of T1 and T2 images. In this paper, we propose to use deep convolutional neural networks (CNNs) for segmenting isointense stage brain tissues using multi-modality MR images. CNNs are a type of deep models in which trainable filters and local neighborhood pooling operations are applied alternatingly on the raw input images, resulting in a hierarchy of increasingly complex features. Specifically, we used multimodality information from T1, T2, and fractional anisotropy (FA) images as inputs and then generated the segmentation maps as outputs. The multiple intermediate layers applied convolution, pooling, normalization, and other operations to capture the highly nonlinear mappings between inputs and outputs. We compared the performance of our approach with that of the commonly used segmentation methods on a set of manually segmented isointense stage brain images. Results showed that our proposed model significantly outperformed prior methods on infant brain tissue segmentation. In addition, our results indicated that integration of multi-modality images led to significant performance improvement. PMID:25562829

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.

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.

Detection of abnormalities in the superficial zone of cartilage repaired using a tissue engineered construct derived from synovial stem cells.

PubMed

Ando, Wataru; Fujie, Hiromichi; Moriguchi, Yu; Nansai, Ryosuke; Shimomura, Kazunori; Hart, David A; Yoshikawa, Hideki; Nakamura, Norimasa

2012-09-28

The present study investigated the surface structure and mechanical properties of repair cartilage generated from a tissue engineered construct (TEC) derived from synovial mesenchymal stem cells at six months post-implantation compared to those of uninjured cartilage. TEC-mediated repair tissue was cartilaginous with Safranin O staining, and had comparable macro-scale compressive properties with uninjured cartilage. However, morphological assessments revealed that the superficial zone of TEC-mediated tissue was more fibrocartilage-like, in contrast to the middle or deep zones that were more hyaline cartilage-like with Safranin O staining. Histological scoring of the TEC-mediated tissue was significantly lower in the superficial zone than in the middle and deep zones. Scanning electron microscopy showed a thick tangential bundle of collagen fibres at the most superficial layer of uninjured cartilage, while no corresponding structure was detected at the surface of TEC-mediated tissue. Immunohistochemical analysis revealed that PRG4 was localised in the superficial area of uninjured cartilage, as well as the TEC-mediated tissue. Friction testing showed that the lubrication properties of the two tissues was similar, however, micro-indentation analysis revealed that the surface stiffness of the TEC-repair tissue was significantly lower than that of uninjured cartilage. Permeability testing indicated that the TEC-mediated tissue exhibited lower water retaining capacity than did uninjured cartilage, specifically at the superficial zone. Thus, TEC-mediated tissue exhibited compromised mechanical properties at the superficial zone, properties which need improvement in the future for maintenance of long term repair cartilage integrity.

The effect of CO2 laser treatment on skin tissue.

PubMed

Baleg, Sana Mohammed Anayb; Bidin, Noriah; Suan, Lau Pik; Ahmad, Muhammad Fakarruddin Sidi; Krishnan, Ganesan; Johari, Abd Rahman; Hamid, Asma

2015-09-01

The aim of this study was to evaluate the effects of multiple pulses on the depth of injury caused by CO2 laser in an in vivo rat model. A 10 600-nm CO2 laser was applied to rat skin, with one side of the rat dorsal skin being exposed, leaving the other side as a control. All of the various laser pulses tested led to gradual loss of epidermal thickness as well as a dramatic increase in thermal damage depth. Collagen coagulation was most effective with ten pulses of CO2 laser, while the strength of irradiated skin tissue increased as the influence of the laser increased. Fundamental laser-skin interaction effects were studied using a CO2 laser. The photodamaged areas obtained from laser interaction were recorded via couple charge device video camera and analyzed via ImageJ software. Photodamage induced by CO2 laser is due to photothermal effects, which involve burning and vaporizing mechanisms to ablate the epidermis layer. The burning area literally expands and penetrates deep into the dermis layer, subsequently causing collagen coagulation. This fundamental study shows in detail the effect of CO2 laser interaction with skin. The CO2 attributed severe burning, producing deep coagulation, and induced strength to treated skin. © 2015 Wiley Periodicals, Inc.

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.

The dynamic deformation of a layered viscoelastic medium under surface excitation

NASA Astrophysics Data System (ADS)

Aglyamov, Salavat R.; Wang, Shang; Karpiouk, Andrei B.; Li, Jiasong; Twa, Michael; Emelianov, Stanislav Y.; Larin, Kirill V.

2015-06-01

In this study the dynamic behavior of a layered viscoelastic medium in response to the harmonic and impulsive acoustic radiation force applied to its surface was investigated both theoretically and experimentally. An analytical solution for a layered viscoelastic compressible medium in frequency and time domains was obtained using the Hankel transform. A special incompressible case was considered to model soft biological tissues. To verify our theoretical model, experiments were performed using tissue-like gel-based phantoms with varying mechanical properties. A 3.5 MHz single-element focused ultrasound transducer was used to apply the radiation force at the surface of the phantoms. A phase-sensitive optical coherence tomography system was used to track the displacements of the phantom surface. Theoretically predicted displacements were compared with experimental measurements. The role of the depth dependence of the elastic properties of a medium in its response to an acoustic pulse at the surface was studied. It was shown that the low-frequency vibrations at the surface are more sensitive to the deep layers than high-frequency ones. Therefore, the proposed model in combination with spectral analysis can be used to evaluate depth-dependent distribution of the mechanical properties based on the measurements of the surface deformation.

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.

In vivo three-photon microscopy of subcortical structures within an intact mouse brain

NASA Astrophysics Data System (ADS)

Horton, Nicholas G.; Wang, Ke; Kobat, Demirhan; Clark, Catharine G.; Wise, Frank W.; Schaffer, Chris B.; Xu, Chris

2013-03-01

Two-photon fluorescence microscopy enables scientists in various fields including neuroscience, embryology and oncology to visualize in vivo and ex vivo tissue morphology and physiology at a cellular level deep within scattering tissue. However, tissue scattering limits the maximum imaging depth of two-photon fluorescence microscopy to the cortical layer within mouse brain, and imaging subcortical structures currently requires the removal of overlying brain tissue or the insertion of optical probes. Here, we demonstrate non-invasive, high-resolution, in vivo imaging of subcortical structures within an intact mouse brain using three-photon fluorescence microscopy at a spectral excitation window of 1,700 nm. Vascular structures as well as red fluorescent protein-labelled neurons within the mouse hippocampus are imaged. The combination of the long excitation wavelength and the higher-order nonlinear excitation overcomes the limitations of two-photon fluorescence microscopy, enabling biological investigations to take place at a greater depth within tissue.

Self-interference 3D super-resolution microscopy for deep tissue investigations.

PubMed

Bon, Pierre; Linarès-Loyez, Jeanne; Feyeux, Maxime; Alessandri, Kevin; Lounis, Brahim; Nassoy, Pierre; Cognet, Laurent

2018-06-01

Fluorescence localization microscopy has achieved near-molecular resolution capable of revealing ultra-structures, with a broad range of applications, especially in cellular biology. However, it remains challenging to attain such resolution in three dimensions and inside biological tissues beyond the first cell layer. Here we introduce SELFI, a framework for 3D single-molecule localization within multicellular specimens and tissues. The approach relies on self-interference generated within the microscope's point spread function (PSF) to simultaneously encode equiphase and intensity fluorescence signals, which together provide the 3D position of an emitter. We combined SELFI with conventional localization microscopy to visualize F-actin 3D filament networks and reveal the spatial distribution of the transcription factor OCT4 in human induced pluripotent stem cells at depths up to 50 µm inside uncleared tissue spheroids. SELFI paves the way to nanoscale investigations of native cellular processes in intact tissues.

Birefringence and vascular imaging of in vivo human skin by Jones-matrix optical coherence tomography

NASA Astrophysics Data System (ADS)

Li, En; Makita, Shuichi; Hong, Young-Joo; Kasaragod, Deepa; Yasuno, Yoshiaki

2017-02-01

A customized 1310-nm Jones-matrix optical coherence tomography (JM-OCT) for dermatological investigation was constructed and used for in vivo normal human skin tissue imaging. This system can simultaneously measure the threedimensional depth-resolved local birefringence, complex-correlation based OCT angiography (OCT-A), degree-ofpolarization- uniformity (DOPU) and scattering OCT intensity. By obtaining these optical properties of tissue, the morphology, vasculature, and collagen content of skin can be deduced and visualized. Structures in the deep layers of the epithelium were observed with depth-resolved local birefringence and polarization uniformity images. These results suggest high diagnostic and investigative potential of JM-OCT for dermatology.

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.

Lung mass density analysis using deep neural network and lung ultrasound surface wave elastography.

PubMed

Zhou, Boran; Zhang, Xiaoming

2018-05-23

Lung mass density is directly associated with lung pathology. Computed Tomography (CT) evaluates lung pathology using the Hounsfield unit (HU) but not lung density directly. We have developed a lung ultrasound surface wave elastography (LUSWE) technique to measure the surface wave speed of superficial lung tissue. The objective of this study was to develop a method for analyzing lung mass density of superficial lung tissue using a deep neural network (DNN) and synthetic data of wave speed measurements with LUSWE. The synthetic training dataset of surface wave speed, excitation frequency, lung mass density, and viscoelasticity from LUSWE (788,000 in total) was used to train the DNN model. The DNN was composed of 3 hidden layers of 1024 neurons for each layer and trained for 10 epochs with a batch size of 4096 and a learning rate of 0.001 with three types of optimizers. The test dataset (4000) of wave speeds at three excitation frequencies (100, 150, and 200 Hz) and shear elasticity of superficial lung tissue was used to predict the lung density and evaluate its accuracy compared with predefined lung mass densities. This technique was then validated on a sponge phantom experiment. The obtained results showed that predictions matched well with test dataset (validation accuracy is 0.992) and experimental data in the sponge phantom experiment. This method may be useful to analyze lung mass density by using the DNN model together with the surface wave speed and lung stiffness measurements. Copyright © 2018 Elsevier B.V. All rights reserved.

Near-infrared optical properties of ex-vivo human skin and subcutaneous tissues using reflectance and transmittance measurements

NASA Astrophysics Data System (ADS)

Simpson, Rebecca; Laufer, Jan G.; Kohl-Bareis, Matthias; Essenpreis, Matthias; Cope, Mark

1997-08-01

The vast majority of 'non-invasive' measurements of human tissues using near infrared spectroscopy rely on passing light through the dermis and subdermis of the skin. Accurate knowledge of the optical properties of these tissues is essential to put into models of light transport and predict the effects of skin perfusion on measurements of deep tissue. Additionally, the skin could be a useful accessible organ for non-invasively determining the constituents of blood flowing through it. Samples of abdominal human skin (including subdermal tissue) were obtained from either post mortem examinations or plastic surgery. The samples were separated into a dermal layer (epidermis and dermis, 1.5 to 2 mm tick), and a sub-cutaneous layer comprised largely of fat. They were enclosed between two glass coverslips and placed in an integrating sphere to measure their reflectance and transmittance over a range of wavelengths from 600 to 1000 nm. The reflectance and transmittance values were converted into average absorption and reduced scattering coefficients by comparison with a Monte Carlo model of light transport. Improvements to the Monte Carlo model and measurement technique removed some previous uncertainties. The results show excellent separation of reduced scattering and absorption coefficient, with clear absorption peaks of hemoglobin, water and lipid. The effect of tissue storage upon measured optical properties was investigated.

Computations in the deep vs superficial layers of the cerebral cortex.

PubMed

Rolls, Edmund T; Mills, W Patrick C

2017-11-01

A fundamental question is how the cerebral neocortex operates functionally, computationally. The cerebral neocortex with its superficial and deep layers and highly developed recurrent collateral systems that provide a basis for memory-related processing might perform somewhat different computations in the superficial and deep layers. Here we take into account the quantitative connectivity within and between laminae. Using integrate-and-fire neuronal network simulations that incorporate this connectivity, we first show that attractor networks implemented in the deep layers that are activated by the superficial layers could be partly independent in that the deep layers might have a different time course, which might because of adaptation be more transient and useful for outputs from the neocortex. In contrast the superficial layers could implement more prolonged firing, useful for slow learning and for short-term memory. Second, we show that a different type of computation could in principle be performed in the superficial and deep layers, by showing that the superficial layers could operate as a discrete attractor network useful for categorisation and feeding information forward up a cortical hierarchy, whereas the deep layers could operate as a continuous attractor network useful for providing a spatially and temporally smooth output to output systems in the brain. A key advance is that we draw attention to the functions of the recurrent collateral connections between cortical pyramidal cells, often omitted in canonical models of the neocortex, and address principles of operation of the neocortex by which the superficial and deep layers might be specialized for different types of attractor-related memory functions implemented by the recurrent collaterals. Copyright © 2017 Elsevier Inc. All rights reserved.

Enhanced near-infrared photoacoustic imaging of silica-coated rare-earth doped nanoparticles.

PubMed

Sheng, Yang; Liao, Lun-De; Bandla, Aishwarya; Liu, Yu-Hang; Yuan, Jun; Thakor, Nitish; Tan, Mei Chee

2017-01-01

Near-infrared photoacoustic (PA) imaging is an emerging diagnostic technology that utilizes the tissue transparent window to achieve improved contrast and spatial resolution for deep tissue imaging. In this study, we investigated the enhancement effect of the SiO 2 shell on the PA property of our core/shell rare-earth nanoparticles (REs) consisting of an active rare-earth doped core of NaYF 4 :Yb,Er (REDNPs) and an undoped NaYF 4 shell. We observed that the PA signal amplitude increased with SiO 2 shell thickness. Although the SiO 2 shell caused an observed decrease in the integrated fluorescence intensity due to the dilution effect, fluorescence quenching of the rare earth emitting ions within the REDNPs cores was successfully prevented by the undoped NaYF 4 shell. Therefore, our multilayer structure consisting of an active core with successive functional layers was demonstrated to be an effective design for dual-modal fluorescence and PA imaging probes with improved PA property. The result from this work addresses a critical need for the development of dual-modal contrast agent that advances deep tissue imaging with high resolution and signal-to-noise ratio. Copyright © 2016 Elsevier B.V. All rights reserved.

Maximizing fluorescence collection efficiency in multiphoton microscopy

PubMed Central

Zinter, Joseph P.; Levene, Michael J.

2011-01-01

Understanding fluorescence propagation through a multiphoton microscope is of critical importance in designing high performance systems capable of deep tissue imaging. Optical models of a scattering tissue sample and the Olympus 20X 0.95NA microscope objective were used to simulate fluorescence propagation as a function of imaging depth for physiologically relevant scattering parameters. The spatio-angular distribution of fluorescence at the objective back aperture derived from these simulations was used to design a simple, maximally efficient post-objective fluorescence collection system. Monte Carlo simulations corroborated by data from experimental tissue phantoms demonstrate collection efficiency improvements of 50% – 90% over conventional, non-optimized fluorescence collection geometries at large imaging depths. Imaging performance was verified by imaging layer V neurons in mouse cortex to a depth of 850 μm. PMID:21934897

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.

Recent progress in tissue optical clearing for spectroscopic application

NASA Astrophysics Data System (ADS)

Sdobnov, A. Yu.; Darvin, M. E.; Genina, E. A.; Bashkatov, A. N.; Lademann, J.; Tuchin, V. V.

2018-05-01

This paper aims to review recent progress in optical clearing of the skin and over naturally turbid biological tissues and blood using this technique in vivo and in vitro with multiphoton microscopy, confocal Raman microscopy, confocal microscopy, NIR spectroscopy, optical coherence tomography, and laser speckle contrast imaging. Basic principles of the technique, its safety, advantages and limitations are discussed. The application of optical clearing agent on a tissue allows for controlling the optical properties of tissue. Optical clearing-induced reduction of tissue scattering significantly facilitates the observation of deep-located tissue regions, at the same time improving the resolution and image contrast for a variety of optical imaging methods suitable for clinical applications, such as diagnostics and laser treatment of skin diseases, mucosal tumor imaging, laser disruption of pathological abnormalities, etc. Structural images of different skin layers obtained ex vivo for porcine ear skin samples at application of Omnipaque™ and glycerol solutions during 60 min. Red color corresponds to TPEAF signal channel. Green color corresponds to SHG signal channel.

Embryonic wound healing by apical contraction and ingression in Xenopus laevis.

PubMed

Davidson, Lance A; Ezin, Akouavi M; Keller, Ray

2002-11-01

We have characterized excisional wounds in the animal cap of early embryos of the frog Xenopus laevis and found that these wounds close accompanied by three distinct processes: (1) the assembly of an actin purse-string in the epithelial cells at the wound margin, (2) contraction and ingression of exposed deep cells, and (3) protrusive activity of epithelial cells at the margin. Microsurgical manipulation allowing fine control over the area and depth of the wound combined with videomicroscopy and confocal analysis enabled us to describe the kinematics and challenge the mechanics of the closing wound. Full closure typically occurs only when the deep, mesenchymal cell-layer of the ectoderm is left intact; in contrast, when deep cells are removed along with the superficial, epithelial cell-layer of the ectoderm, wounds do not close. Actin localizes to the superficial epithelial cell-layer at the wound margin immediately after wounding and forms a contiguous "purse-string" in those cells within 15 min. However, manipulation and closure kinematics of shaped wounds and microsurgical cuts made through the purse-string rule out a major force-generating role for the purse-string. Further analysis of the cell behaviors within the wound show that deep, mesenchymal cells contract their apical surfaces and ingress from the exposed surface. High resolution time-lapse sequences of cells at the leading edge of the wound show that these cells undergo protrusive activity only during the final phases of wound closure as the ectoderm reseals. We propose that assembly of the actin purse-string works to organize and maintain the epithelial sheet at the wound margin, that contraction and ingression of deep cells pulls the wound margins together, and that protrusive activity of epithelial cells at the wound margin reseals the ectoderm and re-establishes tissue integrity during wound healing in the Xenopus embryonic ectoderm. Copyright 2002 Wiley-Liss, Inc.

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.

Role of gap junctions on synchronization in human neocortical networks.

PubMed

Gigout, S; Deisz, R A; Dehnicke, C; Turak, B; Devaux, B; Pumain, R; Louvel, J

2016-04-15

Gap junctions (GJ) have been implicated in the synchronization of epileptiform activities induced by 4-aminopyrine (4AP) in slices from human epileptogenic cortex. Previous evidence implicated glial GJ to govern the frequency of these epileptiform events. The synchrony of these events (evaluated by the phase unlocking index, PUI) in adjacent areas however was attributed to neuronal GJ. In the present study, we have investigated the effects of GAP-134, a recently developed specific activator of glial GJ, on both the PUI and the frequency of the 4AP-induced epileptiform activities in human neocortical slices of temporal lobe epilepsy tissue. To delineate the impact of GJ on spatial spread of synchronous activity we evaluated the effects of carbenoxolone (CBX, a non-selective GJ blocker) on the spread in three axes 1. vertically in a given cortical column, 2. laterally within the deep cortical layers and 3. laterally within the upper cortical layers. GAP-134 slightly increased the frequency of the 4AP-induced spontaneous epileptiform activities while leaving the PUI unaffected. CBX had no effect on the PUI within a cortical column or on the PUI in the deep cortical layers. CBX increased the PUI for long interelectrodes distances in the upper cortical layers. In conclusion we provide new arguments toward the role played by glial GJ to maintain the frequency of spontaneous activities. We show that neuronal GJ control the PUI only in upper cortical layers. Copyright © 2016 Elsevier B.V. All rights reserved.

Deep stroma investigation by confocal microscopy

NASA Astrophysics Data System (ADS)

Rossi, Francesca; Tatini, Francesca; Pini, Roberto; Valente, Paola; Ardia, Roberta; Buzzonetti, Luca; Canovetti, Annalisa; Malandrini, Alex; Lenzetti, Ivo; Menabuoni, Luca

2015-03-01

Laser assisted keratoplasty is nowadays largely used to perform minimally invasive surgery and partial thickness keratoplasty [1-3]. The use of the femtosecond laser enables to perform a customized surgery, solving the specific problem of the single patient, designing new graft profiles and partial thickness keratoplasty (PTK). The common characteristics of the PTKs and that make them eligible respect to the standard penetrating keratoplasty, are: the preservation of eyeball integrity, a reduced risk of graft rejection, a controlled postoperative astigmatism. On the other hand, the optimal surgical results after these PTKs are related to a correct comprehension of the deep stroma layers morphology, which can help in the identification of the correct cleavage plane during surgeries. In the last years some studies were published, giving new insights about the posterior stroma morphology in adult subjects [4,5]. In this work we present a study performed on two groups of tissues: one group is from 20 adult subjects aged 59 +/- 18 y.o., and the other group is from 15 young subjects, aged 12+/-5 y.o.. The samples were from tissues not suitable for transplant in patients. Confocal microscopy and Environmental Scanning Electron Microscopy (ESEM) were used for the analysis of the deep stroma. The preliminary results of this analysis show the main differences in between young and adult tissues, enabling to improve the knowledge of the morphology and of the biomechanical properties of human cornea, in order to improve the surgical results in partial thickness keratoplasty.

Material and physical model for evaluation of deep brain activity contribution to EEG recordings

NASA Astrophysics Data System (ADS)

Ye, Yan; Li, Xiaoping; Wu, Tiecheng; Li, Zhe; Xie, Wenwen

2015-12-01

Deep brain activity is conventionally recorded with surgical implantation of electrodes. During the neurosurgery, brain tissue damage and the consequent side effects to patients are inevitably incurred. In order to eliminate undesired risks, we propose that deep brain activity should be measured using the noninvasive scalp electroencephalography (EEG) technique. However, the deeper the neuronal activity is located, the noisier the corresponding scalp EEG signals are. Thus, the present study aims to evaluate whether deep brain activity could be observed from EEG recordings. In the experiment, a three-layer cylindrical head model was constructed to mimic a human head. A single dipole source (sine wave, 10 Hz, altering amplitudes) was embedded inside the model to simulate neuronal activity. When the dipole source was activated, surface potential was measured via electrodes attached on the top surface of the model and raw data were recorded for signal analysis. Results show that the dipole source activity positioned at 66 mm depth in the model, equivalent to the depth of deep brain structures, is clearly observed from surface potential recordings. Therefore, it is highly possible that deep brain activity could be observed from EEG recordings and deep brain activity could be measured using the noninvasive scalp EEG technique.

Tissue bioengineering and artificial organs.

PubMed

Llames, Sara; García, Eva; Otero Hernández, Jesús; Meana, Alvaro

2012-01-01

The scarcity of organs and tissues for transplant and the need of immunosuppressive drugs to avoid rejection constitute two reasons that justify organ and tissue production in the laboratory. Tissue engineering based tissues (TE) could allow to regenerate the whole organ from a fragment or even to produce several organs from an organ donor for grafting purposes. TE is based in: (1) the ex vivo expansion of cells, (2) the seeding of these expanded cells in tridimensional structures that mimic physiological conditions and, (3) grafting the prototype. In order to graft big structures it is necessary that the organ or tissue produced "ex vivo" bears a vascular tree to ensure the nutrition of its deep layers. At present, no technology has been developed to provide this vascular tree to TE derived products. Thus, these tissues must be thin enough to acquire nutrients during the first days by diffusion from surrounding tissues. This fact constitutes nowadays the greatest limitation of technologies for organ development in the laboratory.In this chapter, all these problems and their possible solutions are commented. Also, the present status of TE techniques in the regeneration of different organ systems is reviewed.

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.

CELL SEGREGATION, MIXING, AND TISSUE PATTERN IN THE SPINAL CORD OF THE XENOPUS LAEVIS NEURULA

PubMed Central

Davidson, Lance A.; Keller, Raymond E.

2014-01-01

Background During Xenopus laevis neurulation, neural ectodermal cells of the spinal cord are patterned at the same time that they intercalate mediolaterally and radially, moving within and between two cell layers. Curious if these rearrangements disrupt early cell identities, we lineage-traced cells in each layer from neural plate stages to the closed neural tube, and used in situ hybridization to assay gene expression in the moving cells. Results Our biotin- and fluorescent labeling of deep and superficial cells reveals that mediolateral intercalation does not disrupt cell cohorts, in other words it is conservative. However, outside the midline notoplate, later radial intercalation does displace superficial cells dorsoventrally, radically disrupting cell cohorts. The tube roof is composed almost exclusively of superficial cells, including some displaced from ventral positions; gene expression in these displaced cells must now be surveyed further. Superficial cells also flank the tube’s floor, which is, itself, almost exclusively composed of deep cells. Conclusions Our data provide: 1) a fate map of superficial- and deep-cell positions within the Xenopus neural tube, 2) the paths taken to these positions, and 3) preliminary evidence of re-patterning in cells carried out of one environment and into another, during neural morphogenesis. PMID:23813905

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.

Context aware decision support in neurosurgical oncology based on an efficient classification of endomicroscopic data.

PubMed

Li, Yachun; Charalampaki, Patra; Liu, Yong; Yang, Guang-Zhong; Giannarou, Stamatia

2018-06-13

Probe-based confocal laser endomicroscopy (pCLE) enables in vivo, in situ tissue characterisation without changes in the surgical setting and simplifies the oncological surgical workflow. The potential of this technique in identifying residual cancer tissue and improving resection rates of brain tumours has been recently verified in pilot studies. The interpretation of endomicroscopic information is challenging, particularly for surgeons who do not themselves routinely review histopathology. Also, the diagnosis can be examiner-dependent, leading to considerable inter-observer variability. Therefore, automatic tissue characterisation with pCLE would support the surgeon in establishing diagnosis as well as guide robot-assisted intervention procedures. The aim of this work is to propose a deep learning-based framework for brain tissue characterisation for context aware diagnosis support in neurosurgical oncology. An efficient representation of the context information of pCLE data is presented by exploring state-of-the-art CNN models with different tuning configurations. A novel video classification framework based on the combination of convolutional layers with long-range temporal recursion has been proposed to estimate the probability of each tumour class. The video classification accuracy is compared for different network architectures and data representation and video segmentation methods. We demonstrate the application of the proposed deep learning framework to classify Glioblastoma and Meningioma brain tumours based on endomicroscopic data. Results show significant improvement of our proposed image classification framework over state-of-the-art feature-based methods. The use of video data further improves the classification performance, achieving accuracy equal to 99.49%. This work demonstrates that deep learning can provide an efficient representation of pCLE data and accurately classify Glioblastoma and Meningioma tumours. The performance evaluation analysis shows the potential clinical value of the technique.

Simulation of laser propagation through a three-layer human skin model in the spectral range from 1000 to 1900 nm.

PubMed

Nasouri, Babak; Murphy, Thomas E; Berberoglu, Halil

2014-01-01

For understanding the mechanisms of low-level laser/light therapy (LLLT), accurate knowledge of light interaction with tissue is necessary. We present a three-dimensional, multilayer reduced-variance Monte Carlo simulation tool for studying light penetration and absorption in human skin. Local profiles of light penetration and volumetric absorption were calculated for uniform as well as Gaussian profile beams with different spreads over the spectral range from 1000 to 1900 nm. The results showed that lasers within this wavelength range could be used to effectively and safely deliver energy to specific skin layers as well as achieve large penetration depths for treating deep tissues, without causing skin damage. In addition, by changing the beam profile from uniform to Gaussian, the local volumetric dosage could increase as much as three times for otherwise similar lasers. We expect that this tool along with the results presented will aid researchers in selecting wavelength and laser power in LLLT.

Superficial heat reduction technique for a hybrid microwave-optical device.

PubMed

Al-Armaghany, A; Tong, K; Leung, T S

2013-01-01

Microwave applicator in the form of a circularly polarized microstrip patch antenna is proposed to provide localized deep heating in biological tissue, which causes blood vessels to dilate leading to changes in tissue oxygenation. These changes are monitored by an integrated optical system for studying thermoregulation in different parts of the human body. Using computer simulations, this paper compares circularly and linearly polarized antennas in terms of the efficiency of depositing electromagnetic (EM) energy and the heating patterns. The biological model composes of the skin, fat and muscle layers with appropriate dielectric and thermal properties. The results show that for the same specific absorption rate (SAR) in the muscle, the circularly polarized antenna results in a lower SAR in the skin-fat interface than the linearly polarized antenna. The thermal distribution is also presented based on the biological heat equation. The proposed circularly polarized antenna shows heat reduction in the superficial layers in comparison to the linearly polarized antenna.

Simulation of laser propagation through a three-layer human skin model in the spectral range from 1000 to 1900 nm

NASA Astrophysics Data System (ADS)

Nasouri, Babak; Murphy, Thomas E.; Berberoglu, Halil

2014-07-01

For understanding the mechanisms of low-level laser/light therapy (LLLT), accurate knowledge of light interaction with tissue is necessary. We present a three-dimensional, multilayer reduced-variance Monte Carlo simulation tool for studying light penetration and absorption in human skin. Local profiles of light penetration and volumetric absorption were calculated for uniform as well as Gaussian profile beams with different spreads over the spectral range from 1000 to 1900 nm. The results showed that lasers within this wavelength range could be used to effectively and safely deliver energy to specific skin layers as well as achieve large penetration depths for treating deep tissues, without causing skin damage. In addition, by changing the beam profile from uniform to Gaussian, the local volumetric dosage could increase as much as three times for otherwise similar lasers. We expect that this tool along with the results presented will aid researchers in selecting wavelength and laser power in LLLT.

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.

Anatomy and histology of the transverse humeral ligament.

PubMed

Snow, Brian J; Narvy, Steven J; Omid, Reza; Atkinson, Roscoe D; Vangsness, C Thomas

2013-10-01

The classic literature describes the transverse humeral ligament (THL) as a distinct anatomic structure with a role in biceps tendon stability; however, recent literature suggests that it is not a distinct anatomic structure. The purpose of this study was to evaluate the gross and microscopic anatomy of the THL, including a specific investigation of the histology of this ligament. Thirty frozen, embalmed cadaveric specimens were dissected to determine the gross anatomy of the THL. Seven specimens were evaluated histologically for the presence of mechanoreceptors and free nerve endings. Two tissue layers were identified in the area described as the THL. In the deep layer, fibers of the subscapularis tendon were found to span the bicipital groove with contributions from the coracohumeral ligament and the supraspinatus tendon. Superficial to this layer was a fibrous fascial covering consisting of distinct bands of tissue. Neurohistology staining revealed the presence of free nerve endings but no mechanoreceptors. This study's findings demonstrate that the THL is a distinct structure continuous with the rotator cuff tendons and the coracohumeral ligament. The finding of free nerve endings in the THL suggests a potential role as a shoulder pain generator. Copyright 2013, SLACK Incorporated.

Theoretical simulation of the dual-heat-flux method in deep body temperature measurements.

PubMed

Huang, Ming; Chen, Wenxi

2010-01-01

Deep body temperature reveals individual physiological states, and is important in patient monitoring and chronobiological studies. An innovative dual-heat-flux method has been shown experimentally to be competitive with the conventional zero-heat-flow method in its performance, in terms of measurement accuracy and step response to changes in the deep temperature. We have utilized a finite element method to model and simulate the dynamic process of a dual-heat-flux probe in deep body temperature measurements to validate the fundamental principles of the dual-heat-flux method theoretically, and to acquire a detailed quantitative description of the thermal profile of the dual-heat-flux probe. The simulation results show that the estimated deep body temperature is influenced by the ambient temperature (linearly, at a maximum rate of 0.03 °C/°C) and the blood perfusion rate. The corresponding depth of the estimated temperature in the skin and subcutaneous tissue layer is consistent when using the dual-heat-flux probe. Insights in improving the performance of the dual-heat-flux method were discussed for further studies of dual-heat-flux probes, taking into account structural and geometric considerations.

The effect of adjunctive noncontact low frequency ultrasound on deep tissue pressure injury.

PubMed

Honaker, Jeremy S; Forston, Michael R; Davis, Emily A; Weisner, Michelle M; Morgan, Jennifer A; Sacca, Emily

2016-11-01

The optimal treatment for deep tissue pressure injuries has not been determined. Deep tissue pressure injuries represent a more ominous early stage pressure injury that may evolve into full thickness ulceration despite implementing the standard of care for pressure injury. A longitudinal prospective historical case control study design was used to determine the effectiveness of noncontact low frequency ultrasound plus standard of care (treatment group) in comparison to standard of care (control group) in reducing deep tissue pressure injury severity, total surface area, and final pressure injury stage. The Honaker Suspected Deep Tissue Injury Severity Scale (range 3-18[more severe]) was used to determine deep tissue pressure injury severity at enrollment (Time 1) and discharge (Time 2). A total of 60 subjects (Treatment = 30; Control= 30) were enrolled in the study. In comparison to the control group mean deep tissue pressure injury total surface area change at Time 2 (0.3 cm 2 ), the treatment group had a greater decrease (8.8 cm 2 ) that was significant (t = 2.41, p = 0.014, r 2  = 0.10). In regards to the Honaker Suspected Deep Tissue Injury Severity Scale scores, the treatment group had a significantly lower score (7.6) in comparison to the control group (11.9) at time 2, with a mean difference of 4.6 (t = 6.146, p = 0.0001, r 2  = 0.39). When considering the final pressure ulcer stage at Time 2, the control group were mostly composed of unstageable pressure ulcer (57%) and deep tissue pressure injury severity (27%). In contrast, the treatment group final pressure ulcer stages were less severe and were mostly composed of stage 2 pressure injury (50%) and deep tissue pressure injury severity (23%) were the most common at time 2. The results of this study have shown that deep tissue pressure injury severity treated with noncontact low frequency ultrasound within 5 days of onset and in conjunction with standard of care may improve outcomes as compared to standard of care only. © 2016 by the Wound Healing Society.

Enzymatic debridement of deeply burned faces: Healing and early scarring based on tissue preservation compared to traditional surgical debridement.

PubMed

Schulz, Alexandra; Fuchs, Paul Christian; Rothermundt, Irene; Hoffmann, Alexandra; Rosenberg, Lior; Shoham, Yaron; Oberländer, Henrik; Schiefer, Jennifer

2017-09-01

Facial burns occur frequently and depending on the injured skin layers often heal with scars which may cause permanent functional and cosmetic sequelae. Preservation of the sensitive facial skin layers, especially of the dermis is essential for scarless epithelialisation. Enzymatic debridement of deep thermal burns has already been shown to assist with preserving viable dermis. However, up to date, there are no published reports on wound healing and in the long term aesthetic outcome after enzymatic debridement of facial burns. Therefore we performed a-single centre clinical trial that included 26 subjects aged 18-78 years with facial burns clinically evaluated as deep dermal or deeper. Burns were treated either with enzymatic debridement or excisional surgical debridement. Then we compared both groups regarding debridement selectivity, wound closure and scar quality after more than 12 months. Enzymatic debridement significantly reduced time to complete wound closure after admission (19.85 days versus 42.23 days, p=0.002), and after enzymatic eschar removal (18.92 days versus 35.62 days, p=0.042). The number of procedures to complete debridement were significantly lower in the enzymatic debridement group (1.00 versus 1.77, p=0.003). 77% of facial burns that had been debrided enzymatically were found to be more superficially burned than initially estimated. Wounds undergoing autografting of any size were significantly reduced by enzymatic debridement (15% versus 77%, p=0.002). Scar quality after enzymatic debridement was superior compared to surgical debridement after 12 months regarding pigmentation (p=0.016), thickness (p=0.16), relief (p=0.10), pliability (p=0.01), surface area (p=0.004), stiffness (p=0.023), thickness (0.011) and scar irregularity (p=0.011). Regarding erythema and melanin, viscoelasticity and pliability, trans-epidermal water loss or laser tissue oxygen saturation, haemoglobin level and microcirculation we found no significant differences for treated and untreated skin in the EDNX group. In our current study we found Bromelain based enzymatic debridement better in some aspects of tissue preservation in deep dermal facial burn. Copyright © 2017 Elsevier Ltd and ISBI. All rights reserved.

[Design of an microwave applicator using for tumor in superficial layer].

PubMed

Sun, Bing; Lu, Xiaofeng; Cao, Yi

2010-05-01

A 2.45 GHz microstrip applicator using single rectangle sheet structure is presented. Based on the radiant principle of microstrip antenna, the applicator's parameter is designed and the simulating model is set and optimized in HFSS. Measured by network analyzer, the technical target of this applicator is complied with design demand. During irradiation experiment, based on 30 W power, 30 mm radiation distance and 15 min duration experiment condition, the thermal field distribution map of phantom is obtained from the far-infrared image instrument. The 3D map shows that the region of thermal field centre has small radius and deep heat penetration. The microwave energy from this applicator can reach the tumor in superficial layer without heat injuring normal tissue around it.

Laminar Neural Field Model of Laterally Propagating Waves of Orientation Selectivity

PubMed Central

2015-01-01

We construct a laminar neural-field model of primary visual cortex (V1) consisting of a superficial layer of neurons that encode the spatial location and orientation of a local visual stimulus coupled to a deep layer of neurons that only encode spatial location. The spatially-structured connections in the deep layer support the propagation of a traveling front, which then drives propagating orientation-dependent activity in the superficial layer. Using a combination of mathematical analysis and numerical simulations, we establish that the existence of a coherent orientation-selective wave relies on the presence of weak, long-range connections in the superficial layer that couple cells of similar orientation preference. Moreover, the wave persists in the presence of feedback from the superficial layer to the deep layer. Our results are consistent with recent experimental studies that indicate that deep and superficial layers work in tandem to determine the patterns of cortical activity observed in vivo. PMID:26491877

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.

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.

Sensory processing of deep tissue nociception in the rat spinal cord and thalamic ventrobasal complex.

PubMed

Sikandar, Shafaq; West, Steven J; McMahon, Stephen B; Bennett, David L; Dickenson, Anthony H

2017-07-01

Sensory processing of deep somatic tissue constitutes an important component of the nociceptive system, yet associated central processing pathways remain poorly understood. Here, we provide a novel electrophysiological characterization and immunohistochemical analysis of neural activation in the lateral spinal nucleus (LSN). These neurons show evoked activity to deep, but not cutaneous, stimulation. The evoked responses of neurons in the LSN can be sensitized to somatosensory stimulation following intramuscular hypertonic saline, an acute model of muscle pain, suggesting this is an important spinal relay site for the processing of deep tissue nociceptive inputs. Neurons of the thalamic ventrobasal complex (VBC) mediate both cutaneous and deep tissue sensory processing, but in contrast to the lateral spinal nucleus our electrophysiological studies do not suggest the existence of a subgroup of cells that selectively process deep tissue inputs. The sensitization of polymodal and thermospecific VBC neurons to mechanical somatosensory stimulation following acute muscle stimulation with hypertonic saline suggests differential roles of thalamic subpopulations in mediating cutaneous and deep tissue nociception in pathological states. Overall, our studies at both the spinal (lateral spinal nucleus) and supraspinal (thalamic ventrobasal complex) levels suggest a convergence of cutaneous and deep somatosensory inputs onto spinothalamic pathways, which are unmasked by activation of muscle nociceptive afferents to produce consequent phenotypic alterations in spinal and thalamic neural coding of somatosensory stimulation. A better understanding of the sensory pathways involved in deep tissue nociception, as well as the degree of labeled line and convergent pathways for cutaneous and deep somatosensory inputs, is fundamental to developing targeted analgesic therapies for deep pain syndromes. © 2017 University College London. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

Trophic dynamics of deep-sea megabenthos are mediated by surface productivity.

PubMed

Tecchio, Samuele; van Oevelen, Dick; Soetaert, Karline; Navarro, Joan; Ramírez-Llodra, Eva

2013-01-01

Most deep-sea benthic ecosystems are food limited and, in the majority of cases, are driven by the organic matter falling from the surface or advected downslope. Species may adapt to this scarceness by applying a wide variety of responses, such as feeding specialisation, niche width variation, and reduction in metabolic rates. The Mediterranean Sea hosts a gradient of food availability at the deep seafloor over its wide longitudinal transect. In the Mediterranean, broad regional studies on trophic habits are almost absent, and the response of deep-sea benthos to different trophic conditions is still speculative. Here, we show that both primary and secondary production processes taking place at surface layers are key drivers of deep-sea food web structuring. By employing an innovative statistical tool, we interpreted bulk-tissue δ(13)C and δ(15)N isotope ratios in benthic megafauna, and associated surface and mesopelagic components from the 3 basins of the Mediterranean Sea at 3 different depths (1200, 2000, and 3000 m). The trophic niche width and the amplitude of primary carbon sources were positively correlated with both primary and secondary surface production indicators. Moreover, mesopelagic organic matter utilization processes showed an intermediate position between surface and deep benthic components. These results shed light on the understanding of deep-sea ecosystems functioning and, at the same time, they demand further investigation.

Trophic Dynamics of Deep-Sea Megabenthos Are Mediated by Surface Productivity

PubMed Central

Tecchio, Samuele; van Oevelen, Dick; Soetaert, Karline; Navarro, Joan; Ramírez-Llodra, Eva

2013-01-01

Most deep-sea benthic ecosystems are food limited and, in the majority of cases, are driven by the organic matter falling from the surface or advected downslope. Species may adapt to this scarceness by applying a wide variety of responses, such as feeding specialisation, niche width variation, and reduction in metabolic rates. The Mediterranean Sea hosts a gradient of food availability at the deep seafloor over its wide longitudinal transect. In the Mediterranean, broad regional studies on trophic habits are almost absent, and the response of deep-sea benthos to different trophic conditions is still speculative. Here, we show that both primary and secondary production processes taking place at surface layers are key drivers of deep-sea food web structuring. By employing an innovative statistical tool, we interpreted bulk-tissue δ13C and δ15N isotope ratios in benthic megafauna, and associated surface and mesopelagic components from the 3 basins of the Mediterranean Sea at 3 different depths (1200, 2000, and 3000 m). The trophic niche width and the amplitude of primary carbon sources were positively correlated with both primary and secondary surface production indicators. Moreover, mesopelagic organic matter utilization processes showed an intermediate position between surface and deep benthic components. These results shed light on the understanding of deep-sea ecosystems functioning and, at the same time, they demand further investigation. PMID:23691098

Combined use of Doppler OCT and en face OCT functions for discrimination of an aneurysm in the lamina cribrosa from a disc hemorrhage.

PubMed

Holló, Gábor

2015-12-01

In addition to retinal nerve fiber layer thickness measurements, the recently introduced AngioVue optical coherence tomography (OCT) offers corresponding layer-by-layer Doppler OCT and en face OCT functions, for simultaneous evaluation of perfusion and structure of the optic nerve head. We investigated the clinical usefulness of combined use of Doppler and en face Fourier-domain OCT functions of the AngioVue Fourier-domain OCT for discrimination of a disc hemorrhage and a disc hemorrhage-like atypical vessel structure located deep in the lamina cribrosa. We present our findings with AngioVue OCT on a disc hemorrhage and a spatially related retinal nerve fiber layer bundle defect in a glaucomatous eye (case 1). Both alterations were detected on en face OCT images without any Doppler OCT signal. We also report on an aneurysm suggestive for a disc hemorrhage on clinical examination and disc photography in a treated ocular hypertensive eye (case 2). The aneurysm was within the lamina cribrosa tissue at the border of the cup and the neuroretinal rim. This vascular structure produced strong Doppler signals but no structurally detectable signs on the en face OCT images. Combined evaluation of corresponding Doppler OCT and en face OCT images enables ophthalmologists to easily separate true disc hemorrhages from disc hemorrhage-like deep vascular structures. This is of clinical significance in preventing unnecessary intensification of pressure-lowering treatment in glaucoma.

Adaptation of a MR imaging protocol into a real-time clinical biometric ultrasound protocol for persons with spinal cord injury at risk for deep tissue injury: A reliability study.

PubMed

Swaine, Jillian M; Moe, Andrew; Breidahl, William; Bader, Daniel L; Oomens, Cees W J; Lester, Leanne; O'Loughlin, Edmond; Santamaria, Nick; Stacey, Michael C

2018-02-01

High strain in soft tissues that overly bony prominences are considered a risk factor for pressure ulcers (PUs) following spinal cord impairment (SCI) and have been computed using Finite Element methods (FEM). The aim of this study was to translate a MRI protocol into ultrasound (US) and determine between-operator reliability of expert sonographers measuring diameter of the inferior curvature of the ischial tuberosity (IT) and the thickness of the overlying soft tissue layers on able-bodied (AB) and SCI using real-time ultrasound. Part 1: Fourteen AB participants with a mean age of 36.7 ± 12.09 years with 7 males and 7 females had their 3 soft tissue layers in loaded and unloaded sitting measured independently by 2 sonographers: tendon/muscle, skin/fat and total soft tissue and the diameter of the IT in its short and long axis. Part 2: Nineteen participants with SCI were screened, three were excluded due to abnormal skin signs, and eight participants (42%) were excluded for abnormal US signs with normal skin. Eight SCI participants with a mean age of 31.6 ± 13.6 years and all male with 4 paraplegics and 4 tetraplegics were measured by the same sonographers for skin, fat, tendon, muscle and total. Skin/fat and tendon/muscle were computed. AB between-operator reliability was good (ICC = 0.81-0.90) for 3 soft tissues layers in unloaded and loaded sitting and poor for both IT short and long axis (ICC = -0.028 and -0.01). SCI between-operator reliability was good in unloaded and loaded for total, muscle, fat, skin/fat, tendon/muscle (ICC = 0.75-0.97) and poor for tendon (ICC = 0.26 unloaded and ICC = -0.71 loaded) and skin (ICC = 0.37 unloaded and ICC = 0.10). A MRI protocol was successfully adapted for a reliable 3 soft tissue layer model and could be used in a 2-D FEM model designed to estimate soft tissue strain as a novel risk factor for the development of a PU. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Deep Undercooling of Tissue Water and Winter Hardiness Limitations in Timberline Flora 1

PubMed Central

Becwar, Michael R.; Rajashekar, Channa; Bristow, Katherine J. Hansen; Burke, Michael J.

1981-01-01

Deep undercooled tissue water, which froze near −40 C, was found in winter collected stem and leaf tissue of the dominant timberline tree species of the Colorado Rocky Mountains, Engelmann spruce (Picea engelmannii (Parry) Engelm.) and subalpine fir (Abies lasiocarpa (Hook.) Nutt.), and in numerous other woody species in and below the subalpine vegetation zone. Previous work on numerous woody plants indicates that deep undercooling in xylem makes probable a −40 C winter hardiness limit in stem tissue. Visual injury determinations and electrolyte loss measurements on stem tissue revealed injury near −40 C associated with the freezing of the deep undercooled stem tissue water. These results suggest that the winter hardiness limit of this woody flora is near −40 C. The relevance of deep undercooling in relation to timberline, the upper elevational limit of the subalpine forest, is discussed. PMID:16661852

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.

Deep Sequencing of the Fruit Transcriptome and Lipid Accumulation in a Non-Seed Tissue of Chinese Tallow, a Potential Biofuel Crop.

PubMed

Divi, Uday K; Zhou, Xue-Rong; Wang, Penghao; Butlin, Jamie; Zhang, Dong-Mei; Liu, Qing; Vanhercke, Thomas; Petrie, James R; Talbot, Mark; White, Rosemary G; Taylor, Jennifer M; Larkin, Philip; Singh, Surinder P

2016-01-01

Chinese tallow (Triadica sebifera) is a valuable oilseed-producing tree that can grow in a variety of conditions without competing for food production, and is a promising biofuel feedstock candidate. The fruits are unique in that they contain both saturated and unsaturated fat present in the tallow and seed layer, respectively. The tallow layer is poorly studied and is considered only as an external fatty deposition secreted from the seed. In this study we show that tallow is in fact a non-seed cellular tissue capable of triglyceride synthesis. Knowledge of lipid synthesis and storage mechanisms in tissues other than seed is limited but essential to generate oil-rich biomass crops. Here, we describe the annotated transcriptome assembly generated from the fruit coat, tallow and seed tissues of Chinese tallow. The final assembly was functionally annotated, allowing for the identification of candidate genes and reconstruction of lipid pathways. A tallow tissue-specific paralog for the transcription factor gene WRINKLED1 (WRI1) and lipid droplet-associated protein genes, distinct from those expressed in seed tissue, were found to be active in tallow, underpinning the mode of oil synthesis and packaging in this tissue. Our data have established an excellent knowledge base that can provide genetic and biochemical insights for engineering non-seed tissues to accumulate large amounts of oil. In addition to the large data set of annotated transcripts, the study also provides gene-based simple sequence repeat and single nucleotide polymorphism markers. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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.

Raman spectroscopy of normal oral buccal mucosa tissues: study on intact and incised biopsies

NASA Astrophysics Data System (ADS)

Deshmukh, Atul; Singh, S. P.; Chaturvedi, Pankaj; Krishna, C. Murali

2011-12-01

Oral squamous cell carcinoma is one of among the top 10 malignancies. Optical spectroscopy, including Raman, is being actively pursued as alternative/adjunct for cancer diagnosis. Earlier studies have demonstrated the feasibility of classifying normal, premalignant, and malignant oral ex vivo tissues. Spectral features showed predominance of lipids and proteins in normal and cancer conditions, respectively, which were attributed to membrane lipids and surface proteins. In view of recent developments in deep tissue Raman spectroscopy, we have recorded Raman spectra from superior and inferior surfaces of 10 normal oral tissues on intact, as well as incised, biopsies after separation of epithelium from connective tissue. Spectral variations and similarities among different groups were explored by unsupervised (principal component analysis) and supervised (linear discriminant analysis, factorial discriminant analysis) methodologies. Clusters of spectra from superior and inferior surfaces of intact tissues show a high overlap; whereas spectra from separated epithelium and connective tissue sections yielded clear clusters, though they also overlap on clusters of intact tissues. Spectra of all four groups of normal tissues gave exclusive clusters when tested against malignant spectra. Thus, this study demonstrates that spectra recorded from the superior surface of an intact tissue may have contributions from deeper layers but has no bearing from the classification of a malignant tissues point of view.

Simulation study of interaction of pulse laser with tumor-embedded gastric tissue using finite element analysis

NASA Astrophysics Data System (ADS)

Liu, Lantian; Li, Zhifang; Li, Hui

2018-01-01

The study of interaction of laser with tumor-embedded gastric tissue is of great theoretical and practical significance for the laser diagnosis and treatment of gastric cancer in medicine. A finite element (FE)-based simulation model has been developed incorporating light propagation and heat transfer in soft tissues using a commercial FE simulation package, COMSOL Multiphysics. In this study, FE model is composed of three parts of 1) homogeneous background soft tissues submerged in water, 2) tumor tissue inclusion, and 3) different wavelengths of short pulsed laser source (450nm, 550nm, 632nm and 800nm). The laser point source is placed right under the tissues submerged in water. This laser source light propagation through the multi-layer tissues using the diffusion equation and bioheat transfer in tissues is simulated using bioheat equation for temperature change. The simulation results show that the penetration depth and light energy distribution mainly depend on the optical parameters of the different wavelengths of the tissue. In the process of biological heat transfer, the temperature of the tissue decreases exponentially with the depth and the deep tissues are almost unaffected. The results are helpful to optimize the laser source in a photoacoustic imaging system and provide some significance for the further study of the early diagnosis of gastric cancer.

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

A Non-Invasive Deep Tissue PH Monitor.

DTIC Science & Technology

1995-08-11

disturbances in acid-base regulation may have serious effects on metabolic activity, circulation, and the central nervous system. Currently, acid-base...to tissue ischemia than is arterial pH. Consequently, a non-invasive deep tissue pH monitor has enormous value as a mechanism for rapid and effective ...achieved, and improve our understanding of what physical effects are important to successful non-invasive deep tissue pH monitoring. This last statement

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.

Anatomy and biomechanics of the vertebral aponeurosis part of the posterior layer of the thoracolumbar fascia.

PubMed

Loukas, Marios; Shoja, Mohammadali M; Thurston, Todd; Jones, Virginia L; Linganna, Sanjay; Tubbs, R Shane

2008-03-01

There is significant paucity in the literature regarding vertebral aponeurosis. We were able to find only a few descriptions of this specific fascia in the extant medical literature. To elucidate further the anatomy of this structure, forty adult human cadavers were dissected. Both quantitation and anatomical observations were made of the vertebral aponeurosis. The vertebral aponeurosis was identified in 100% of specimens. This fascia was identified as a thin fibrous layer consisting of longitudinal and transverse connective tissue fibers blended together deep to the latissimus dorsi muscle. It attached medially to the spinous processes of the of the thoracic vertebrae; laterally to the angles of ribs; inferiorly to the fascia covering the serratus posterior inferior muscle (superficial lamina of the posterior layer of thoracolumbar fascia); superiorly it ran deep to the serratus posterior superior and splenius capitis muscles to blend with the deep fascia of the neck. At the level of the serratus posterior inferior muscle, the vertebral aponeurosis fused to form a continuous layer descending toward the sacrotuberous ligament covering the erector spinae muscle. Morphometrically, the mean length of the vertebral aponeurosis was 38 cm and the mean width was 24 cm. The mean thickness was three mm. There was no significant difference between left and right sides, gender or age with regard to vertebral aponeurosis length, width, or thickness (P > 0.05). During manual tension of the vertebral aponeurosis, the tensile force necessary for failure had a mean of 38.7 N. In all specimens, the vertebral aponeurosis was capable of holding sutures placed through its substance. We hope that these data will be of use for descriptive purposes and may potentially add to our understanding of the biomechanics involved in movements of the back. As back pain is perhaps the most common reason patients visit their physicians, additional knowledge of this anatomical region is important.

[A modified technique of liposuction with excision for gynecomastia].

PubMed

Yang, Hong-Yan; Xu, Jun; Yan, Xiao-Qing; You, Lei

2007-11-20

To introduce a modified technique of liposuction with excision for gynecomastia. From 2003 to 2007, 32 cases of gynecomastia were treated with the modified technique: the operative region was divided into central and periphery parts, liposuction was performed only in the periphery part and the deep layer of the central part, while the breast gland in the superficial layer of the central part underwent sharp dissection, the subcutaneous tissue of the central part was conserved, and blood supply was reserved and saucer deformity was avoided. Follow-up was conducted for 3.0 - 18.5 months. Normal men breast appearance was achieved. No complication happened such as hematoma, seroma, saucer deformity, and necrosis in nipple and areola. This modified operative technique for gynecomastia proves to be an excellent and effective technique.

Skin permeation and antioxidant efficacy of topically applied resveratrol.

PubMed

Alonso, Cristina; Martí, M; Barba, C; Carrer, V; Rubio, L; Coderch, L

2017-08-01

The permeation of resveratrol was assessed by in vitro and in vivo experiments 24 h after topical administration. The in vitro profile of resveratrol was assessed by Raman spectroscopy. Human skin permeation was analysed in vivo by the tape stripping method with the progressive removal of the stratum corneum layers using adhesive tape strips. Moreover, the free radical scavenging activity of resveratrol after its topical application was determined using the DPPH assay. The Raman spectra indicated that the topically applied resveratrol penetrates deep into the skin. The results showed high amounts of resveratrol in the different stratum corneum layers close to the surface and a constant lower amount in the upper layers of the viable epidermis. The concentration of resveratrol present in the outermost stratum corneum layers was obtained by tape stripping after in vivo application. The results demonstrated that resveratrol mainly remained in the human stratum corneum layers. After topical application, resveratrol maintained its antiradical activity. The antioxidant efficacy of the compound was higher in the inner layers of the stratum corneum. As these results have demonstrated, topically applied resveratrol reinforces the antioxidant system of the stratum corneum and provides an efficient means of increasing the tissue levels of antioxidants in the human epidermis.

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.

Enhancement of transmission of laser and other radiation by soft turbid physical and biological media

NASA Astrophysics Data System (ADS)

Askar'yan, G. A.

1982-07-01

An analysis is made and experimental results are reported of studies of the transmission of laser and other radiation by turbid physical and biological media, such as layers of a scattering medium or human tissue of thickness much greater than the characteristic attenuation length. It is reported that the transmission increases strongly as a result of depression and piercing of soft scattering media. A local pressure applied to a biological tissue produces a transmission enhancement considerably greater than compression of a layer of a physically turbid medium: this is due to the displacement of blood and of muscle out of the compressed region. A reduction in the scattering and absorption is expected to occur also in the case of rf and ionizing radiations, such as charged particles, x rays, gamma rays, etc. It is pointed out that this could be useful in deep irradiation carried out with the aim of inhibiting internal morbid processes (for example, in the spinal cord) and in treatment of neuroinfectious diseases (amyotrophic lateral sclerosis, multiple sclerosis, poliomyelitis, etc.), as well as in oncological conditions, ulcers, etc.

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

Role of interstitial branching in the development of visual corticocortical connections: a time-lapse and fixed-tissue analysis.

PubMed

Ruthazer, Edward S; Bachleda, Amelia R; Olavarria, Jaime F

2010-12-15

We combined fixed-tissue and time-lapse analyses to investigate the axonal branching phenomena underlying the development of topographically organized ipsilateral projections from area 17 to area 18a in the rat. These complementary approaches allowed us to relate static, large-scale information provided by traditional fixed-tissue analysis to highly dynamic, local, small-scale branching phenomena observed with two-photon time-lapse microscopy in acute slices of visual cortex. Our fixed-tissue data revealed that labeled area 17 fibers invaded area 18a gray matter at topographically restricted sites, reaching superficial layers in significant numbers by postnatal day 6 (P6). Moreover, most parental axons gave rise to only one or occasionally a small number of closely spaced interstitial branches beneath 18a. Our time-lapse data showed that many filopodium-like branches emerged along parental axons in white matter or deep layers in area 18a. Most of these filopodial branches were transient, often disappearing after several minutes to hours of exploratory extension and retraction. These dynamic behaviors decreased significantly from P4, when the projection is first forming, through the second postnatal week, suggesting that the expression of, or sensitivity to, cortical cues promoting new branch addition in the white matter is developmentally down-regulated coincident with gray matter innervation. Together, these data demonstrate that the development of topographically organized corticocortical projections in rats involves extensive exploratory branching along parental axons and invasion of cortex by only a small number of interstitial branches, rather than the widespread innervation of superficial cortical layers by an initially exuberant population of branches. © 2010 Wiley-Liss, Inc.

Role of Interstitial Branching in the Development of Visual Corticocortical Connections: A Time-Lapse and Fixed-Tissue Analysis

PubMed Central

Ruthazer, Edward S.; Bachleda, Amelia R.; Olavarria, Jaime F.

2013-01-01

We combined fixed-tissue and time-lapse analyses to investigate the axonal branching phenomena underlying the development of topographically organized ipsilateral projections from area 17 to area 18a in the rat. These complementary approaches allowed us to relate static, large-scale information provided by traditional fixed-tissue analysis to highly dynamic, local, small-scale branching phenomena observed with two-photon time-lapse microscopy in acute slices of visual cortex. Our fixed-tissue data revealed that labeled area 17 fibers invaded area 18a gray matter at topographically restricted sites, reaching superficial layers in significant numbers by postnatal day 6 (P6). Moreover, most parental axons gave rise to only one or occasionally a small number of closely spaced interstitial branches beneath 18a. Our time-lapse data showed that many filopodium-like branches emerged along parental axons in white matter or deep layers in area 18a. Most of these filopo-dial branches were transient, often disappearing after several minutes to hours of exploratory extension and retraction. These dynamic behaviors decreased significantly from P4, when the projection is first forming, through the second postnatal week, suggesting that the expression of, or sensitivity to, cortical cues promoting new branch addition in the white matter is developmentally down-regulated coincident with gray matter innervation. Together, these data demonstrate that the development of topographically organized corticocortical projections in rats involves extensive exploratory branching along parental axons and invasion of cortex by only a small number of interstitial branches, rather than the widespread innervation of superficial cortical layers by an initially exuberant population of branches. PMID:21031561

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.

Deep Tissue Fluorescent Imaging in Scattering Specimens Using Confocal Microscopy

PubMed Central

Clendenon, Sherry G.; Young, Pamela A.; Ferkowicz, Michael; Phillips, Carrie; Dunn, Kenneth W.

2015-01-01

In scattering specimens, multiphoton excitation and nondescanned detection improve imaging depth by a factor of 2 or more over confocal microscopy; however, imaging depth is still limited by scattering. We applied the concept of clearing to deep tissue imaging of highly scattering specimens. Clearing is a remarkably effective approach to improving image quality at depth using either confocal or multiphoton microscopy. Tissue clearing appears to eliminate the need for multiphoton excitation for deep tissue imaging. PMID:21729357

Reflection-artifact-free photoacoustic imaging using PAFUSion (photoacoustic-guided focused ultrasound)

NASA Astrophysics Data System (ADS)

Kuniyil Ajith Singh, Mithun; Jaeger, Michael; Frenz, Martin; Steenbergen, Wiendelt

2016-03-01

Reflection artifacts caused by acoustic inhomogeneities are a main challenge to deep-tissue photoacoustic imaging. Photoacoustic transients generated by the skin surface and superficial vasculature will propagate into the tissue and reflect back from echogenic structures to generate reflection artifacts. These artifacts can cause problems in image interpretation and limit imaging depth. In its basic version, PAFUSion mimics the inward travelling wave-field from blood vessel-like PA sources by applying focused ultrasound pulses, and thus provides a way to identify reflection artifacts. In this work, we demonstrate reflection artifact correction in addition to identification, towards obtaining an artifact-free photoacoustic image. In view of clinical applications, we implemented an improved version of PAFUSion in which photoacoustic data is backpropagated to imitate the inward travelling wave-field and thus the reflection artifacts of a more arbitrary distribution of PA sources that also includes the skin melanin layer. The backpropagation is performed in a synthetic way based on the pulse-echo acquisitions after transmission on each single element of the transducer array. We present a phantom experiment and initial in vivo measurements on human volunteers where we demonstrate significant reflection artifact reduction using our technique. The results provide a direct confirmation that reflection artifacts are prominent in clinical epi-photoacoustic imaging, and that PAFUSion can reduce these artifacts significantly to improve the deep-tissue photoacoustic imaging.

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.

Speckle contrast optical tomography: A new method for deep tissue three-dimensional tomography of blood flow

PubMed Central

Varma, Hari M.; Valdes, Claudia P.; Kristoffersen, Anna K.; Culver, Joseph P.; Durduran, Turgut

2014-01-01

A novel tomographic method based on the laser speckle contrast, speckle contrast optical tomography (SCOT) is introduced that allows us to reconstruct three dimensional distribution of blood flow in deep tissues. This method is analogous to the diffuse optical tomography (DOT) but for deep tissue blood flow. We develop a reconstruction algorithm based on first Born approximation to generate three dimensional distribution of flow using the experimental data obtained from tissue simulating phantoms. PMID:24761306

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.

Thigh muscle and subcutaneous tissue thickness measured using ultrasound imaging in older females living in extended care: a preliminary study.

PubMed

Welch, Daniella; Ndanyo, Laetitia Sungu; Brown, Simon; Agyapong-Badu, Sandra; Warner, Martin; Stokes, Maria; Samuel, Dinesh

2018-05-01

Thigh tissue thickness has not been examined in older females living in extended care in UK as an indicator of musculoskeletal health. This study examined the feasibility of using ultrasound imaging to measure the thickness of superficial (fat) and deep layers (muscle) of the thigh in older females living in extended care. In ten older females in extended care (aged 80-98 years, mean 88 ± 6.8; body mass: 56.5 ± 12.6 kg) images of the anterior thigh (dominant) were taken in supine using B-mode ultrasound imaging. Superficial and deep layers were measured and percentage thickness was calculated. Independent t tests compared data from those in extended care to ten sedentary females living independently (aged 80-90 years, mean 84 ± 3.6; body mass: 61.6 ± 10.0 kg). Thickness of the superficial layers was not significantly different between the two groups (CI -0.017 to 0.815, p = 0.059). However, those living in extended care had greater (p < 0.001) muscle thickness (mean 2.75 ± 0.48 cm) than those living independently (mean 1.83 ± 0.3 cm), which was similarly significant when normalised for body mass (extended care 0.51 ± 0.16; independent living 0.30 ± 0.06). These novel findings showed it is feasible to use ultrasound to measure muscles in older females in extended care and that muscle thickness was larger than in those living independently. The reason for the difference seen between groups would need to be confirmed by a larger study that also examined factors related to risk of sarcopenia and frailty, such as nutrition and physical activity levels.

A Wearable Real-Time and Non-Invasive Thoracic Cavity Monitoring System

NASA Astrophysics Data System (ADS)

Salman, Safa

A surgery-free on-body monitoring system is proposed to evaluate the dielectric constant of internal body tissues (especially lung and heart) and effectively determine irregularities in real-time. The proposed surgery-free on-body monitoring system includes a sensor, a post-processing technique, and an automated data collection circuit. Data are automatically collected from the sensor electrodes and then post processed to extract the electrical properties of the underlying biological tissue(s). To demonstrate the imaging concept, planar and wrap-around sensors are devised. These sensors are designed to detect changes in the dielectric constant of inner tissues (lung and heart). The planar sensor focuses on a single organ while the wrap-around sensors allows for imaging of the thoracic cavity's cross section. Moreover, post-processing techniques are proposed to complement sensors for a more complete on-body monitoring system. The idea behind the post-processing technique is to suppress interference from the outer layers (skin, fat, muscle, and bone). The sensors and post-processing techniques yield high signal (from the inner layers) to noise (from the outer layers) ratio. Additionally, data collection circuits are proposed for a more robust and stand-alone system. The circuit design aims to sequentially activate each port of the sensor and portions of the propagating signal are to be received at all passive ports in the form of a voltage at the probes. The voltages are converted to scattering parameters which are then used in the post-processing technique to obtain epsilonr. The concept of wearability is also considered through the use of electrically conductive fibers (E-fibers). These fibers show matching performance to that of copper, especially at low frequencies making them a viable substitute. For the cases considered, the proposed sensors show promising results in recovering the permittivity of deep tissues with a maximum error of 13.5%. These sensors provide a way for a new class of medical sensors through accuracy improvements and avoidance of inverse scattering techniques.

Newer concepts in the pathophysiology of ischemic heart disease.

PubMed

Kirk, E S; Factor, S; Sonnenblick, E H

1984-11-01

Thus the thrust of these studies suggests that blood flow is the overwhelming factor in determining the consequences of the imbalance of oxygen supply and demand. Moreover, the factors that determine the requirements for tissue survival in the presence of deep ischemia are not the same as those shown for the normal myocardium in figure 1. In deep ischemia, contraction ceases, and metabolism shifts from aerobic to anaerobic pathways. Survival rather than contractile function then becomes the agenda. Not only does supply tend to overshadow demand in determining extent of transmural necrosis, but the anatomical pattern of supply precisely delineates the region at risk following a coronary occlusion as well as the ultimate extent of infarction. These views are summarized in the model presented in figures 12 and 13. The anatomic distribution of the ligated artery determines the lateral limits of the ischemic region (Fig. 12) and thus the lateral extension of necrosis (Fig. 13). The extension of the necrosis across the heart wall depends largely on the status of perfusion within the ischemic region. Extension of an infarct, should it occur, has to be explained by other mechanisms. These might include: (i) vascular obstruction in adjacent vascular systems that were not involved in the first occlusion, (ii) relative ischemia in the normal tissue surrounding the ischemic tissue due to an increased wall stress at the demarcation between contracting and noncontracting tissue, or (9) interruption of vessels supplying large interdigitations of normal tissue within the originally ischemic tissue due to changes associated with the process of infarction of ischemia. Alternatively, much that is called extension of infarction may involve more of the wall transmurally without lateral extension. Additional features of the development of myocardial infarction in figures 12 and 13 include: (i) the development of collateral vessel function resulting in an increased capacity to supply the ischemic area, and (ii) a redistribution of collateral blood flow from necrotic to surviving myocardium within the ischemic area. Thus, as coronary collaterals develop, collateral blood flow becomes increasingly heterogeneous within the ischemic area. Following a coronary occlusion, blood flow is reduced more in the subendocardium, and infarction occurs. Resistance to flow in infarcting tissue increase and causes a redistribution of flow to adjacent surviving layers of myocardium that life toward the epicardium. The process continues and combined with the enlargement of collateral vessels results in a sufficient flow to the epicardial layers so that they may survive.

Sex differences and hormonal modulation of deep tissue pain

PubMed Central

Traub, Richard J.; Ji, Yaping

2013-01-01

Women disproportionately suffer from many deep tissue pain conditions. Experimental studies show that women have lower pain thresholds, higher pain ratings and less tolerance to a range of painful stimuli. Most clinical and epidemiological reports suggest female gonadal hormones modulate pain for some, but not all, conditions. Similarly, animal studies support greater nociceptive sensitivity in females in many deep tissue pain models. Gonadal hormones modulate responses in primary afferents, dorsal horn neurons and supraspinal sites, but the direction of modulation is variable. This review will examine sex differences in deep tissue pain in humans and animals focusing on the role of gonadal hormones (mainly estradiol) as an underlying component of the modulation of pain sensitivity. PMID:23872333

Double-excitation fluorescence spectral imaging: eliminating tissue auto-fluorescence from in vivo PPIX measurements

NASA Astrophysics Data System (ADS)

Torosean, Sason; Flynn, Brendan; Samkoe, Kimberley S.; Davis, Scott C.; Gunn, Jason; Axelsson, Johan; Pogue, Brian W.

2012-02-01

An ultrasound coupled handheld-probe-based optical fluorescence molecular tomography (FMT) system has been in development for the purpose of quantifying the production of Protoporphyrin IX (PPIX) in aminolevulinic acid treated (ALA), Basal Cell Carcinoma (BCC) in vivo. The design couples fiber-based spectral sampling of PPIX fluorescence emission with a high frequency ultrasound imaging system, allowing regionally localized fluorescence intensities to be quantified [1]. The optical data are obtained by sequential excitation of the tissue with a 633nm laser, at four source locations and five parallel detections at each of the five interspersed detection locations. This method of acquisition permits fluorescence detection for both superficial and deep locations in ultrasound field. The optical boundary data, tissue layers segmented from ultrasound image and diffusion theory are used to estimate the fluorescence in tissue layers. To improve the recovery of the fluorescence signal of PPIX, eliminating tissue autofluorescence is of great importance. Here the approach was to utilize measurements which straddled the steep Qband excitation peak of PPIX, via the integration of an additional laser source, exciting at 637 nm; a wavelength with a 2 fold lower PPIX excitation value than 633nm.The auto-fluorescence spectrum acquired from the 637 nm laser is then used to spectrally decouple the fluorescence data and produce an accurate fluorescence emission signal, because the two wavelengths have very similar auto-fluorescence but substantially different PPIX excitation levels. The accuracy of this method, using a single source detector pair setup, is verified through animal tumor model experiments, and the result is compared to different methods of fluorescence signal recovery.

High-Resolution Ultrasound-Switchable Fluorescence Imaging in Centimeter-Deep Tissue Phantoms with High Signal-To-Noise Ratio and High Sensitivity via Novel Contrast Agents

PubMed Central

Cheng, Bingbing; Bandi, Venugopal; Wei, Ming-Yuan; Pei, Yanbo; D’Souza, Francis; Nguyen, Kytai T.; Hong, Yi; Yuan, Baohong

2016-01-01

For many years, investigators have sought after high-resolution fluorescence imaging in centimeter-deep tissue because many interesting in vivo phenomena—such as the presence of immune system cells, tumor angiogenesis, and metastasis—may be located deep in tissue. Previously, we developed a new imaging technique to achieve high spatial resolution in sub-centimeter deep tissue phantoms named continuous-wave ultrasound-switchable fluorescence (CW-USF). The principle is to use a focused ultrasound wave to externally and locally switch on and off the fluorophore emission from a small volume (close to ultrasound focal volume). By making improvements in three aspects of this technique: excellent near-infrared USF contrast agents, a sensitive frequency-domain USF imaging system, and an effective signal processing algorithm, for the first time this study has achieved high spatial resolution (~ 900 μm) in 3-centimeter-deep tissue phantoms with high signal-to-noise ratio (SNR) and high sensitivity (3.4 picomoles of fluorophore in a volume of 68 nanoliters can be detected). We have achieved these results in both tissue-mimic phantoms and porcine muscle tissues. We have also demonstrated multi-color USF to image and distinguish two fluorophores with different wavelengths, which might be very useful for simultaneously imaging of multiple targets and observing their interactions in the future. This work has opened the door for future studies of high-resolution centimeter-deep tissue fluorescence imaging. PMID:27829050

High-Resolution Ultrasound-Switchable Fluorescence Imaging in Centimeter-Deep Tissue Phantoms with High Signal-To-Noise Ratio and High Sensitivity via Novel Contrast Agents.

PubMed

Cheng, Bingbing; Bandi, Venugopal; Wei, Ming-Yuan; Pei, Yanbo; D'Souza, Francis; Nguyen, Kytai T; Hong, Yi; Yuan, Baohong

2016-01-01

For many years, investigators have sought after high-resolution fluorescence imaging in centimeter-deep tissue because many interesting in vivo phenomena-such as the presence of immune system cells, tumor angiogenesis, and metastasis-may be located deep in tissue. Previously, we developed a new imaging technique to achieve high spatial resolution in sub-centimeter deep tissue phantoms named continuous-wave ultrasound-switchable fluorescence (CW-USF). The principle is to use a focused ultrasound wave to externally and locally switch on and off the fluorophore emission from a small volume (close to ultrasound focal volume). By making improvements in three aspects of this technique: excellent near-infrared USF contrast agents, a sensitive frequency-domain USF imaging system, and an effective signal processing algorithm, for the first time this study has achieved high spatial resolution (~ 900 μm) in 3-centimeter-deep tissue phantoms with high signal-to-noise ratio (SNR) and high sensitivity (3.4 picomoles of fluorophore in a volume of 68 nanoliters can be detected). We have achieved these results in both tissue-mimic phantoms and porcine muscle tissues. We have also demonstrated multi-color USF to image and distinguish two fluorophores with different wavelengths, which might be very useful for simultaneously imaging of multiple targets and observing their interactions in the future. This work has opened the door for future studies of high-resolution centimeter-deep tissue fluorescence imaging.

Factors affecting the microbiological condition of the deep tissues of mechanically tenderized beef.

PubMed

Gill, C O; McGinnis, J C

2005-04-01

Whole or halved top butt prime beef cuts were treated in two types of mechanical tenderizing machines that both pierced the meat with thin blades but that used blades of different forms. Aerobes on meat surfaces and in the deep tissues of cuts after treatments were counted. When cuts were treated at a laboratory using a Lumar machine, the contamination of deep tissues increased significantly (P < 0.01) with increasing numbers of aerobic bacteria on meat surfaces and decreased significantly (P < 0.001) with increasing distance from the incised surface. However, contamination did not increase significantly (P > 0.1) with repeated incising of the meat. When halved cuts were incised one or eight times using a commercially cleaned Ross machine at a retail store, the numbers of aerobes recovered from deep tissues were similar with both treatments. When halved cuts were treated in one or other machine, deep tissue contamination was greater with the Lumar machine than with the Ross machine. Contamination of deep tissues as a result of tenderizing by piercing with thin blades can be minimized if the blades are designed to limit the number of bacteria carried into the meat and the microbiological condition of incised surface is well controlled.

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.

Estimating the time and temperature relationship for causation of deep-partial thickness skin burns.

PubMed

Abraham, John P; Plourde, Brian; Vallez, Lauren; Stark, John; Diller, Kenneth R

2015-12-01

The objective of this study is to develop and present a simple procedure for evaluating the temperature and exposure-time conditions that lead to causation of a deep-partial thickness burn and the effect that the immediate post-burn thermal environment can have on the process. A computational model has been designed and applied to predict the time required for skin burns to reach a deep-partial thickness level of injury. The model includes multiple tissue layers including the epidermis, dermis, hypodermis, and subcutaneous tissue. Simulated exposure temperatures ranged from 62.8 to 87.8°C (145-190°F). Two scenarios were investigated. The first and worst case scenario was a direct exposure to water (characterized by a large convection coefficient) with the clothing left on the skin following the exposure. A second case consisted of a scald insult followed immediately by the skin being washed with cool water (20°C). For both cases, an Arrhenius injury model was applied whereby the extent and depth of injury were calculated and compared for the different post-burn treatments. In addition, injury values were compared with experiment data from the literature to assess verification of the numerical methodology. It was found that the clinical observations of injury extent agreed with the calculated values. Furthermore, inundation with cool water decreased skin temperatures more quickly than the clothing insulating case and led to a modest decrease in the burn extent. Copyright © 2015 Elsevier Ltd and ISBI. All rights reserved.

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.

Adipocyte Origins: Weighing the Possibilities

PubMed Central

Majka, Susan M.; Barak, Yaacov; Klemm, Dwight J.

2012-01-01

Adipose tissue is the primary energy reservoir in the body and an important endocrine organ that plays roles in energy homeostasis, feeding, insulin sensitivity and inflammation. While it was tacitly assumed that fat in different anatomical locations had a common origin and homogenous function, it is now clear that regional differences exist in adipose tissue characteristics and function. This is exemplified by the link between increased deep abdominal or visceral fat, but not peripheral adipose tissue, and the metabolic disturbances associated with obesity. Regional differences in fat function are due in large part to distinct adipocyte populations that comprise the different fat depots. Evidence accrued primarily in the last decade indicate that the distinct adipocyte populations are generated by a number of processes during and after development. These include the production of adipocytes from different germ cell layers, the formation of distinct preadipocyte populations from mesenchymal progenitors of mesodermal origin, and the production of adipocytes from hematopoietic stem cells from the bone marrow. This review will examine each of these process and their relevance to normal adipose tissue formation and contribution to obesity-related diseases. PMID:21544899

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.

Volumetric imaging of fast biological dynamics in deep tissue via wavefront engineering

NASA Astrophysics Data System (ADS)

Kong, Lingjie; Tang, Jianyong; Cui, Meng

2016-03-01

To reveal fast biological dynamics in deep tissue, we combine two wavefront engineering methods that were developed in our laboratory, namely optical phase-locked ultrasound lens (OPLUL) based volumetric imaging and iterative multiphoton adaptive compensation technique (IMPACT). OPLUL is used to generate oscillating defocusing wavefront for fast axial scanning, and IMPACT is used to compensate the wavefront distortions for deep tissue imaging. We show its promising applications in neuroscience and immunology.

Echinococcus granulosus equinus: variation in the germinal layer of murine hydatids and evidence of autophagy.

PubMed

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

1984-08-01

The germinal layer of sterile 9-month-old murine peritoneal cysts of Echinococcus granulosus equinus shows interrelated variation in depth, tissue integrity, metabolic reserves and the number of autophagic lamellar bodies present. These features are similar in large and medium-sized cysts from the same host, whether occurring singly or within cyst masses. Deep germinal layers (greater than 16 micron) are lipid- and glycogen-rich and possess numerous autophagic vacuoles with 6 nm period lamellar stacks asymmetrically disposed peripherally; shallow layers (less than 12 micron), with indications of degeneration, have depleted metabolic reserves and fewer lamellar bodies. These bodies are formed by smooth endoplasmic reticulum encirclement of small glycogen masses followed by further sequestration, and eventually definition of glycogen particles may be lost. Autophagy of mitochondria and cytoplasmic vesicles also occurs. The presence of lysosomal enzymes within the layer suggests autolysosomal compartmentalization of excess substrate and effete material. Mucopolysaccharide bodies, containing material similar to that exocytosed to form the laminated layer matrix, occur and are formed from fusion and autophagy of Golgi-derived vesicles. These bodies may also develop peripheral 6 nm period lamellar stacks, but of limited depth. Mucopolysaccharide bodies are the dominant feature of the germinal layer of very small cyst-mass cysts in which laminated layer production is considered to be arrested. They thus represent a repository for the unreleased mucopolysaccharide material.

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…

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.

Her2Net: A Deep Framework for Semantic Segmentation and Classification of Cell Membranes and Nuclei in Breast Cancer Evaluation.

PubMed

Saha, Monjoy; Chakraborty, Chandan

2018-05-01

We present an efficient deep learning framework for identifying, segmenting, and classifying cell membranes and nuclei from human epidermal growth factor receptor-2 (HER2)-stained breast cancer images with minimal user intervention. This is a long-standing issue for pathologists because the manual quantification of HER2 is error-prone, costly, and time-consuming. Hence, we propose a deep learning-based HER2 deep neural network (Her2Net) to solve this issue. The convolutional and deconvolutional parts of the proposed Her2Net framework consisted mainly of multiple convolution layers, max-pooling layers, spatial pyramid pooling layers, deconvolution layers, up-sampling layers, and trapezoidal long short-term memory (TLSTM). A fully connected layer and a softmax layer were also used for classification and error estimation. Finally, HER2 scores were calculated based on the classification results. The main contribution of our proposed Her2Net framework includes the implementation of TLSTM and a deep learning framework for cell membrane and nucleus detection, segmentation, and classification and HER2 scoring. Our proposed Her2Net achieved 96.64% precision, 96.79% recall, 96.71% F-score, 93.08% negative predictive value, 98.33% accuracy, and a 6.84% false-positive rate. Our results demonstrate the high accuracy and wide applicability of the proposed Her2Net in the context of HER2 scoring for breast cancer evaluation.

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.

Sacrificial-layer free transfer of mammalian cells using near infrared femtosecond laser pulses

PubMed Central

Zhang, Jun; Hartmann, Bastian; Siegel, Julian; Marchi, Gabriele; Clausen-Schaumann, Hauke; Sudhop, Stefanie; Huber, Heinz P.

2018-01-01

Laser-induced cell transfer has been developed in recent years for the flexible and gentle printing of cells. Because of the high transfer rates and the superior cell survival rates, this technique has great potential for tissue engineering applications. However, the fact that material from an inorganic sacrificial layer, which is required for laser energy absorption, is usually transferred to the printed target structure, constitutes a major drawback of laser based cell printing. Therefore alternative approaches using deep UV laser sources and protein based acceptor films for energy absorption, have been introduced. Nevertheless, deep UV radiation can introduce DNA double strand breaks, thereby imposing the risk of carcinogenesis. Here we present a method for the laser-induced transfer of hydrogels and mammalian cells, which neither requires any sacrificial material for energy absorption, nor the use of UV lasers. Instead, we focus a near infrared femtosecond (fs) laser pulse (λ = 1030 nm, 450 fs) directly underneath a thin cell layer, suspended on top of a hydrogel reservoir, to induce a rapidly expanding cavitation bubble in the gel, which generates a jet of material, transferring cells and hydrogel from the gel/cell reservoir to an acceptor stage. By controlling laser pulse energy, well-defined cell-laden droplets can be transferred with high spatial resolution. The transferred human (SCP1) and murine (B16F1) cells show high survival rates, and good cell viability. Time laps microscopy reveals unaffected cell behavior including normal cell proliferation. PMID:29718923

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.

Deep learning based tissue analysis predicts outcome in colorectal cancer.

PubMed

Bychkov, Dmitrii; Linder, Nina; Turkki, Riku; Nordling, Stig; Kovanen, Panu E; Verrill, Clare; Walliander, Margarita; Lundin, Mikael; Haglund, Caj; Lundin, Johan

2018-02-21

Image-based machine learning and deep learning in particular has recently shown expert-level accuracy in medical image classification. In this study, we combine convolutional and recurrent architectures to train a deep network to predict colorectal cancer outcome based on images of tumour tissue samples. The novelty of our approach is that we directly predict patient outcome, without any intermediate tissue classification. We evaluate a set of digitized haematoxylin-eosin-stained tumour tissue microarray (TMA) samples from 420 colorectal cancer patients with clinicopathological and outcome data available. The results show that deep learning-based outcome prediction with only small tissue areas as input outperforms (hazard ratio 2.3; CI 95% 1.79-3.03; AUC 0.69) visual histological assessment performed by human experts on both TMA spot (HR 1.67; CI 95% 1.28-2.19; AUC 0.58) and whole-slide level (HR 1.65; CI 95% 1.30-2.15; AUC 0.57) in the stratification into low- and high-risk patients. Our results suggest that state-of-the-art deep learning techniques can extract more prognostic information from the tissue morphology of colorectal cancer than an experienced human observer.

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.

Subsurface thermal coagulation of tissues using near infrared lasers

NASA Astrophysics Data System (ADS)

Chang, Chun-Hung Jack

Noninvasive laser therapy is currently limited primarily to cosmetic dermatological applications such as skin resurfacing, hair removal, tattoo removal and treatment of vascular birthmarks. In order to expand applications of noninvasive laser therapy, deeper optical penetration of laser radiation in tissue as well as more aggressive cooling of the tissue surface is necessary. The near-infrared laser wavelength of 1075 nm was found to be the optimal laser wavelength for creation of deep subsurface thermal lesions in liver tissue, ex vivo, with contact cooling, preserving a surface tissue layer of 2 mm. Monte Carlo light transport, heat transfer, and Arrhenius integral thermal damage simulations were conducted at this wavelength, showing good agreement between experiment and simulations. Building on the initial results, our goal is to develop new noninvasive laser therapies for application in urology, specifically for treatment of female stress urinary incontinence (SUI). Various laser balloon probes including side-firing and diffusing fibers were designed and tested for both transvaginal and transurethral approaches to treatment. The transvaginal approach showed the highest feasibility. To further increase optical penetration depth, various types and concentrations of optical clearing agents were also explored. Three cadavers studies were performed to investigate and demonstrate the feasibility of laser treatment for SUI.

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.

Experimentally increased nutrient availability at the permafrost thaw front selectively enhances biomass production of deep-rooting subarctic peatland species.

PubMed

Keuper, Frida; Dorrepaal, Ellen; van Bodegom, Peter M; van Logtestijn, Richard; Venhuizen, Gemma; van Hal, Jurgen; Aerts, Rien

2017-10-01

Climate warming increases nitrogen (N) mineralization in superficial soil layers (the dominant rooting zone) of subarctic peatlands. Thawing and subsequent mineralization of permafrost increases plant-available N around the thaw-front. Because plant production in these peatlands is N-limited, such changes may substantially affect net primary production and species composition. We aimed to identify the potential impact of increased N-availability due to permafrost thawing on subarctic peatland plant production and species performance, relative to the impact of increased N-availability in superficial organic layers. Therefore, we investigated whether plant roots are present at the thaw-front (45 cm depth) and whether N-uptake ( 15 N-tracer) at the thaw-front occurs during maximum thaw-depth, coinciding with the end of the growing season. Moreover, we performed a unique 3-year belowground fertilization experiment with fully factorial combinations of deep- (thaw-front) and shallow-fertilization (10 cm depth) and controls. We found that certain species are present with roots at the thaw-front (Rubus chamaemorus) and have the capacity (R. chamaemorus, Eriophorum vaginatum) for N-uptake from the thaw-front between autumn and spring when aboveground tissue is largely senescent. In response to 3-year shallow-belowground fertilization (S) both shallow- (Empetrum hermaphroditum) and deep-rooting species increased aboveground biomass and N-content, but only deep-rooting species responded positively to enhanced nutrient supply at the thaw-front (D). Moreover, the effects of shallow-fertilization and thaw-front fertilization on aboveground biomass production of the deep-rooting species were similar in magnitude (S: 71%; D: 111% increase compared to control) and additive (S + D: 181% increase). Our results show that plant-available N released from thawing permafrost can form a thus far overlooked additional N-source for deep-rooting subarctic plant species and increase their biomass production beyond the already established impact of warming-driven enhanced shallow N-mineralization. This may result in shifts in plant community composition and may partially counteract the increased carbon losses from thawing permafrost. © 2017 John Wiley & Sons Ltd.

Biomimetic remineralization of demineralized dentine using scaffold of CMC/ACP nanocomplexes in an in vitro tooth model of deep caries.

PubMed

Chen, Zhen; Cao, Shansong; Wang, Haorong; Li, Yanqiu; Kishen, Anil; Deng, Xuliang; Yang, Xiaoping; Wang, Yinghui; Cong, Changhong; Wang, Huajun; Zhang, Xu

2015-01-01

Currently, it is still a tough task for dentists to remineralize dentine in deep caries. The aim of this study was to remineralize demineralized dentine in a tooth model of deep caries using nanocomplexes of carboxymethyl chitosan/amorphous calcium phosphate (CMC/ACP) based on mimicking the stabilizing effect of dentine matrix protein 1 (DMP1) on ACP in the biomineralization of dentine. The experimental results indicate that CMC can stabilize ACP to form nanocomplexes of CMC/ACP, which is able to be processed into scaffolds by lyophilization. In the single-layer collagen model, ACP nanoparticles are released from scaffolds of CMC/ACP nanocomplexes dissolved and then infiltrate into collagen fibrils via the gap zones (40 nm) to accomplish intrafibrillar mineralization of collagen. With this method, the completely demineralized dentine was partially remineralized in the tooth mode. This is a bottom-up remineralizing strategy based on non-classical crystallization theory. Since nanocomplexes of CMC/ACP show a promising effect of remineralization on demineralized dentine via biomimetic strategy, thereby preserving dentinal tissue to the maximum extent possible, it would be a potential indirect pulp capping (IPC) material for the management of deep caries during vital pulp therapy based on the concept of minimally invasive dentistry (MID).

Biomimetic Remineralization of Demineralized Dentine Using Scaffold of CMC/ACP Nanocomplexes in an In Vitro Tooth Model of Deep Caries

PubMed Central

Chen, Zhen; Cao, Shansong; Wang, Haorong; Li, Yanqiu; Kishen, Anil; Deng, Xuliang; Yang, Xiaoping; Wang, Yinghui; Cong, Changhong; Wang, Huajun; Zhang, Xu

2015-01-01

Currently, it is still a tough task for dentists to remineralize dentine in deep caries. The aim of this study was to remineralize demineralized dentine in a tooth model of deep caries using nanocomplexes of carboxymethyl chitosan/amorphous calcium phosphate (CMC/ACP) based on mimicking the stabilizing effect of dentine matrix protein 1 (DMP1) on ACP in the biomineralization of dentine. The experimental results indicate that CMC can stabilize ACP to form nanocomplexes of CMC/ACP, which is able to be processed into scaffolds by lyophilization. In the single-layer collagen model, ACP nanoparticles are released from scaffolds of CMC/ACP nanocomplexes dissolved and then infiltrate into collagen fibrils via the gap zones (40 nm) to accomplish intrafibrillar mineralization of collagen. With this method, the completely demineralized dentine was partially remineralized in the tooth mode. This is a bottom-up remineralizing strategy based on non-classical crystallization theory. Since nanocomplexes of CMC/ACP show a promising effect of remineralization on demineralized dentine via biomimetic strategy, thereby preserving dentinal tissue to the maximum extent possible, it would be a potential indirect pulp capping (IPC) material for the management of deep caries during vital pulp therapy based on the concept of minimally invasive dentistry (MID). PMID:25587986

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.

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.

Improvement of depth resolution on photoacoustic imaging using multiphoton absorption

NASA Astrophysics Data System (ADS)

Yamaoka, Yoshihisa; Fujiwara, Katsuji; Takamatsu, Tetsuro

2007-07-01

Commercial imaging systems, such as computed tomography and magnetic resonance imaging, are frequently used powerful tools for observing structures deep within the human body. However, they cannot precisely visualized several-tens micrometer-sized structures for lack of spatial resolution. In this presentation, we propose photoacoustic imaging using multiphoton absorption technique to generate ultrasonic waves as a means of improving depth resolution. Since the multiphoton absorption occurs at only the focus point and the employed infrared pulses deeply penetrate living tissues, it enables us to extract characteristic features of structures embedded in the living tissue. When nanosecond pulses from a 1064-nm Nd:YAG laser were focused on Rhodamine B/chloroform solution (absorption peak: 540 nm), the peak intensity of the generated photoacoustic signal was proportional to the square of the input pulse energy. This result shows that the photoacoustic signals can be induced by the two-photon absorption of infrared nanosecond pulse laser and also can be detected by a commercial low-frequency MHz transducer. Furthermore, in order to evaluate the depth resolution of multiphoton-photoacoustic imaging, we investigated the dependence of photoacoustic signal on depth position using a 1-mm-thick phantom in a water bath. We found that the depth resolution of two-photon photoacoustic imaging (1064 nm) is greater than that of one-photon photoacoustic imaging (532 nm). We conclude that evolving multiphoton-photoacoustic imaging technology renders feasible the investigation of biomedical phenomena at the deep layer in living tissue.

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.

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.

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.

Subcutaneous and Intramuscular Hemodynamics and Oxygenation After Cold-Spray Application as Monitored by Near-Infrared Spectroscopy

PubMed Central

Shadgan, Babak; Pakravan, Amir H.; Hoens, Alison; Reid, W. Darlene

2015-01-01

Context Vapocoolant spray, commonly known as cold spray (CS), is a cryotherapy modality used in sports medicine, athletic training, and rehabilitation settings. Proposed physiologic effects of cryotherapy modalities include reductions in tissue blood flow, oxygenation, and cell metabolism in addition to attenuation of pain perception attributed to reduced superficial nerve conduction velocity. Objective To examine the effects of CS on subcutaneous and intramuscular blood flow and oxygenation on the thigh muscle using near-infrared spectroscopy, an optical method to monitor changes in tissue oxygenated (O2Hb), deoxygenated (HHb), and total (tHb) hemoglobin. Design Cross-sectional study. Setting Muscle Biophysics Laboratory. Patients or Other Participants Participants were 13 healthy adults (8 men, 5 women; age = 37.4 ± 6 years, body mass index = 27.4 ± 2.6, adipose tissue thickness = 7.2 ± 1.8 mm). Intervention(s) Conventional CS was applied to the vastus medialis muscles. Main Outcome Measure(s) Changes in chromophore concentrations of O2Hb, HHb, and tHb at superficial and deep layers were monitored for 5 minutes using a 2-channel near-infrared spectroscopy. Results Thirty seconds after CS application, we observed a decrease from baseline in O2Hb and tHb only in the superficial layer that was maintained for 3 minutes. Conclusions Application of CS induced a transient change in blood flow and oxygenation of the superficial tissues with no change in deeper tissues over the healthy vastus medialis muscle. The limited physiologic effect of CS on the superficial hemodynamics and oxygenation of limb muscles may limit the therapeutic benefit of this cryotherapy modality to a temporary analgesic effect, a hypothesis that warrants a clinical trial on traumatized muscles. PMID:26098273

Initial evaluation of an ultrasound measure for assessing the activity of skin lesions in juvenile localized scleroderma.

PubMed

Li, S C; Liebling, M S; Haines, K A; Weiss, J E; Prann, A

2011-05-01

To evaluate the construct validity of 2 proposed measures (the Ultrasound Disease Activity [U-DA] and the Tissue Thickness Score [TTS]) for evaluating sonographic differences in juvenile localized scleroderma skin lesions. We conducted a retrospective review of juvenile localized scleroderma patients who had ultrasound scans of their skin lesions between October 2005 and February 2009. Imaged lesions were classified as active or inactive based upon clinical assessment. Lesions had to have been imaged within 1 month of a clinic visit or have the same clinical assessment during both the visit before and the visit after the scan. Two physicians scored the scans using the U-DA, which scores for differences in lesion echogenicity and vascularity compared with normal tissue. Tissue thickness differences were evaluated by percent differences and by using the TTS. Wilcoxon's rank sum test was performed to assess differences. We studied 52 scans from 21 patients, 32 scans of active skin lesions and 20 scans of inactive skin lesions. Features reported by clinicians as indicative of active disease included erythema, warmth, violaceous color, new lesion, expansion of lesion, and induration. The U-DA was significantly different between active and inactive skin lesions (P = 0.0010) with significant differences found for the parameters of total echogenicity, hypodermis echogenicity, and deep tissue layer vascularity (P = 0.0014, P = 0.0023, and P = 0.0374, respectively). No significant differences were found for tissue layer thickness or TTS. The U-DA may be a useful tool in the identification of localized scleroderma activity. Further study is needed to prospectively evaluate the validity, reliability, and sensitivity of this potential monitoring tool. Copyright © 2011 by the American College of Rheumatology.

Application of CO laser for laser balloon angioplasty

NASA Astrophysics Data System (ADS)

Miyamoto, Akira; Sakurada, Masami; Mizuno, Kyoichi; Kurita, Akira; Nakamura, Haruo; Suda, Akira; Arai, Tsunenori; Kikuchi, Makoto

1990-07-01

CO laser may be efficient for thermal fusion of intima of arterial wall without adventitial tissue damage because of high tissue absorption. To investigate the efficacy of CO laser as a laser bam for laser balloon angioplasty (LBA). CO laser was irradiated to aortic tissue through 3Oim polyethylene membrane and tissue temperature was measured by a thermistor. At 2Owatt/cm2 200joules/cm2 continuous laser exposure (CE), tissue temperature was above 100°C within a depth of 1mm and rapidly decreased to 60 °C or below between 2 and 3mm in depth. Moreover, adventitial temperature could be decreased by changing duty ratio (exposure duration/interval) of intermittent laser exposure (IE) despite of the same laser energy. Light microscopy showed high degree of medial coagulation necrosis in CE, however thermal coagulation was observed only at the surface of intima of aortic tissue in IE at duty ratio 1 / 2. These findings suggested CO laser could coagulate intimal layer with less deep thermal damage compared to Nd- YAG laser and that IE was better for superficial welding than CE at the same energy. We concluded that CO laser might be more efficient as a laser beam for LBA than Nd-YAG laser.

Deep lamellar keratoplasty on air with lyophilised tissue.

PubMed Central

Chau, G K; Dilly, S A; Sheard, C E; Rostron, C K

1992-01-01

Deep lamellar keratoplasty on air involves injecting air into the corneal stroma to expand it to several times its normal thickness. This method is designed to facilitate dissection of the deep stroma and reduce the risk of perforation of Descemet's membrane when carrying out deep lamellar keratoplasty. We have modified the technique by using prelathed freeze-dried donor tissue and report our results in a series of patients with corneal stromal scarring owing to a variety of corneal problems, namely, keratoconus, pterygium, and herpes zoster ophthalmicus. All patients achieved best corrected postoperative visual acuity of 6/12 or better without problems associated with graft failure or rejection. Histopathological examination of corneal tissue following air injection showed surgical emphysema within the cornea and separation of deep stromal fibres from the underlying Descemet's membrane. Images PMID:1477037

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.

Photoelectron Transfer at ZnTPyP Self-Assembly/TiO2 Interfaces for Enhanced Two-Photon Photodynamic Therapy.

PubMed

Liu, Yanyan; Meng, Xianfu; Wang, Han; Tang, Zhongmin; Zuo, Changjing; He, Mingyuan; Bu, Wenbo

2018-01-17

Two-photon (TP) absorption nanomaterials are highly desirable for deep-tissue clinical diagnostics and orthotopic disease treatment. Here, a well-designed core/shell nanostructure was successfully synthesized with a ZnTPyP self-assembly nanocrystal (ZSN) inner core coated by a homogeneous TiO 2 layer outside (ZSN-TO). The ZSN is a good photosemiconductor, showing both one-photon (OP) and TP absorption properties for red fluorescence emission and electron-hole pair generation; TiO 2 with good biocompatibility acts as the electron acceptor, which can transfer photoelectron from ZSN to TiO 2 for highly effective electron-hole separation, favoring the production of long-life superoxide anion (O 2 •- ) by electrons and oxygen and strong oxidizing hydroxyl radical (•OH) by holes and surrounding H 2 O. Once pretreated with ZSN-TO, the simultaneous OP-405 nm or TP-800 nm laser stimulation and fluorescent imaging of reactive oxygen species (ROS) showed dynamical and continuous generation of ROS in HeLa cells, with cytotoxicity significantly increasing via the type-1-like photodynamic therapy process. The results demonstrated that the combination of organic ZSN with inorganic TiO 2 has great applications as an excellent photosensitizer for deep-tissue fluorescent imaging and noninvasive disease treatment via TP photodynamic therapy.

Convolutional Neural Network for Histopathological Analysis of Osteosarcoma.

PubMed

Mishra, Rashika; Daescu, Ovidiu; Leavey, Patrick; Rakheja, Dinesh; Sengupta, Anita

2018-03-01

Pathologists often deal with high complexity and sometimes disagreement over osteosarcoma tumor classification due to cellular heterogeneity in the dataset. Segmentation and classification of histology tissue in H&E stained tumor image datasets is a challenging task because of intra-class variations, inter-class similarity, crowded context, and noisy data. In recent years, deep learning approaches have led to encouraging results in breast cancer and prostate cancer analysis. In this article, we propose convolutional neural network (CNN) as a tool to improve efficiency and accuracy of osteosarcoma tumor classification into tumor classes (viable tumor, necrosis) versus nontumor. The proposed CNN architecture contains eight learned layers: three sets of stacked two convolutional layers interspersed with max pooling layers for feature extraction and two fully connected layers with data augmentation strategies to boost performance. The use of a neural network results in higher accuracy of average 92% for the classification. We compare the proposed architecture with three existing and proven CNN architectures for image classification: AlexNet, LeNet, and VGGNet. We also provide a pipeline to calculate percentage necrosis in a given whole slide image. We conclude that the use of neural networks can assure both high accuracy and efficiency in osteosarcoma classification.

Surgical management of advanced ocular adnexal amyloidosis.

PubMed

Patrinely, J R; Koch, D D

1992-06-01

Ocular adnexal amyloidosis is characterized by amyloid deposition within the deep connective tissue layers of the eyelids, conjunctiva, and anterior orbit. Management of advanced cases has traditionally been unsatisfactory, with either no surgery offered because of fear of hemorrhage or an en bloc resection performed of the entire involved area. We present two cases of advanced periorbital amyloidosis successfully managed by preserving the anatomic planes of the eyelids and meticulously debulking the deposits with a spooned curette. Lax eyelid tendons and aponeuroses were simultaneously repaired, and no sacrifice of eyelid tissues was necessary. One patient remained asymptomatic for 2 years after surgery before developing early reaccumulation in the lower eyelids. The other patient required additional eyelid debulking and ptosis revision 8 months after surgery, but was in stable condition at follow-up 2 years after surgery. This technique offers safe, easily repeatable, nondestructive treatment for advanced periocular amyloidosis.

Coherence-Gated Sensorless Adaptive Optics Multiphoton Retinal Imaging

PubMed Central

Cua, Michelle; Wahl, Daniel J.; Zhao, Yuan; Lee, Sujin; Bonora, Stefano; Zawadzki, Robert J.; Jian, Yifan; Sarunic, Marinko V.

2016-01-01

Multiphoton microscopy enables imaging deep into scattering tissues. The efficient generation of non-linear optical effects is related to both the pulse duration (typically on the order of femtoseconds) and the size of the focused spot. Aberrations introduced by refractive index inhomogeneity in the sample distort the wavefront and enlarge the focal spot, which reduces the multiphoton signal. Traditional approaches to adaptive optics wavefront correction are not effective in thick or multi-layered scattering media. In this report, we present sensorless adaptive optics (SAO) using low-coherence interferometric detection of the excitation light for depth-resolved aberration correction of two-photon excited fluorescence (TPEF) in biological tissue. We demonstrate coherence-gated SAO TPEF using a transmissive multi-actuator adaptive lens for in vivo imaging in a mouse retina. This configuration has significant potential for reducing the laser power required for adaptive optics multiphoton imaging, and for facilitating integration with existing systems. PMID:27599635

Coherence-Gated Sensorless Adaptive Optics Multiphoton Retinal Imaging.

PubMed

Cua, Michelle; Wahl, Daniel J; Zhao, Yuan; Lee, Sujin; Bonora, Stefano; Zawadzki, Robert J; Jian, Yifan; Sarunic, Marinko V

2016-09-07

Multiphoton microscopy enables imaging deep into scattering tissues. The efficient generation of non-linear optical effects is related to both the pulse duration (typically on the order of femtoseconds) and the size of the focused spot. Aberrations introduced by refractive index inhomogeneity in the sample distort the wavefront and enlarge the focal spot, which reduces the multiphoton signal. Traditional approaches to adaptive optics wavefront correction are not effective in thick or multi-layered scattering media. In this report, we present sensorless adaptive optics (SAO) using low-coherence interferometric detection of the excitation light for depth-resolved aberration correction of two-photon excited fluorescence (TPEF) in biological tissue. We demonstrate coherence-gated SAO TPEF using a transmissive multi-actuator adaptive lens for in vivo imaging in a mouse retina. This configuration has significant potential for reducing the laser power required for adaptive optics multiphoton imaging, and for facilitating integration with existing systems.

Increased Liposome Extravasation in Selected Tissues: Effect of Substance P

NASA Astrophysics Data System (ADS)

Rosenecker, Joseph; Zhang, Weiming; Hong, Keelung; Lausier, James; Geppetti, Pierangelo; Yoshihara, Shigemi; Papahadjopoulos, Demetrios; Nadel, Jay A.

1996-07-01

We have used a pharmacologic mediator to open intercellular connections in selected vessels to allow liposomes to escape from the blood stream and to extravasate into tissues that have appropriate receptors. We have examined the effects of substance P (SP), a peptide known to increase vascular permeability in selected tissues, such as trachea, esophagus, and urinary bladder in rats. We used quantitative fluorescence analysis of tissues to measure two fluorescent markers, one attached to the lipid (rhodamine-phosphatidylethanolamine) and another, doxorubicin (an antitumor drug), encapsulated within the aqueous interior. We have also examined the deposition of liposomes microscopically by the use of encapsulated colloidal gold and silver enhancement. Analysis of the biochemical and morphological observations indicate the following: (i) Injection of SP produces a striking increase in both liposome labels, but only in tissues that possess receptors for SP in postcapillary venules; (ii) liposome material in these tissues has extravasated and is found extracellularly near a variety of cells beyond the endothelial layer over the first few hours; (iii) 24 h following injection of liposomes and SP, liposome material is found in these tissues, localized intracellularly in both endothelial cells and macrophages. We propose that appropriate application of tissue-specific mediators can result in liposome extravasation deep within tissues that normally do not take up significant amounts of liposomes from the blood. Such liposomes are able to carry a variety of pharmacological agents that can be released locally within selected target tissues for therapeutic purposes.

Resolution enhancement in deep-tissue nanoparticle imaging based on plasmonic saturated excitation microscopy

NASA Astrophysics Data System (ADS)

Deka, Gitanjal; Nishida, Kentaro; Mochizuki, Kentaro; Ding, Hou-Xian; Fujita, Katsumasa; Chu, Shi-Wei

2018-03-01

Recently, many resolution enhancing techniques are demonstrated, but most of them are severely limited for deep tissue applications. For example, wide-field based localization techniques lack the ability of optical sectioning, and structured light based techniques are susceptible to beam distortion due to scattering/aberration. Saturated excitation (SAX) microscopy, which relies on temporal modulation that is less affected when penetrating into tissues, should be the best candidate for deep-tissue resolution enhancement. Nevertheless, although fluorescence saturation has been successfully adopted in SAX, it is limited by photobleaching, and its practical resolution enhancement is less than two-fold. Recently, we demonstrated plasmonic SAX which provides bleaching-free imaging with three-fold resolution enhancement. Here we show that the three-fold resolution enhancement is sustained throughout the whole working distance of an objective, i.e., 200 μm, which is the deepest super-resolution record to our knowledge, and is expected to extend into deeper tissues. In addition, SAX offers the advantage of background-free imaging by rejecting unwanted scattering background from biological tissues. This study provides an inspirational direction toward deep-tissue super-resolution imaging and has the potential in tumor monitoring and beyond.

Computational analysis of transcranial magnetic stimulation in the presence of deep brain stimulation probes

NASA Astrophysics Data System (ADS)

Syeda, F.; Holloway, K.; El-Gendy, A. A.; Hadimani, R. L.

2017-05-01

Transcranial Magnetic Stimulation is an emerging non-invasive treatment for depression, Parkinson's disease, and a variety of other neurological disorders. Many Parkinson's patients receive the treatment known as Deep Brain Stimulation, but often require additional therapy for speech and swallowing impairment. Transcranial Magnetic Stimulation has been explored as a possible treatment by stimulating the mouth motor area of the brain. We have calculated induced electric field, magnetic field, and temperature distributions in the brain using finite element analysis and anatomically realistic heterogeneous head models fitted with Deep Brain Stimulation leads. A Figure of 8 coil, current of 5000 A, and frequency of 2.5 kHz are used as simulation parameters. Results suggest that Deep Brain Stimulation leads cause surrounding tissues to experience slightly increased E-field (Δ Emax =30 V/m), but not exceeding the nominal values induced in brain tissue by Transcranial Magnetic Stimulation without leads (215 V/m). The maximum temperature in the brain tissues surrounding leads did not change significantly from the normal human body temperature of 37 °C. Therefore, we ascertain that Transcranial Magnetic Stimulation in the mouth motor area may stimulate brain tissue surrounding Deep Brain Stimulation leads, but will not cause tissue damage.

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.

[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.

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

"Deep-media culture condition" promoted lumen formation of endothelial cells within engineered three-dimensional tissues in vitro.

PubMed

Sekiya, Sachiko; Shimizu, Tatsuya; Yamato, Masayuki; Okano, Teruo

2011-03-01

In the field of tissue engineering, the induction of microvessels into tissues is an important task because of the need to overcome diffusion limitations of oxygen and nutrients within tissues. Powerful methods to create vessels in engineered tissues are needed for creating real living tissues. In this study, we utilized three-dimensional (3D) highly cell dense tissues fabricated by cell sheet technology. The 3D tissue constructs are close to living-cell dense tissue in vivo. Additionally, creating an endothelial cell (EC) network within tissues promoted neovascularization promptly within the tissue after transplantation in vivo. Compared to the conditions in vivo, however, common in vitro cell culture conditions provide a poor environment for creating lumens within 3D tissue constructs. Therefore, for determining adequate conditions for vascularizing engineered tissue in vitro, our 3D tissue constructs were cultured under a "deep-media culture conditions." Compared to the control conditions, the morphology of ECs showed a visibly strained cytoskeleton, and the density of lumen formation within tissues increased under hydrostatic pressure conditions. Moreover, the increasing expression of vascular endothelial cadherin in the lumens suggested that the vessels were stabilized in the stimulated tissues compared with the control. These findings suggested that deep-media culture conditions improved lumen formation in engineered tissues in vitro.

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.

VoxResNet: Deep voxelwise residual networks for brain segmentation from 3D MR images.

PubMed

Chen, Hao; Dou, Qi; Yu, Lequan; Qin, Jing; Heng, Pheng-Ann

2018-04-15

Segmentation of key brain tissues from 3D medical images is of great significance for brain disease diagnosis, progression assessment and monitoring of neurologic conditions. While manual segmentation is time-consuming, laborious, and subjective, automated segmentation is quite challenging due to the complicated anatomical environment of brain and the large variations of brain tissues. We propose a novel voxelwise residual network (VoxResNet) with a set of effective training schemes to cope with this challenging problem. The main merit of residual learning is that it can alleviate the degradation problem when training a deep network so that the performance gains achieved by increasing the network depth can be fully leveraged. With this technique, our VoxResNet is built with 25 layers, and hence can generate more representative features to deal with the large variations of brain tissues than its rivals using hand-crafted features or shallower networks. In order to effectively train such a deep network with limited training data for brain segmentation, we seamlessly integrate multi-modality and multi-level contextual information into our network, so that the complementary information of different modalities can be harnessed and features of different scales can be exploited. Furthermore, an auto-context version of the VoxResNet is proposed by combining the low-level image appearance features, implicit shape information, and high-level context together for further improving the segmentation performance. Extensive experiments on the well-known benchmark (i.e., MRBrainS) of brain segmentation from 3D magnetic resonance (MR) images corroborated the efficacy of the proposed VoxResNet. Our method achieved the first place in the challenge out of 37 competitors including several state-of-the-art brain segmentation methods. Our method is inherently general and can be readily applied as a powerful tool to many brain-related studies, where accurate segmentation of brain structures is critical. Copyright © 2017 Elsevier Inc. All rights reserved.

[Observation on changes of oxygen partial pressure in the deep tissues along the large intestine meridian during acupuncture in healthy subjects].

PubMed

Chen, Ming; Hu, Xiang-long; Wu, Zu-xing

2010-06-01

To observe changes of the partial oxygen pressure in the deep tissues along the Large Intestine Meridian (LIM) during acupuncture stimulation, so as to reveal the characteristics of energy metabolism in the tissues along the LIM. Thirty-one healthy volunteer subjects were enlisted in the present study. Partial oxygen pressure (POP) in the tissues (at a depth of about 1.5 cm) of acupoints Binao (LI 14), Shouwuli (LI 13), Shousanli (LI 10), 2 non-acupoints [the midpoints between Quchi (LI 11) and LI 14, and between Yangxi (LI 5) and LI 11) of the LIM, and 10 non-meridian points, 1.5-2.0 cm lateral and medial to each of the tested points of the LIM was detected before, during and after electroacupuncture (EA) stimulation of Hegu (LI 4) by using a tissue oxygen tension needle-like sensor. In normal condition, the POP values in the deep tissues along the LIM were significantly higher than those of the non-meridian control points on its bilateral sides. During and after EA of Hegu (LI 4), the POP levels decreased significantly in the deep tissues along the LIM in comparison with pre-EA (P < 0.01), and had no apparent changes in the non-meridian control points (P > 0.05). POP is significantly higher in the deep tissues along the LIM of healthy subjects under normal conditions, which can be downregulated by EA of Hegu (LI 4), suggesting an increase of both the utilization rate of oxygen and energy metabolism after EA.

Layer-by-Layer Bioprinting of Stem Cells for Retinal Tissue Regeneration

DTIC Science & Technology

2015-10-01

AWARD NUMBER: W81XWH-14-1-0522 TITLE: Layer-by-Layer Bioprinting of Stem Cells for Retinal Tissue Regeneration PRINCIPAL INVESTIGATOR...TITLE AND SUBTITLE Layer-by-Layer Bioprinting of Stem Cells for Retinal Tissue Regeneration 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-14-1-0522 5c...bioprinting process using stem cells for retinal tissue regeneration. The LBL nature of the bioprinting process matches nicely with the native

A deep learning model observer for use in alterative forced choice virtual clinical trials

NASA Astrophysics Data System (ADS)

Alnowami, M.; Mills, G.; Awis, M.; Elangovanr, P.; Patel, M.; Halling-Brown, M.; Young, K. C.; Dance, D. R.; Wells, K.

2018-03-01

Virtual clinical trials (VCTs) represent an alternative assessment paradigm that overcomes issues of dose, high cost and delay encountered in conventional clinical trials for breast cancer screening. However, to fully utilize the potential benefits of VCTs requires a machine-based observer that can rapidly and realistically process large numbers of experimental conditions. To address this, a Deep Learning Model Observer (DLMO) was developed and trained to identify lesion targets from normal tissue in small (200 x 200 pixel) image segments, as used in Alternative Forced Choice (AFC) studies. The proposed network consists of 5 convolutional layers with 2x2 kernels and ReLU (Rectified Linear Unit) activations, followed by max pooling with size equal to the size of the final feature maps and three dense layers. The class outputs weights from the final fully connected dense layer are used to consider sets of n images in an n-AFC paradigm to determine the image most likely to contain a target. To examine the DLMO performance on clinical data, a training set of 2814 normal and 2814 biopsy-confirmed malignant mass targets were used. This produced a sensitivity of 0.90 and a specificity of 0.92 when presented with a test data set of 800 previously unseen clinical images. To examine the DLMOs minimum detectable contrast, a second dataset of 630 simulated backgrounds and 630 images with simulated lesion and spherical targets (4mm and 6mm diameter), produced contrast thresholds equivalent to/better than human observer performance for spherical targets, and comparable (12 % difference) for lesion targets.

Photocleavable Hydrogel-Coated Upconverting Nanoparticles: A Multifunctional Theranostic Platform for NIR Imaging and On-Demand Macromolecular Delivery.

PubMed

Jalani, Ghulam; Naccache, Rafik; Rosenzweig, Derek H; Haglund, Lisbet; Vetrone, Fiorenzo; Cerruti, Marta

2016-01-27

Lanthanide-doped upconverting nanoparticles (UCNPs) have emerged as excellent nanotransducers for converting longer wavelength near-infrared (NIR) light to shorter wavelengths spanning the ultraviolet (UV) to the visible (Vis) regions of the spectrum via a multiphoton absorption process, known as upconversion. Here, we report the development of NIR to UV-Vis-NIR UCNPs consisting of LiYF4:Yb(3+)/Tm(3+)@SiO2 individually coated with a 10 ± 2 nm layer of chitosan (CH) hydrogel cross-linked with a photocleavable cross-linker (PhL). We encapsulated fluorescent-bovine serum albumin (FITC-BSA) inside the gel. Under 980 nm excitation, the upconverted UV emission cleaves the PhL cross-links and instantaneously liberates the FITC-BSA under 2 cm thick tissue. The release is immediately arrested if the excitation source is switched off. The upconverted NIR light allows for the tracking of particles under the tissue. Nucleus pulposus (NP) cells cultured with UCNPs are viable both in the presence and in the absence of laser irradiation. Controlled drug delivery of large biomolecules and deep tissue imaging make this system an excellent theranostic platform for tissue engineering, biomapping, and cellular imaging applications.

Laser-induced lipolysis on adipose cells

NASA Astrophysics Data System (ADS)

Solarte, Efrain; Gutierrez, O.; Neira, Rodrigo; Arroyave, J.; Isaza, Carolina; Ramirez, Hugo; Rebolledo, Aldo F.; Criollo, Willian; Ortiz, C.

2004-10-01

Recently, a new liposuction technique, using a low-level laser (LLL) device and Ultrawet solution prior to the procedure, demonstrated the movement of fat from the inside to the outside of the adipocyte (Neira et al., 2002). To determine the mechanisms involved, we have performed Scanning and Transmission Electron Microscopy studies; Light transmittance measurements on adipocyte dilutions; and a study of laser light propagation in adipose tissue. This studies show: 1. Cellular membrane alterations. 2. LLL is capable to reach the deep adipose tissue layer, and 3. The tumescence solution enhances the light propagation by clearing the tissue. MRI studies demonstrated the appearance of fat on laser treated abdominal tissue. Besides, adipocytes were cultivated and irradiated to observe the effects on isolated cells. These last studies show: 1. 635 nm-laser alone is capable of mobilizing cholesterol from the cell membrane; this action is enhanced by the presence of adrenaline and lidocaine. 2. Intracellular fat is released from adipocytes by co joint action of adrenaline, aminophyline and 635 nm-laser. Results are consistent with a laser induced cellular process, which causes fat release from the adipocytes into the intercellular space, besides the modification of the cellular membranes.

[THE PECULIARITIES OF UTERINE STRUCTURE AFTER DELIVERY IN RATS WITH THE MYOMETRIAL SCAR].

PubMed

Maiborodin, I V; Pekarev, O G; Yakimova, N V; Pekareva, Ye O; Maiborodina, V I; Perminova, Ye I

2015-01-01

The uterine tissues of female rats (n=30) with a scarred myometrium were examined by methods of light microscopy after the delivery. 1.5-2 months after the delivery no significant differences in the parameters of blood and lymph flow in the deep layers of the endometrium, myometrium and the myometrial scar tissue were found between the intact rats, nulliparous rats with a scarred uterus, rats that gave birth after laparotomy only and those that gave birth under the conditions of myometrial scar. In the course of pregnancy and labor activity, the damage of the tissues was observed not in the uterine scar proper, but at its borders with the myometrium. This is supported by the old hemorrhages and lymphostasis phenomena, greater number of lymphocytes, neutrophils, monocytes, macrophages and erythrocytes. In determining the indications and contraindications to vaginal childbirth in women with scarred uterus it is necessary to examine not only the scar proper, but also its border with the myometrium. The myometrial scar by itself, is not an absolute contraindication to vaginal delivery, the natural delivery is feasible in the absence of cavities with liquid and hemorrhages in the tissues of the uterine scar and at its border with myometrium.

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.

Transmission in near-infrared optical windows for deep brain imaging.

PubMed

Shi, Lingyan; Sordillo, Laura A; Rodríguez-Contreras, Adrián; Alfano, Robert

2016-01-01

Near-infrared (NIR) radiation has been employed using one- and two-photon excitation of fluorescence imaging at wavelengths 650-950 nm (optical window I) for deep brain imaging; however, longer wavelengths in NIR have been overlooked due to a lack of suitable NIR-low band gap semiconductor imaging detectors and/or femtosecond laser sources. This research introduces three new optical windows in NIR and demonstrates their potential for deep brain tissue imaging. The transmittances are measured in rat brain tissue in the second (II, 1,100-1,350 nm), third (III, 1,600-1,870 nm), and fourth (IV, centered at 2,200 nm) NIR optical tissue windows. The relationship between transmission and tissue thickness is measured and compared with the theory. Due to a reduction in scattering and minimal absorption, window III is shown to be the best for deep brain imaging, and windows II and IV show similar but better potential for deep imaging than window I. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Calibrating amino acid δ13C and δ15N offsets between polyp and protein skeleton to develop proteinaceous deep-sea corals as paleoceanographic archives

NASA Astrophysics Data System (ADS)

McMahon, Kelton W.; Williams, Branwen; Guilderson, Thomas P.; Glynn, Danielle S.; McCarthy, Matthew D.

2018-01-01

Compound-specific stable isotopes of amino acids (CSI-AA) from proteinaceous deep-sea coral skeletons have the potential to improve paleoreconstructions of plankton community composition, and our understanding of the trophic dynamics and biogeochemical cycling of sinking organic matter in the Ocean. However, the assumption that the molecular isotopic values preserved in protein skeletal material reflect those of the living coral polyps has never been directly investigated in proteinaceous deep-sea corals. We examined CSI-AA from three genera of proteinaceous deep-sea corals from three oceanographically distinct regions of the North Pacific: Primnoa from the Gulf of Alaska, Isidella from the Central California Margin, and Kulamanamana from the North Pacific Subtropical Gyre. We found minimal offsets in the δ13C values of both essential and non-essential AAs, and in the δ15N values of source AAs, between paired samples of polyp tissue and protein skeleton. Using an essential AA δ13C fingerprinting approach, we show that estimates of the relative contribution of eukaryotic microalgae and prokaryotic cyanobacteria to the sinking organic matter supporting deep-sea corals are the same when calculated from polyp tissue or recently deposited skeletal tissue. The δ15N values of trophic AAs in skeletal tissue, on the other hand, were consistently 3-4‰ lower than polyp tissue for all three genera. We hypothesize that this offset reflects a partitioning of nitrogen flux through isotopic branch points in the synthesis of polyp (fast turnover tissue) and skeleton (slow, unidirectional incorporation). This offset indicates an underestimation, albeit correctable, of approximately half a trophic position from gorgonin protein-based deep-sea coral skeleton. Together, our observations open the door for applying many of the rapidly evolving CSI-AA based tools developed for metabolically active tissues in modern systems to archival coral tissues in a paleoceanographic context.

Pre-operative intra-articular deep tissue sampling with novel retrograde forceps improves the diagnostics in periprosthetic joint infection.

PubMed

Wimmer, Matthias D; Ploeger, Milena M; Friedrich, Max J; Hügle, Thomas; Gravius, Sascha; Randau, Thomas M

2017-07-01

Histopathological tissue analysis is a key parameter within the diagnostic algorithm for suspected periprosthetic joint infections (PJIs), conventionally acquired in open surgery. In 2014, Hügle and co-workers introduced novel retrograde forceps for retrograde synovial biopsy with simultaneous fluid aspiration of the knee joint. We hypothesised that tissue samples acquired by retrograde synovial biopsy are equal to intra-operatively acquired deep representative tissue samples regarding bacterial detection and differentiation of periprosthetic infectious membranes. Thirty patients (male n = 15, 50%; female n = 15, 50%) with 30 suspected PJIs in painful total hip arthroplasties (THAs) were included in this prospective, controlled, non-blinded trial. The results were compared with intra-operatively obtained representative deep tissue samples. In summary, 27 out of 30 patients were diagnosed correctly as infected (17/17) or non-infected (10/13). The sensitivity to predict a PJI using the Retroforce® sampling forceps in addition to standard diagnostics was 85%, the specificity 100%. Retrograde synovial biopsy is a new and rapid diagnostic procedure under local anaesthesia in patients with painful THAs with similar histological results compared to deep tissue sampling.

Ultrasound elastomicroscopy for articular cartilage: from static to transient and 1D to 2D

NASA Astrophysics Data System (ADS)

Zheng, Yongping; Bridal, Sharon L.; Shi, Jun; Saied, Amena; Lu, Minghua; Jaffre, Britta; Mak, Arthur F. T.; Laugier, Pascal; Qin, Ling

2003-05-01

Articular cartilage (AC) is a biological weight-bearing tissue covering the ends of articulating bones within synovial joints. Its function very much depends on the unique multi-layered structure and the depth-dependent material properties, which have not been well invetigated nondestructively. In this study, transient depth-dependent material properties of bovine patella cartilage were measured using ultrasound elastomicroscopy methods. A 50 MHz focused ultrasound transducer was used to collect A-mode ultrasound echoes from the articular cartilage during the compression and subsequent force-relaxation. The transient displacements of the cartilage tissues at different depths were calculated from the ultrasound echoes using a cross-correlation technique. It was observed that the strains in the superficial zone were much larger than those in the middle and deep zones as the equilibrium state was approached. The tissues inside the AC layer continued to move during the force-relaxation phase after the compression was completed. This process has been predicted by a biphasic theory. In this study, it has been verified experimentally. It was also observed that the tissue deformations at different depths of AC were much more evenly distributed before force-relaxation. AC specimens were also investigated using a 2D ultrasound elastomicroscopy system that included a 3D translating system for moving the ultrasound transducer over the specimens. B-mode RF ultrasound signals were collected from the specimens under different loading levels applied with a specially designed compressor. Preliminary results demonstrated that the scanning was repeatable with high correlation of radio frequency signals obtained from the same site during different scans when compression level was unchanged (R2 > 0.97). Strains of the AC specimens were mapped using data collected with this ultrasound elastomicroscope. This system can also be potentially used for the assessment of other biological tissues, bioengineered tissues or biomaterials with fine structures.

Effects of protein-coated nanofibers on conformation of gingival fibroblast spheroids: potential utility for connective tissue regeneration.

PubMed

Kaufman, Gili; Whitescarver, Ryan A; Nunes, Laiz; Palmer, Xavier-Lewis; Skrtic, Drago; Tutak, Wojtek

2018-01-24

Deep wounds in the gingiva caused by trauma or surgery require a rapid and robust healing of connective tissues. We propose utilizing gas-brushed nanofibers coated with collagen and fibrin for that purpose. Our hypotheses are that protein-coated nanofibers will: (i) attract and mobilize cells in various spatial orientations, and (ii) regulate the expression levels of specific extracellular matrix (ECM)-associated proteins, determining the initial conformational nature of dense and soft connective tissues. Gingival fibroblast monolayers and 3D spheroids were cultured on ECM substrate and covered with gas-blown poly-(DL-lactide-co-glycolide) (PLGA) nanofibers (uncoated/coated with collagen and fibrin). Cell attraction and rearrangement was followed by F-actin staining and confocal microscopy. Thicknesses of the cell layers, developed within the nanofibers, were quantified by ImageJ software. The expression of collagen1α1 chain (Col1α1), fibronectin, and metalloproteinase 2 (MMP2) encoding genes was determined by quantitative reverse transcription analysis. Collagen- and fibrin- coated nanofibers induced cell migration toward fibers and supported cellular growth within the scaffolds. Both proteins affected the spatial rearrangement of fibroblasts by favoring packed cell clusters or intermittent cell spreading. These cell arrangements resembled the structural characteristic of dense and soft connective tissues, respectively. Within three days of incubation, fibroblast spheroids interacted with the fibers, and grew robustly by increasing their thickness compared to monolayers. While the ECM key components, such as fibronectin and MMP2 encoding genes, were expressed in both protein groups, Col1α1 was predominantly expressed in bundled fibroblasts grown on collagen fibers. This enhanced expression of collagen1 is typical for dense connective tissue. Based on results of this study, our gas-blown, collagen- and fibrin-coated PLGA nanofibers are viable candidates for engineering soft and dense connective tissues with the required structural characteristics and functions needed for wound healing applications. Rapid regeneration of these layers should enhance healing of open wounds in a harsh oral environment.

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.

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.

A Neocortical Delta Rhythm Facilitates Reciprocal Interlaminar Interactions via Nested Theta Rhythms

PubMed Central

Carracedo, Lucy M.; Kjeldsen, Henrik; Cunnington, Leonie; Jenkins, Alastair; Schofield, Ian; Cunningham, Mark O.; Davies, Ceri H.; Traub, Roger D.

2013-01-01

Delta oscillations (1–4 Hz) associate with deep sleep and are implicated in memory consolidation and replay of cortical responses elicited during wake states. A potent local generator has been characterized in thalamus, and local generators in neocortex have been suggested. Here we demonstrate that isolated rat neocortex generates delta rhythms in conditions mimicking the neuromodulatory state during deep sleep (low cholinergic and dopaminergic tone). The rhythm originated in an NMDA receptor-driven network of intrinsic bursting (IB) neurons in layer 5, activating a source of GABAB receptor-mediated inhibition. In contrast, regular spiking (RS) neurons in layer 5 generated theta-frequency outputs. In layer 2/3 principal cells, outputs from IB cells associated with IPSPs, whereas those from layer 5 RS neurons related to nested bursts of theta-frequency EPSPs. Both interlaminar spike and field correlations revealed a sequence of events whereby sparse spiking in layer 2/3 was partially reflected back from layer 5 on each delta period. We suggest that these reciprocal, interlaminar interactions may represent a “Helmholtz machine”-like process to control synaptic rescaling during deep sleep. PMID:23804097

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.

Amelioration of ethanol induced apoptotic DNA damage and ulcerative injuries in the mice gastric tissues by starch oral administration.

PubMed

Hamad, Sherin Ramadan; Hamad Mohamed, Hanan Ramadan

2018-02-01

Nowadays, gastric ulcers have become very common gastrointestinal disorders and numerous natural plant extracts exert promising anti-ulcerative effects. Therefore, this study was designed to evaluate the possible protective effect of dietary starch against ethanol induced gastric ulcers in mice. Post-administration of dietary starch for three consecutive days caused remarkable ameliorations in hemorrhagic lesions in gastric mucus and significant suppression in % incidence of ulceration, ulcer index and ulcer score induced by ethanol single administration. Indeed, deep ulceration, necrosis, disruption and degeneration in large areas of mucosa layer together with dense inflammatory cells infiltration and edema in sub-mucosal layer induced by ethanol administration were attenuated by starch post-administration and normalized the tissue architecture of the stomach. This potential protective effect could be attributed to the potent anti-oxidative capacity of starch that causes scavenger of the reactive oxygen species and thereby decreasing single and double DNA stranded break inductions and apoptotic DNA damage revealed by returning the p53 and caspase-3 expression levels to the normal level compared to the ethanol treated group. In conclusion, dietary starch has a potent therapeutic effect against ethanol induced gastric ulcer in mice via its free radical scavengers ability. Thus, we recommended further studies on its possible use as antiulcer drugs.

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.

Biophotonic applications of eigenchannels in a scattering medium (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kim, Moonseok; Choi, Wonjun; Choi, Youngwoon; Yoon, Changhyeong; Choi, Wonshik

2016-03-01

When waves travel through disordered media such as ground glass and skin tissues, they are scattered multiple times. Most of the incoming energy bounces back at the superficial layers and only a small fraction can penetrate deep inside. This has been a limiting factor for the working depth of various optical techniques. We present a systematic method to enhance wave penetration to the scattering media. Specifically, we measured the reflection matrix of a disordered medium with wide angular coverage for each orthogonal polarization states. From the reflection matrix, we identified reflection eigenchannels of the medium, and shaped the incident wave into the reflection eigenchannel with smallest eigenvalue, which we call anti-reflection mode. This makes reflectance reduced and wave penetration increased as a result of the energy conservation. We demonstrated transmission enhancement by more than a factor of 3 by the coupling of the incident waves to the anti-reflection modes. Based on the uneven distribution of eigenvalues of reflection eigenchannels, we further developed an iterative feedback control method for finding and coupling light to anti-reflection modes. Since this adaptive control method can keep up with sample perturbation, it promotes the applicability of exploiting reflection eigenchannels. Our approach of delivering light deep into the scattering media will contribute to enhancing the sensitivity of detecting objects hidden under scattering layers, which is universal problem ranging from geology to life science.

Superiority of the EF-120-00-3F biopsy forceps in the histopathological evaluation of upper urinary tract specimens.

PubMed

Kramer, Mario W; Abbas, Mahmoud; Kabbani, Mohammad; Imkamp, Florian; Nagele, Udo; Bach, Thorsten; Jutzi, Stephan; von Klot, Christoph; Becker, Jan; Merseburger, Axel S; Kuczyk, Markus A; Kreipe, Hans H; Herrmann, Thomas R

2014-08-01

The purpose of this study was to analyze the efficacy of two different biopsy forceps with respect to their functionality and quality for histological assessment of upper urinary tract biopsies. We compared flow rates, active deflection angle and histological quality of specimens taken from upper urinary tract biopsies of 40 consecutively treated patients between October 2011 and October 2012. Two different biopsy forceps [group A = 20 patients: "Piranha (®) " (Boston Scientific, Natick, USA) versus group B = 20 patients: "EF-120-00-3F" (Euromedical GmbH, Siegsdorf, GER)] were assessed. The specimens obtained with the "EF-120-00-3F" were superior in terms of tissue preservation such as intact urothelium/tissue fragmentation and the prevention of artifacts due to tissue compression (existence of artifacts/nucleus evaluation). Furthermore, due to superiority of tissue preservation, tissues obtained with the "EF-120-00-3F" showed better tissue orientation in the sense of anatomic evaluation of invasion and deep layer involvement. Irrigation flow rates did not differ significantly while deflection angle was more impaired with the "Piranha" biopsy forceps. No difference was observed with the handling of both biopsy forceps. We conclude that the "EF-120-00-3F" biopsy forceps represent a valuable modification of antegradely insertable instruments that qualifies for improved and correct staging as well as diagnosis of upper urinary specimens in comparison with standard biopsy forcipes.

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.

3D printing of tissue-simulating phantoms as a traceable standard for biomedical optical measurement

NASA Astrophysics Data System (ADS)

Dong, Erbao; Wang, Minjie; Shen, Shuwei; Han, Yilin; Wu, Qiang; Xu, Ronald

2016-01-01

Optical phantoms are commonly used to validate and calibrate biomedical optical devices in order to ensure accurate measurement of optical properties in biological tissue. However, commonly used optical phantoms are based on homogenous materials that reflect neither optical properties nor multi-layer heterogeneities of biological tissue. Using these phantoms for optical calibration may result in significant bias in biological measurement. We propose to characterize and fabricate tissue simulating phantoms that simulate not only the multi-layer heterogeneities but also optical properties of biological tissue. The tissue characterization module detects tissue structural and functional properties in vivo. The phantom printing module generates 3D tissue structures at different scales by layer-by-layer deposition of phantom materials with different optical properties. The ultimate goal is to fabricate multi-layer tissue simulating phantoms as a traceable standard for optimal calibration of biomedical optical spectral devices.

Photoacoustic design parameter optimization for deep tissue imaging by numerical simulation

NASA Astrophysics Data System (ADS)

Wang, Zhaohui; Ha, Seunghan; Kim, Kang

2012-02-01

A new design of light illumination scheme for deep tissue photoacoustic (PA) imaging, a light catcher, is proposed and evaluated by in silico simulation. Finite element (FE)-based numerical simulation model was developed for photoacoustic (PA) imaging in soft tissues. In this in silico simulation using a commercially available FE simulation package (COMSOL MultiphysicsTM, COMSOL Inc., USA), a short-pulsed laser point source (pulse length of 5 ns) was placed in water on the tissue surface. Overall, four sets of simulation models were integrated together to describe the physical principles of PA imaging. Light energy transmission through background tissues from the laser source to the target tissue or contrast agent was described by diffusion equation. The absorption of light energy and its conversion to heat by target tissue or contrast agent was modeled using bio-heat equation. The heat then causes the stress and strain change, and the resulting displacement of the target surface produces acoustic pressure. The created wide-band acoustic pressure will propagate through background tissues to the ultrasound detector, which is governed by acoustic wave equation. Both optical and acoustical parameters in soft tissues such as scattering, absorption, and attenuation are incorporated in tissue models. PA imaging performance with different design parameters of the laser source and energy delivery scheme was investigated. The laser light illumination into the deep tissues can be significantly improved by up to 134.8% increase of fluence rate by introducing a designed compact light catcher with highly reflecting inner surface surrounding the light source. The optimized parameters through this simulation will guide the design of PA system for deep tissue imaging, and help to form the base protocols of experimental evaluations in vitro and in vivo.

Regional and depth variability of porcine meniscal mechanical properties through biaxial testing.

PubMed

Kahlon, A; Hurtig, M B; Gordon, K D

2015-01-01

The menisci in the knee joint undergo complex loading in-vivo resulting in a multidirectional stress distribution. Extensive mechanical testing has been conducted to investigate the tissue properties of the knee meniscus, but the testing conditions do not replicate this complex loading regime. Biaxial testing involves loading tissue along two different directions simultaneously, which more accurately simulates physiologic loading conditions. The purpose of this study was to report mechanical properties of meniscal tissue resulting from biaxial testing, while simultaneously investigating regional variations in properties. Ten left, fresh porcine joints were obtained, and the medial and lateral menisci were harvested from each joint (twenty menisci total). Each menisci was divided into an anterior, middle and posterior region; and three slices (femoral, deep and tibial layers) were obtained from each region. Biaxial and constrained uniaxial testing was performed on each specimen, and Young's moduli were calculated from the resulting stress strain curves. Results illustrated significant differences in regional mechanical properties, with the medial anterior (Young's modulus (E)=11.14 ± 1.10 MPa), lateral anterior (E=11.54 ± 1.10 MPa) and lateral posterior (E=9.0 ± 1.2 MPa) regions exhibiting the highest properties compared to the medial central (E=5.0 ± 1.22 MPa), medial posterior (E=4.16 ± 1.13 MPa) and lateral central (E=5.6 ± 1.20 MPa) regions. Differences with depth were also significant on the lateral meniscus, with the femoral (E=12.7 ± 1.22 MPa) and tibial (E=8.6 ± 1.22 MPa) layers exhibiting the highest Young's moduli. This data may form the basis for future modeling of meniscal tissue, or may aid in the design of synthetic replacement alternatives. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Tomographic reconstruction of layered tissue structures

NASA Astrophysics Data System (ADS)

Hielscher, Andreas H.; Azeez-Jan, Mohideen; Bartel, Sebastian

2001-11-01

In recent years the interest in the determination of optical properties of layered tissue structure has resurfaced. Applications include, for example, studies on layered skin tissue and underlying muscles, imaging of the brain underneath layers of skin, skull, and meninges, and imaging of the fetal head in utero beneath the layered structures of the maternal abdomen. In this work we approach the problem of layered structures in the framework of model-based iterative image reconstruction schemes. These schemes are currently developed to determine the optical properties inside tissue from measurement on the surface. If applied to layered structure these techniques yield substantial improvements over currently available semi-analytical approaches.

Design and optimization of an ultra wideband and compact microwave antenna for radiometric monitoring of brain temperature.

PubMed

Rodrigues, Dario B; Maccarini, Paolo F; Salahi, Sara; Oliveira, Tiago R; Pereira, Pedro J S; Limao-Vieira, Paulo; Snow, Brent W; Reudink, Doug; Stauffer, Paul R

2014-07-01

We present the modeling efforts on antenna design and frequency selection to monitor brain temperature during prolonged surgery using noninvasive microwave radiometry. A tapered log-spiral antenna design is chosen for its wideband characteristics that allow higher power collection from deep brain. Parametric analysis with the software HFSS is used to optimize antenna performance for deep brain temperature sensing. Radiometric antenna efficiency (η) is evaluated in terms of the ratio of power collected from brain to total power received by the antenna. Anatomical information extracted from several adult computed tomography scans is used to establish design parameters for constructing an accurate layered 3-D tissue phantom. This head phantom includes separate brain and scalp regions, with tissue equivalent liquids circulating at independent temperatures on either side of an intact skull. The optimized frequency band is 1.1-1.6 GHz producing an average antenna efficiency of 50.3% from a two turn log-spiral antenna. The entire sensor package is contained in a lightweight and low-profile 2.8 cm diameter by 1.5 cm high assembly that can be held in place over the skin with an electromagnetic interference shielding adhesive patch. The calculated radiometric equivalent brain temperature tracks within 0.4 °C of the measured brain phantom temperature when the brain phantom is lowered 10 °C and then returned to the original temperature (37 °C) over a 4.6-h experiment. The numerical and experimental results demonstrate that the optimized 2.5-cm log-spiral antenna is well suited for the noninvasive radiometric sensing of deep brain temperature.

Superficial and deep changes of histology, texture and particle size distribution in broiler wooden breast muscle during refrigerated storage.

PubMed

Soglia, Francesca; Gao, Jingxian; Mazzoni, Maurizio; Puolanne, Eero; Cavani, Claudio; Petracci, Massimiliano; Ertbjerg, Per

2017-09-01

Recently the poultry industry faced an emerging muscle abnormality termed wooden breast (WB), the prevalence of which has dramatically increased in the past few years. Considering the incomplete knowledge concerning this condition and the lack of information on possible variations due to the intra-fillet sampling locations (superficial vs. deep position) and aging of the samples, this study aimed at investigating the effect of 7-d storage of broiler breast muscles on histology, texture, and particle size distribution, evaluating whether the sampling position exerts a relevant role in determining the main features of WB. With regard to the histological observations, severe myodegeneration accompanied by accumulation of connective tissue was observed within the WB cases, irrespective of the intra-fillet sampling position. No changes in the histological traits took place during the aging in either the normal or the WB samples. As to textural traits, although a progressive tenderization process took place during storage (P ≤ 0.001), the differences among the groups were mainly detected when raw meat rather than cooked was analyzed, with the WB samples exhibiting the highest (P ≤ 0.001) 80% compression values. In spite of the increased amount of connective tissue components in the WB cases, their thermally labile cross-links will account for the similar compression and shear-force values as normal breast cases when measured on cooked samples. Similarly, the enlargement of extracellular matrix and fibrosis might contribute in explaining the different fragmentation patterns observed between the superficial and the deep layer in the WB samples, with the superficial part exhibiting a higher amount of larger particles and an increase in particles with larger size during storage, compared to normal breasts. © 2017 Poultry Science Association Inc.

Tissue Damage Characterization Using Non-invasive Optical Modalities

NASA Astrophysics Data System (ADS)

Diaz, David

The ability to determine the degree of cutaneous and subcutaneous tissue damage is essential for proper wound assessment and a significant factor for determining patient treatment and morbidity. Accurate characterization of tissue damage is critical for a number of medical applications including surgical removal of nonviable tissue, severity assessment of subcutaneous ulcers, and depth assessment of visually open wounds. The main objective of this research was to develop a non-invasive method for identifying the extent of tissue damage underneath intact skin that is not apparent upon visual examination. This work investigated the relationship between tissue optical properties, blood flow, and tissue viability by testing the hypotheses that (a) changes in tissue oxygenation and/or microcirculatory blood flow measurable by Diffuse Near Infrared Spectroscopy (DNIRS) and Diffuse Correlation Spectroscopy (DCS) differ between healthy and damaged tissue and (b) the magnitude of those changes differs for different degrees of tissue damage. This was accomplished by developing and validating a procedure for measuring microcirculatory blood flow and tissue oxygenation dynamics at multiple depths (up to 1 centimeter) using non-invasive DCS and DNIRS technologies. Due to the lack of pressure ulcer animal models that are compatible with our optical systems, a proof of concept was conducted in a porcine burn model prior to conducting clinical trials in order to assess the efficacy of the system in-vivo. A reduction in total hemoglobin was observed for superficial (5%) and deep burns (35%) along with a statistically significant difference between the optical properties of superficial and deep burns (p < 0.05). Burn depth and viable vessel density were estimated via histological samples. 42% of vessels in the dermal layer were viable for superficial burns, compared to 25% for deep burns. The differences detected in optical properties and hemoglobin content by optical measurements correlated with the extent of tissue injury observed in histological stains. After proof of concept in animals, a human study was conducted and optical data was collected from 20 healthy subjects and 8 patients at risk of developing pressure ulcers. Blood flow index (BFI) values from the sacral region of patients were compared with those of healthy volunteers. Prior to loading measurements, baseline BFI values were measured in subjects in lateral position. These values were systematically higher for patients who developed open ulcers than for the other research subjects. While under the loading position, patients who developed a pressure ulcer had a decrease in BFI from baseline values an order of magnitude larger than healthy subjects (p < 0.01) and patients whose redness dissipated (p < 0.01). The hyperemic response, when pressure was released as the patient was moved back to a lateral position, showed a decreasing trend from one session to the next for patients who developed open ulcers. Overall, this work presents a novel non-invasive method of pressure ulcer assessment and provides an improvement over current assessment methods. The obtained results suggest the system may potentially predict whether non-blanchable redness will develop into an advanced pressure ulcer within four weeks from initial observation.

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.

13-fold resolution gain through turbid layer via translated unknown speckle illumination

PubMed Central

Guo, Kaikai; Zhang, Zibang; Jiang, Shaowei; Liao, Jun; Zhong, Jingang; Eldar, Yonina C.; Zheng, Guoan

2017-01-01

Fluorescence imaging through a turbid layer holds great promise for various biophotonics applications. Conventional wavefront shaping techniques aim to create and scan a focus spot through the turbid layer. Finding the correct input wavefront without direct access to the target plane remains a critical challenge. In this paper, we explore a new strategy for imaging through turbid layer with a large field of view. In our setup, a fluorescence sample is sandwiched between two turbid layers. Instead of generating one focus spot via wavefront shaping, we use an unshaped beam to illuminate the turbid layer and generate an unknown speckle pattern at the target plane over a wide field of view. By tilting the input wavefront, we raster scan the unknown speckle pattern via the memory effect and capture the corresponding low-resolution fluorescence images through the turbid layer. Different from the wavefront-shaping-based single-spot scanning, the proposed approach employs many spots (i.e., speckles) in parallel for extending the field of view. Based on all captured images, we jointly recover the fluorescence object, the unknown optical transfer function of the turbid layer, the translated step size, and the unknown speckle pattern. Without direct access to the object plane or knowledge of the turbid layer, we demonstrate a 13-fold resolution gain through the turbid layer using the reported strategy. We also demonstrate the use of this technique to improve the resolution of a low numerical aperture objective lens allowing to obtain both large field of view and high resolution at the same time. The reported method provides insight for developing new fluorescence imaging platforms and may find applications in deep-tissue imaging. PMID:29359102

Characterisation of signal enhancements achieved when utilizing a photon diode in deep Raman spectroscopy of tissue

PubMed Central

Vardaki, Martha Z.; Matousek, Pavel; Stone, Nicholas

2016-01-01

We characterise the performance of a beam enhancing element (‘photon diode’) for use in deep Raman spectroscopy (DRS) of biological tissues. The optical component enhances the number of laser photons coupled into a tissue sample by returning escaping photons back into it at the illumination zone. The method is compatible with transmission Raman spectroscopy, a deep Raman spectroscopy concept, and its implementation leads to considerable enhancement of detected Raman photon rates. In the past, the enhancement concept was demonstrated with a variety of samples (pharmaceutical tablets, tissue, etc) but it was not systematically characterized with biological tissues. In this study, we investigate the enhancing properties of the photon diode in the transmission Raman geometry as a function of: a) the depth and b) the optical properties of tissue samples. Liquid tissue phantoms were employed to facilitate systematic variation of optical properties. These were chosen to mimic optical properties of human tissues, including breast and prostate. The obtained results evidence that a photon diode can enhance Raman signals of tissues by a maximum of × 2.4, although it can also decrease the signals created towards the back of samples that exhibit high scattering or absorption properties. PMID:27375932

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.

Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data.

PubMed

Alakwaa, Fadhl M; Chaudhary, Kumardeep; Garmire, Lana X

2018-01-05

Metabolomics holds the promise as a new technology to diagnose highly heterogeneous diseases. Conventionally, metabolomics data analysis for diagnosis is done using various statistical and machine learning based classification methods. However, it remains unknown if deep neural network, a class of increasingly popular machine learning methods, is suitable to classify metabolomics data. Here we use a cohort of 271 breast cancer tissues, 204 positive estrogen receptor (ER+), and 67 negative estrogen receptor (ER-) to test the accuracies of feed-forward networks, a deep learning (DL) framework, as well as six widely used machine learning models, namely random forest (RF), support vector machines (SVM), recursive partitioning and regression trees (RPART), linear discriminant analysis (LDA), prediction analysis for microarrays (PAM), and generalized boosted models (GBM). DL framework has the highest area under the curve (AUC) of 0.93 in classifying ER+/ER- patients, compared to the other six machine learning algorithms. Furthermore, the biological interpretation of the first hidden layer reveals eight commonly enriched significant metabolomics pathways (adjusted P-value <0.05) that cannot be discovered by other machine learning methods. Among them, protein digestion and absorption and ATP-binding cassette (ABC) transporters pathways are also confirmed in integrated analysis between metabolomics and gene expression data in these samples. In summary, deep learning method shows advantages for metabolomics based breast cancer ER status classification, with both the highest prediction accuracy (AUC = 0.93) and better revelation of disease biology. We encourage the adoption of feed-forward networks based deep learning method in the metabolomics research community for classification.

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.

Computed tomography of deep fat masses in multiple symmetrical lipomatosis

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

Enzi, G.; Biondetti, P.R.; Fiore, D.

1982-07-01

Deep fat masses were evaluated by computed tomography (CT) in 15 patients with multiple symmetrical lipomatosis. In 4 patients, peritracheal accumulations of fat were observed. In 3 of them, tracheal compression by lipomatous tissue was demonstrated: 2 were asymptomatic and the third severe respiratory insufficiency secondary to blockage of the air was by the vocal cords as the result of recurrent nerve palsy. In 6 patients, lipomatous tissue occupied the potential space between the spina scapulae and the trapezius, supraspinatus, and infraspinatus muscles. In 2, calcification of lipomatous masses was observed. There was no relationship between extension of subcutaneous fatmore » and accumulation at deep sites. CT facilitates early detection of peritracheal lipomatous tissue and is helpful in follow-up when deep fat accumulation is responsible for space-occupying lesions requiring surgery.« less

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

Mild closed head injury promotes a selective trigeminal hypernociception: implications for the acute emergence of post-traumatic headache.

PubMed

Benromano, T; Defrin, R; Ahn, A H; Zhao, J; Pick, C G; Levy, D

2015-05-01

Headache is one of the most common symptoms following traumatic head injury. The mechanisms underlying the emergence of such post-traumatic headache (PTH) remain unknown but may be related to injury of deep cranial tissues or damage to central pain processing pathways, as a result of brain injury. A mild closed head injury in mice combined with the administration of cranial or hindpaw formalin tests was used to examine post-traumatic changes in the nociceptive processing from deep cranial tissues or the hindpaw. Histological analysis was used to examine post-traumatic pro-inflammatory changes in the calvarial periosteum, a deep cranial tissue. At 48 h after head injury, mice demonstrated enhanced nociceptive responses following injection of formalin into the calvarial periosteum, a deep cranial tissue, but no facilitation of the nociceptive responses following injection of formalin into an extracranial tissue, the hindpaw. Mice also showed an increase in the number of activated periosteal mast cells 48 h following mild head trauma, suggesting an inflammatory response. Our study demonstrates that mild closed head injury is associated with enhanced processing of nociceptive information emanating from trigeminal-innervated deep cranial tissues, but not from non-cranial tissues. Based on these finding as well as the demonstration of head injury-evoked degranulation of calvarial periosteal mast cells, we propose that inflammatory-evoked enhancement of peripheral cranial nociception, rather than changes in supraspinal pain mechanisms play a role in the initial emergence of PTH. Peripheral targeting of nociceptors that innervate the calvaria may be used to ameliorate PTH pain. © 2014 European Pain Federation - EFIC®

Estimation and imaging of breast lesions using a two-layer tissue structure by ultrasound-guided optical tomography

PubMed Central

Xu, Yan; Zhu, Quing

2015-01-01

Abstract. A new two-step estimation and imaging method is developed for a two-layer breast tissue structure consisting of a breast tissue layer and a chest wall underneath. First, a smaller probe with shorter distance source-detector pairs was used to collect the reflected light mainly from the breast tissue layer. Then, a larger probe with 9×14 source-detector pairs and a centrally located ultrasound transducer was used to collect reflected light from the two-layer tissue structure. The data collected from the smaller probe were used to estimate breast tissue optical properties. With more accurate estimation of the average breast tissue properties, the second layer properties can be assessed from data obtained from the larger probe. Using this approach, the unknown variables have been reduced from four to two and the estimated bulk tissue optical properties are more accurate and robust. In addition, a two-step reconstruction using a genetic algorithm and conjugate gradient method is implemented to simultaneously reconstruct the absorption and reduced scattering maps of targets inside a two-layer tissue structure. Simulations and phantom experiments have been performed to validate the new reconstruction method, and a clinical example is given to demonstrate the feasibility of this approach. PMID:26046722

3D Deep Learning Angiography (3D-DLA) from C-arm Conebeam CT.

PubMed

Montoya, J C; Li, Y; Strother, C; Chen, G-H

2018-05-01

Deep learning is a branch of artificial intelligence that has demonstrated unprecedented performance in many medical imaging applications. Our purpose was to develop a deep learning angiography method to generate 3D cerebral angiograms from a single contrast-enhanced C-arm conebeam CT acquisition in order to reduce image artifacts and radiation dose. A set of 105 3D rotational angiography examinations were randomly selected from an internal data base. All were acquired using a clinical system in conjunction with a standard injection protocol. More than 150 million labeled voxels from 35 subjects were used for training. A deep convolutional neural network was trained to classify each image voxel into 3 tissue types (vasculature, bone, and soft tissue). The trained deep learning angiography model was then applied for tissue classification into a validation cohort of 8 subjects and a final testing cohort of the remaining 62 subjects. The final vasculature tissue class was used to generate the 3D deep learning angiography images. To quantify the generalization error of the trained model, we calculated the accuracy, sensitivity, precision, and Dice similarity coefficients for vasculature classification in relevant anatomy. The 3D deep learning angiography and clinical 3D rotational angiography images were subjected to a qualitative assessment for the presence of intersweep motion artifacts. Vasculature classification accuracy and 95% CI in the testing dataset were 98.7% (98.3%-99.1%). No residual signal from osseous structures was observed for any 3D deep learning angiography testing cases except for small regions in the otic capsule and nasal cavity compared with 37% (23/62) of the 3D rotational angiographies. Deep learning angiography accurately recreated the vascular anatomy of the 3D rotational angiography reconstructions without a mask. Deep learning angiography reduced misregistration artifacts induced by intersweep motion, and it reduced radiation exposure required to obtain clinically useful 3D rotational angiography. © 2018 by American Journal of Neuroradiology.

Quantum dots versus organic fluorophores in fluorescent deep-tissue imaging--merits and demerits.

PubMed

Bakalova, Rumiana; Zhelev, Zhivko; Gadjeva, Veselina

2008-12-01

The use of fluorescence in deep-tissue imaging is rapidly expanding in last several years. The progress in fluorescent molecular probes and fluorescent imaging techniques gives an opportunity to detect single cells and even molecular targets in live organisms. The highly sensitive and high-speed fluorescent molecular sensors and detection devices allow the application of fluorescence in functional imaging. With the development of novel bright fluorophores based on nanotechnologies and 3D fluorescence scanners with high spatial and temporal resolution, the fluorescent imaging has a potential to become an alternative of the other non-invasive imaging techniques as magnetic resonance imaging, positron-emission tomography, X-ray, computing tomography. The fluorescent imaging has also a potential to give a real map of human anatomy and physiology. The current review outlines the advantages of fluorescent nanoparticles over conventional organic dyes in deep-tissue imaging in vivo and defines the major requirements to the "perfect fluorophore". The analysis proceeds from the basic principles of fluorescence and major characteristics of fluorophores, light-tissue interactions, and major limitations of fluorescent deep-tissue imaging. The article is addressed to a broad readership - from specialists in this field to university students.

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.

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.

Non-invasive therapy of wrinkles and lax skin using a novel multisource phase-controlled radio frequency system.

PubMed

Elman, Monica; Vider, Itzhak; Harth, Yoram; Gottfried, Varda; Shemer, Avner

2010-04-01

Abstract The last few years have shown an increased demand for non-invasive skin tightening to improve body contour. Since light (lasers or intense pulsed light sources) has a limited ability to penetrate deep into the tissue, radio frequency (RF) modalities were introduced for the reduction of lax skin to achieve skin tightening and body circumference reduction. This study presents the use of the novel 3DEEP technology for body contouring. 3DEEP is a next generation RF technology that provides targeted heating to deeper skin layers without pain or other local or systemic side effects associated with the use of the earlier generation RF systems available today. The study included 30 treatment areas on 23 healthy volunteers at two sites. The treatment protocol included four weekly and two bi-weekly (n= 6) treatments on different body areas. Results were evaluated by standardized photography and by circumference measurements at the treatment area, and were compared to changes in body weight. Significant improvement could be observed in wrinkles and skin laxity, and in the appearance of stretch marks and cellulite. Some changes appeared as early as after a single treatment. Circumference changes of up to 4.3 cm were measured.

Growth and regeneration in cultivated fragments of the boreal deep water sponge Geodia barretti Bowerbank, 1858 (Geodiidae, Tetractinellida, Demospongiae).

PubMed

Hoffmann, Friederike; Rapp, Hans Tore; Zöller, Tobias; Reitner, Joachim

2003-01-23

A cultivation method has been developed for the boreal deep-water sponge Geodia barretti (Demospongiae, Geodiidae), a species which is common in the deep Norwegian fjords. The species is known to contain secondary metabolites which are biologically active. Choanosomal fragments of 2-4 cm(3) (approximately 3-7 g) were kept in half-open systems. Cicatrisation and regeneration processes were surveyed by histological examination during 8 months of cultivation. During the first weeks, the weight of the fragments decreased. However, after about 6 weeks the weight equalled the original weight, and after 1 year the weight had increased by about 40% compared to the original weight. The initial decrease was due to complex healing processes and the regeneration of the cortex, a sterrastral layer typical for the family of the Geodiidae. We document, for the first time, the complete cortex reconstruction in an adult G. barretti, as well as the development of egg cells during cultivation. Our study represents the first attempt at biotechnological production of boreal sponge tissue. For successful farming of G. barretti and other boreal and arctic sponges, however, further investigation is needed on factors stimulating growth and secondary metabolite production in the target species.

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.

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.

A deep learning approach to estimate chemically-treated collagenous tissue nonlinear anisotropic stress-strain responses from microscopy images.

PubMed

Liang, Liang; Liu, Minliang; Sun, Wei

2017-11-01

Biological collagenous tissues comprised of networks of collagen fibers are suitable for a broad spectrum of medical applications owing to their attractive mechanical properties. In this study, we developed a noninvasive approach to estimate collagenous tissue elastic properties directly from microscopy images using Machine Learning (ML) techniques. Glutaraldehyde-treated bovine pericardium (GLBP) tissue, widely used in the fabrication of bioprosthetic heart valves and vascular patches, was chosen to develop a representative application. A Deep Learning model was designed and trained to process second harmonic generation (SHG) images of collagen networks in GLBP tissue samples, and directly predict the tissue elastic mechanical properties. The trained model is capable of identifying the overall tissue stiffness with a classification accuracy of 84%, and predicting the nonlinear anisotropic stress-strain curves with average regression errors of 0.021 and 0.031. Thus, this study demonstrates the feasibility and great potential of using the Deep Learning approach for fast and noninvasive assessment of collagenous tissue elastic properties from microstructural images. In this study, we developed, to our best knowledge, the first Deep Learning-based approach to estimate the elastic properties of collagenous tissues directly from noninvasive second harmonic generation images. The success of this study holds promise for the use of Machine Learning techniques to noninvasively and efficiently estimate the mechanical properties of many structure-based biological materials, and it also enables many potential applications such as serving as a quality control tool to select tissue for the manufacturing of medical devices (e.g. bioprosthetic heart valves). Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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.

Contrasting effects of strabismic amblyopia on metabolic activity in superficial and deep layers of striate cortex

PubMed Central

Adams, Daniel L.; Economides, John R.

2015-01-01

To probe the mechanism of visual suppression, we have raised macaques with strabismus by disinserting the medial rectus muscle in each eye at 1 mo of age. Typically, this operation produces a comitant, alternating exotropia with normal acuity in each eye. Here we describe an unusual occurrence: the development of severe amblyopia in one eye of a monkey after induction of exotropia. Shortly after surgery, the animal demonstrated a strong fixation preference for the left eye, with apparent suppression of the right eye. Later, behavioral testing showed inability to track or to saccade to targets with the right eye. With the left eye occluded, the animal demonstrated no visually guided behavior. Optokinetic nystagmus was absent in the right eye. Metabolic activity in striate cortex was assessed by processing the tissue for cytochrome oxidase (CO). Amblyopia caused loss of CO in one eye's rows of patches, presumably those serving the blind eye. Layers 4A and 4B showed columns of reduced CO, in register with pale rows of patches in layer 2/3. Layers 4C, 5, and 6 also showed columns of CO activity, but remarkably, comparison with more superficial layers showed a reversal in contrast. In other words, pale CO staining in layers 2/3, 4A, and 4B was aligned with dark CO staining in layers 4C, 5, and 6. No experimental intervention or deprivation paradigm has been reported previously to produce opposite effects on metabolic activity in layers 2/3, 4A, and 4B vs. layers 4C, 5, and 6 within a given eye's columns. PMID:25810480

Contrasting effects of strabismic amblyopia on metabolic activity in superficial and deep layers of striate cortex.

PubMed

Adams, Daniel L; Economides, John R; Horton, Jonathan C

2015-05-01

To probe the mechanism of visual suppression, we have raised macaques with strabismus by disinserting the medial rectus muscle in each eye at 1 mo of age. Typically, this operation produces a comitant, alternating exotropia with normal acuity in each eye. Here we describe an unusual occurrence: the development of severe amblyopia in one eye of a monkey after induction of exotropia. Shortly after surgery, the animal demonstrated a strong fixation preference for the left eye, with apparent suppression of the right eye. Later, behavioral testing showed inability to track or to saccade to targets with the right eye. With the left eye occluded, the animal demonstrated no visually guided behavior. Optokinetic nystagmus was absent in the right eye. Metabolic activity in striate cortex was assessed by processing the tissue for cytochrome oxidase (CO). Amblyopia caused loss of CO in one eye's rows of patches, presumably those serving the blind eye. Layers 4A and 4B showed columns of reduced CO, in register with pale rows of patches in layer 2/3. Layers 4C, 5, and 6 also showed columns of CO activity, but remarkably, comparison with more superficial layers showed a reversal in contrast. In other words, pale CO staining in layers 2/3, 4A, and 4B was aligned with dark CO staining in layers 4C, 5, and 6. No experimental intervention or deprivation paradigm has been reported previously to produce opposite effects on metabolic activity in layers 2/3, 4A, and 4B vs. layers 4C, 5, and 6 within a given eye's columns. Copyright © 2015 the American Physiological Society.

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.

Noncontact diffuse correlation spectroscopy for noninvasive deep tissue blood flow measurement

NASA Astrophysics Data System (ADS)

Lin, Yu; He, Lian; Shang, Yu; Yu, Guoqiang

2012-01-01

A noncontact diffuse correlation spectroscopy (DCS) probe has been developed using two separated optical paths for the source and detector. This unique design avoids the interference between the source and detector and allows large source-detector separations for deep tissue blood flow measurements. The noncontact probe has been calibrated against a contact probe in a tissue-like phantom solution and human muscle tissues; flow changes concurrently measured by the two probes are highly correlated in both phantom (R2=0.89, p<10-5) and real-tissue (R2=0.77, p<10-5, n=9) tests. The noncontact DCS holds promise for measuring blood flow in vulnerable (e.g., pressure ulcer) and soft (e.g., breast) tissues without distorting tissue hemodynamic properties.

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.

Diffusive, Displacive Deformations and Local Phase Transformation Govern the Mechanics of Layered Crystals: The Case Study of Tobermorite.

PubMed

Tao, Lei; Shahsavari, Rouzbeh

2017-07-19

Understanding the deformation mechanisms underlying the mechanical behavior of materials is the key to fundamental and engineering advances in materials' performance. Herein, we focus on crystalline calcium-silicate-hydrates (C-S-H) as a model system with applications in cementitious materials, bone-tissue engineering, drug delivery and refractory materials, and use molecular dynamics simulation to investigate its loading geometry dependent mechanical properties. By comparing various conventional (e.g. shear, compression and tension) and nano-indentation loading geometries, our findings demonstrate that the former loading leads to size-independent mechanical properties while the latter results in size-dependent mechanical properties at the nanometer scales. We found three key mechanisms govern the deformation and thus mechanics of the layered C-S-H: diffusive-controlled and displacive-controlled deformation mechanisms, and strain gradient with local phase transformations. Together, these elaborately classified mechanisms provide deep fundamental understanding and new insights on the relationship between the macro-scale mechanical properties and underlying molecular deformations, providing new opportunities to control and tune the mechanics of layered crystals and other complex materials such as glassy C-S-H, natural composite structures, and manmade laminated structures.

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.

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.

Deep Space Gateway as a Platform to Study Synergistic Radiation and Microgravity-Induced Tissue Degeneration Using the Bioculture System Single Cassette Hardware Design

NASA Astrophysics Data System (ADS)

Almeida, E. A. C.

2018-02-01

A major unknown for human exploration of deep space is the question of how the degenerative effects of microgravity unloading of cells and tissues may synergize with radiation. Here we describe cell culture hardware to study those combined effects.

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).

Salzmann's nodular degeneration of the cornea: a review and case series.

PubMed

Das, Sujata; Link, Barbara; Seitz, Berthold

2005-10-01

Salzmann's nodular degeneration is a rare, noninflammatory, slowly progressive, degenerative condition. Bluish-white nodules raised above the surface of the cornea characterize it. It has usually developed in corneas with a history of phlyctenulosis, trachoma, vernal keratoconjunctivitis, measles, scarlet fever, and various other viral diseases. However, today the majority of cases have been seen without recognized previous keratitis. It is composed of dense irregularly arranged collagen tissue with hyalinization between epithelium and Bowman's layer or beyond. Manual removal, phototherapeutic keratectomy (PTK) with or without the use of topical mitomycin-C, lamellar or penetrating keratoplasty have been used in the treatment of this disease. Salzmann's nodular degeneration does not seem to consist of one clinical entity. In some cases, elevated and pannus-like tissue can be separated easily from the corneal surface leaving Bowman's layer almost untouched. In these eyes, subsequent PTK may be necessary to smooth the surface. Recurrences are rare in these eyes. In contrast, some eyes (often with major peripheral vascularization) are left with deep defects in Bowman's layer and superficial stroma after difficult mechanical removal of nodules. In these eyes, multiple masking/laser ablation procedures are mandatory to acquire a homogenous surface. In our experience, the required laser ablation depth is significantly greater and the best-corrected visual acuity to be expected is reduced in contrast to the eyes with easy removal of the nodules. In these eyes recurrences seem to occur more frequently after treatment. Of 35 eyes documented to have Salzmann's nodular degeneration during the last 15 years in our department, 22 needed PTK treatment. Visual acuity increased from 0.4 to 0.7 on average. As a routine, laser ablation should be combined with previous conventional removal of nodules and excessive pannus tissue. By doing so, lamellar and penetrating keratoplasty techniques are hardly ever required in those eyes.

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).

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.

Incidence of deep vein thrombosis in patients undergoing breast reconstruction with autologous tissue transfer.

PubMed

Konoeda, Hisato; Yamaki, Takashi; Hamahata, Atsumori; Ochi, Masakazu; Osada, Atsuyoshi; Hasegawa, Yuki; Kirita, Miho; Sakurai, Hiroyuki

2017-05-01

Background Breast reconstruction is associated with multiple risk factors for venous thromboembolism. However, the incidence of deep vein thrombosis in patients undergoing breast reconstruction is uncertain. Objective The aim of this study was to prospectively evaluate the incidence of deep vein thrombosis in patients undergoing breast reconstruction using autologous tissue transfer and to identify potential risk factors for deep vein thrombosis. Methods Thirty-five patients undergoing breast reconstruction were enrolled. We measured patients' preoperative characteristics including age, body mass index (kg/m 2 ), and risk factors for deep vein thrombosis. The preoperative diameter of each venous segment in the deep veins was measured using duplex ultrasound. All patients received intermittent pneumatic pump and elastic compression stockings for postoperative thromboprophylaxis. Results Among the 35 patients evaluated, 11 (31.4%) were found to have deep vein thrombosis postoperatively, and one patient was found to have pulmonary embolism postoperatively. All instances of deep vein thrombosis developed in the calf and were asymptomatic. Ten of 11 patients underwent free flap transfer, and the remaining one patient received a latissimus dorsi pedicled flap. Deep vein thrombosis incidence did not significantly differ between patients with a free flap or pedicled flap (P = 0.13). Documented risk factors for deep vein thrombosis demonstrated no significant differences between patients with and without deep vein thrombosis. The diameter of the common femoral vein was significantly larger in patients who developed postoperative deep vein thrombosis than in those who did not ( P < 0.05). Conclusions The morbidity of deep vein thrombosis in patients who underwent breast reconstruction using autologous tissue transfer was relatively high. Since only the diameter of the common femoral vein was predictive of developing postoperative deep vein thrombosis, postoperative pharmacological thromboprophylaxis should be considered for all patients undergoing breast reconstruction regardless of operative procedure.

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.

The peri-esophageal connective tissue layers and related compartments: visualization by histology and magnetic resonance imaging.

PubMed

Weijs, T J; Goense, L; van Rossum, P S N; Meijer, G J; van Lier, A L H M W; Wessels, F J; Braat, M N G; Lips, I M; Ruurda, J P; Cuesta, M A; van Hillegersberg, R; Bleys, R L A W

2017-02-01

An organized layer of connective tissue coursing from aorta to esophagus was recently discovered in the mediastinum. The relations with other peri-esophageal fascias have not been described and it is unclear whether this layer can be visualized by non-invasive imaging. This study aimed to provide a comprehensive description of the peri-esophageal fascias and determine whether the connective tissue layer between aorta and esophagus can be visualized by magnetic resonance imaging (MRI). First, T2-weighted MRI scanning of the thoracic region of a human cadaver was performed, followed by histological examination of transverse sections of the peri-esophageal tissue between the thyroid gland and the diaphragm. Secondly, pretreatment motion-triggered MRI scans were prospectively obtained from 34 patients with esophageal cancer and independently assessed by two radiologists for the presence and location of the connective tissue layer coursing from aorta to esophagus. A layer of connective tissue coursing from the anterior aspect of the descending aorta to the left lateral aspect of the esophagus, with a thin extension coursing to the right pleural reflection, was visualized ex vivo in the cadaver on MR images, macroscopic tissue sections, and after histologic staining, as well as on in vivo MR images. The layer connecting esophagus and aorta was named 'aorto-esophageal ligament' and the layer connecting aorta to the right pleural reflection 'aorto-pleural ligament'. These connective tissue layers divides the posterior mediastinum in an anterior compartment containing the esophagus, (carinal) lymph nodes and vagus nerve, and a posterior compartment, containing the azygos vein, thoracic duct and occasionally lymph nodes. The anterior compartment was named 'peri-esophageal compartment' and the posterior compartment 'para-aortic compartment'. The connective tissue layers superior to the aortic arch and at the diaphragm corresponded with the currently available anatomic descriptions. This study confirms the existence of the previously described connective tissue layer coursing from aorta to esophagus, challenging the long-standing paradigm that no such structure exists. A comprehensive, detailed description of the peri-esophageal fascias is provided and, furthermore, it is shown that the connective tissue layer coursing from aorta to esophagus can be visualized in vivo by MRI. © 2016 Anatomical Society.

Sol gel-derived hydroxyapatite films over porous calcium polyphosphate substrates for improved tissue engineering of osteochondral-like constructs.

PubMed

Lee, Whitaik David; Gawri, Rahul; Pilliar, Robert M; Stanford, William L; Kandel, Rita A

2017-10-15

Integration of in vitro-formed cartilage on a suitable substrate to form tissue-engineered implants for osteochondral defect repair is a considerable challenge. In healthy cartilage, a zone of calcified cartilage (ZCC) acts as an intermediary for mechanical force transfer from soft to hard tissue, as well as an effective interlocking structure to better resist interfacial shear forces. We have developed biphasic constructs that consist of scaffold-free cartilage tissue grown in vitro on, and interdigitated with, porous calcium polyphosphate (CPP) substrates. However, as CPP degrades, it releases inorganic polyphosphates (polyP) that can inhibit local mineralization, thereby preventing the formation of a ZCC at the interface. Thus, we hypothesize that coating CPP substrate with a layer of hydroxyapatite (HA) might prevent or limit this polyP release. To investigate this we tested both inorganic or organic sol-gel processing methods, asa barrier coating on CPP substrate to inhibit polyP release. Both types of coating supported the formation of ZCC in direct contact with the substrate, however the ZCC appeared more continuous in the tissue formed on the organic HA sol gel coated CPP. Tissues formed on coated substrates accumulated comparable quantities of extracellular matrix and mineral, but tissues formed on organic sol-gel (OSG)-coated substrates accumulated less polyP than tissues formed on inorganic sol-gel (ISG)-coated substrates. Constructs formed with OSG-coated CPP substrates had greater interfacial shear strength than those formed with ISG-coated and non-coated substrates. These results suggest that the OSG coating method can modify the location and distribution of ZCC and can be used to improve the mechanical integrity of tissue-engineered constructs formed on porous CPP substrates. Articular cartilage interfaces with bone through a zone of calcified cartilage. This study describes a method to generate an "osteochondral-like" implant that mimics this organization using isolated deep zone cartilage cells and a sol-gel hydroxyapatite coated bone substitute material composed of calcium polyphosphate (CPP). Developing a layer of calcified cartilage at the interface should contribute to enhancing the success of this "osteochondral-like" construct following implantation to repair cartilage defects. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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

Risk of Infection After Allograft Anterior Cruciate Ligament Reconstruction: Are Nonprocessed Allografts More Likely to Get Infected? A Cohort Study of Over 10,000 Allografts.

PubMed

Yu, Anthony; Prentice, Heather A; Burfeind, William E; Funahashi, Tadashi; Maletis, Gregory B

2018-03-01

Allograft tissue is frequently used in anterior cruciate ligament reconstruction (ACLR). It is often irradiated and/or chemically processed to decrease the risk of disease transmission, but some tissue is aseptically harvested without further processing. Irradiated and chemically processed allograft tissue appears to have a higher risk of revision, but whether this processing decreases the risk of infection is not clear. To determine the incidence of deep surgical site infection after ACLR with allograft in a large community-based sample and to evaluate the association of allograft processing and the risk of deep infection. Cohort study; Level of evidence, 3. The authors conducted a cohort study using the Kaiser Permanente Anterior Cruciate Ligament Reconstruction Registry. Primary isolated unilateral ACLR with allograft were identified from February 1, 2005 to September 30, 2015. Ninety-day postoperative deep infections were identified via an electronic screening algorithm and then validated through chart review. Logistic regression was used to evaluate the likelihood of 90-day postoperative deep infection per allograft processing method: processed (graft treated chemically and/or irradiated) or nonprocessed (graft not irradiated or chemically processed). Of 10,190 allograft cases, 8425 (82.7%) received a processed allograft, and 1765 (17.3%) received a nonprocessed allograft. There were 15 (0.15%) deep infections during the study period: 4 (26.7%) coagulase-negative Staphylococcus, 4 (26.7%) methicillin-sensitive Staphylococcus aureus, 1 (6.7%) Peptostreptococcus micros, and 6 (40.0%) with no growth. There was no difference in the likelihood for 90-day deep infection for processed versus nonprocessed allografts (odds ratio = 1.36, 95% CI = 0.31-6.04). The overall incidence of deep infection after ACLR with allograft tissue was very low (0.15%), suggesting that the methods currently employed by tissue banks to minimize the risk of infection are effective. In this cohort, no difference in the likelihood of infection between processed and nonprocessed allografts could be identified.

Isolation of tissue layers in hermatypic corals by N-acetylcysteine: morphological and proteomic examinations

NASA Astrophysics Data System (ADS)

Peng, S.-E.; Luo, Y.-J.; Huang, H.-J.; Lee, I.-T.; Hou, L.-S.; Chen, W.-N. U.; Fang, L.-S.; Chen, C.-S.

2008-03-01

Corals are diploblastic in body pattern and include two tissue layers, the epidermis and gastrodermis, interconnected by an acellular matrix mesoglea. During development, cells in these tissue layers differentiate morphologically and functionally. In most hermatypic corals, the gastrodermis further develops an ability to associate with microalgae dinoflagellates. This endosymbiosis occurs inside specific host gastrodermal cells, and its mechanism still remains unclear notwithstanding decades of research. The delay in progress is partly due to the difficulty in separating the gastrodermis and its symbionts from the epidermis for detailed cellular and biochemical investigations. The present study reports a simple method to separate these two tissue layers in hermatypic corals using the reducing agent, N-acetylcysteine (NAC). Efficient tissue and proteomic isolations are demonstrated by microscopy and two-dimensional SDS polyacrylamide gel electrophoresis (2D SDS-PAGE). The NAC treatment was able to separate tissue layers without inducing protein degradation. Furthermore, the sensitivity of protein detection greatly increases in the isolated tissue layers. The application of the present technique provides future research on endosymbiosis and coral development with a tool for higher accuracy and sensitivity.

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.

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.

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

Joint deep shape and appearance learning: application to optic pathway glioma segmentation

NASA Astrophysics Data System (ADS)

Mansoor, Awais; Li, Ien; Packer, Roger J.; Avery, Robert A.; Linguraru, Marius George

2017-03-01

Automated tissue characterization is one of the major applications of computer-aided diagnosis systems. Deep learning techniques have recently demonstrated impressive performance for the image patch-based tissue characterization. However, existing patch-based tissue classification techniques struggle to exploit the useful shape information. Local and global shape knowledge such as the regional boundary changes, diameter, and volumetrics can be useful in classifying the tissues especially in scenarios where the appearance signature does not provide significant classification information. In this work, we present a deep neural network-based method for the automated segmentation of the tumors referred to as optic pathway gliomas (OPG) located within the anterior visual pathway (AVP; optic nerve, chiasm or tracts) using joint shape and appearance learning. Voxel intensity values of commonly used MRI sequences are generally not indicative of OPG. To be considered an OPG, current clinical practice dictates that some portion of AVP must demonstrate shape enlargement. The method proposed in this work integrates multiple sequence magnetic resonance image (T1, T2, and FLAIR) along with local boundary changes to train a deep neural network. For training and evaluation purposes, we used a dataset of multiple sequence MRI obtained from 20 subjects (10 controls, 10 NF1+OPG). To our best knowledge, this is the first deep representation learning-based approach designed to merge shape and multi-channel appearance data for the glioma detection. In our experiments, mean misclassification errors of 2:39% and 0:48% were observed respectively for glioma and control patches extracted from the AVP. Moreover, an overall dice similarity coefficient of 0:87+/-0:13 (0:93+/-0:06 for healthy tissue, 0:78+/-0:18 for glioma tissue) demonstrates the potential of the proposed method in the accurate localization and early detection of OPG.

Mineralization of Alvinella polychaete tubes at hydrothermal vents.

PubMed

Georgieva, M N; Little, C T S; Ball, A D; Glover, A G

2015-03-01

Alvinellid polychaete worms form multilayered organic tubes in the hottest and most rapidly growing areas of deep-sea hydrothermal vent chimneys. Over short periods of time, these tubes can become entirely mineralized within this environment. Documenting the nature of this process in terms of the stages of mineralization, as well as the mineral textures and end products that result, is essential for our understanding of the fossilization of polychaetes at hydrothermal vents. Here, we report in detail the full mineralization of Alvinella spp. tubes collected from the East Pacific Rise, determined through the use of a wide range of imaging and analytical techniques. We propose a new model for tube mineralization, whereby mineralization begins as templating of tube layer and sublayer surfaces and results in fully mineralized tubes comprised of multiple concentric, colloform, pyrite bands. Silica appeared to preserve organic tube layers in some samples. Fine-scale features such as protein fibres, extracellular polymeric substances and two types of filamentous microbial colonies were also found to be well preserved within a subset of the tubes. The fully mineralized Alvinella spp. tubes do not closely resemble known ancient hydrothermal vent tube fossils, corroborating molecular evidence suggesting that the alvinellids are a relatively recent polychaete lineage. We also compare pyrite and silica preservation of organic tissues within hydrothermal vents to soft tissue preservation in sediments and hot springs. © 2014 The Authors. Geobiology Published by John Wiley & Sons Ltd.

Confocal multispot microscope for fast and deep imaging in semicleared tissues

NASA Astrophysics Data System (ADS)

Adam, Marie-Pierre; Müllenbroich, Marie Caroline; Di Giovanna, Antonino Paolo; Alfieri, Domenico; Silvestri, Ludovico; Sacconi, Leonardo; Pavone, Francesco Saverio

2018-02-01

Although perfectly transparent specimens are imaged faster with light-sheet microscopy, less transparent samples are often imaged with two-photon microscopy leveraging its robustness to scattering; however, at the price of increased acquisition times. Clearing methods that are capable of rendering strongly scattering samples such as brain tissue perfectly transparent specimens are often complex, costly, and time intensive, even though for many applications a slightly lower level of tissue transparency is sufficient and easily achieved with simpler and faster methods. Here, we present a microscope type that has been geared toward the imaging of semicleared tissue by combining multispot two-photon excitation with rolling shutter wide-field detection to image deep and fast inside semicleared mouse brain. We present a theoretical and experimental evaluation of the point spread function and contrast as a function of shutter size. Finally, we demonstrate microscope performance in fixed brain slices by imaging dendritic spines up to 400-μm deep.

Deep-tissue focal fluorescence imaging with digitally time-reversed ultrasound-encoded light

PubMed Central

Wang, Ying Min; Judkewitz, Benjamin; DiMarzio, Charles A.; Yang, Changhuei

2012-01-01

Fluorescence imaging is one of the most important research tools in biomedical sciences. However, scattering of light severely impedes imaging of thick biological samples beyond the ballistic regime. Here we directly show focusing and high-resolution fluorescence imaging deep inside biological tissues by digitally time-reversing ultrasound-tagged light with high optical gain (~5×105). We confirm the presence of a time-reversed optical focus along with a diffuse background—a corollary of partial phase conjugation—and develop an approach for dynamic background cancellation. To illustrate the potential of our method, we image complex fluorescent objects and tumour microtissues at an unprecedented depth of 2.5 mm in biological tissues at a lateral resolution of 36 μm×52 μm and an axial resolution of 657 μm. Our results set the stage for a range of deep-tissue imaging applications in biomedical research and medical diagnostics. PMID:22735456

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.

Bedside ultrasound of the soft tissue of the face: a case of early Ludwig's angina.

PubMed

Gaspari, Romolo J

2006-10-01

A case is reported of a 38-year-old man presenting with early Ludwig's angina. It is difficult to differentiate superficial from deep infections of the face and neck by physical examination alone. The diagnosis of this condition with bedside soft tissue ultrasound of the face is described. Ludwig's angina is an uncommon infection of the deep tissues of the face and neck that usually evolves from more superficial infections such as dental abscesses.

Finite difference time domain (FDTD) modeling of implanted deep brain stimulation electrodes and brain tissue.

PubMed

Gabran, S R I; Saad, J H; Salama, M M A; Mansour, R R

2009-01-01

This paper demonstrates the electromagnetic modeling and simulation of an implanted Medtronic deep brain stimulation (DBS) electrode using finite difference time domain (FDTD). The model is developed using Empire XCcel and represents the electrode surrounded with brain tissue assuming homogenous and isotropic medium. The model is created to study the parameters influencing the electric field distribution within the tissue in order to provide reference and benchmarking data for DBS and intra-cortical electrode development.

Layer-by-layer 3-dimensional nanofiber tissue scaffold with controlled gap by electrospinning

NASA Astrophysics Data System (ADS)

Lin, Sai-Jun; Xue, Ya-Ping; Chang, Guoqing; Han, Qiao-Ling; Chen, Li-Fang; Jia, Yan-Bo; Zheng, Yu-Guo

2018-02-01

The development of three-dimensional (3D) nanofiber structures by electrospinning has drawn considerable attention in the field of tissue scaffolds. However, the generation of two dimensional mats using the conventional method limits electrospinning, the electrical charging of polymer liquids, as a means of nanofiber fabrication. In this study, we established a facile method of fabrication of layer-by-layer 3D polycaprolactone (PCL) nanofiber structures by utilizing a booklet collector with controlled morphology. Meanwhile, we explore the application of the manufactured 3D architectures in the field of tissue scaffolds. The approximately 20 μm layer-to-layer distance enhanced the ability of cells to migrate freely into tissues and induce cells in an ordered arrangement.

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 dopamine extravasation injury: a case report.

PubMed

Phillips, Reid A; Andrades, Patricio; Grant, John H; Ray, Peter D

2009-07-01

We report the case of a 3-month-old girl with Down's syndrome, who sustained a deep and massive extravasation of dopamine, resulting in segmented, full-thickness skin necrosis and transient brachial plexus palsy of her left upper extremity. The patient was managed conservatively, including wound care, de-bridement of necrotic tissue, secondary wound healing and intensive physical therapy. The patient showed a satisfactory outcome with complete secondary closure of her wounds and full brachial plexus recovery after 1 year of follow-up. The mechanism of action of dopamine in the deep soft tissue, the difficulties of an adequate diagnosis of a deep dopamine extravasation and alternative treatments are presented in this article.

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.

[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.

Deep Learning MR Imaging-based Attenuation Correction for PET/MR Imaging.

PubMed

Liu, Fang; Jang, Hyungseok; Kijowski, Richard; Bradshaw, Tyler; McMillan, Alan B

2018-02-01

Purpose To develop and evaluate the feasibility of deep learning approaches for magnetic resonance (MR) imaging-based attenuation correction (AC) (termed deep MRAC) in brain positron emission tomography (PET)/MR imaging. Materials and Methods A PET/MR imaging AC pipeline was built by using a deep learning approach to generate pseudo computed tomographic (CT) scans from MR images. A deep convolutional auto-encoder network was trained to identify air, bone, and soft tissue in volumetric head MR images coregistered to CT data for training. A set of 30 retrospective three-dimensional T1-weighted head images was used to train the model, which was then evaluated in 10 patients by comparing the generated pseudo CT scan to an acquired CT scan. A prospective study was carried out for utilizing simultaneous PET/MR imaging for five subjects by using the proposed approach. Analysis of covariance and paired-sample t tests were used for statistical analysis to compare PET reconstruction error with deep MRAC and two existing MR imaging-based AC approaches with CT-based AC. Results Deep MRAC provides an accurate pseudo CT scan with a mean Dice coefficient of 0.971 ± 0.005 for air, 0.936 ± 0.011 for soft tissue, and 0.803 ± 0.021 for bone. Furthermore, deep MRAC provides good PET results, with average errors of less than 1% in most brain regions. Significantly lower PET reconstruction errors were realized with deep MRAC (-0.7% ± 1.1) compared with Dixon-based soft-tissue and air segmentation (-5.8% ± 3.1) and anatomic CT-based template registration (-4.8% ± 2.2). Conclusion The authors developed an automated approach that allows generation of discrete-valued pseudo CT scans (soft tissue, bone, and air) from a single high-spatial-resolution diagnostic-quality three-dimensional MR image and evaluated it in brain PET/MR imaging. This deep learning approach for MR imaging-based AC provided reduced PET reconstruction error relative to a CT-based standard within the brain compared with current MR imaging-based AC approaches. © RSNA, 2017 Online supplemental material is available for this article.

Light dosimetry for focused and defocused beam irradiation in multi-layered tissue models

NASA Astrophysics Data System (ADS)

Petrova, Kremena S.; Stoykova, Elena V.

2006-09-01

Treatment of acupuncture points, trigger points, joint inflammations in low level laser therapy as well as various applications of lasers for treatment of soft tissues in dental medicine, require irradiation by a narrow converging laser beam. The aim of this study is to compare light delivery produced by focused or defocused narrow beam irradiation in a multi-layered skin tissue model at increasing depth of the target. The task is solved by 3-D Monte-Carlo simulation for matched and mismatched refractive indices at the tissue/ambient medium interface. The modeled light beams have a circular cross-section at the tissue entrance with uniform or Gaussian intensity distribution. Three are the tissue models used in simulation : i) a bloodless skin layer; ii) a bloodless skin layer with embedded scattering object; iii) a skin layer with small blood vessels of varying size, which are modeled as infinite cylinders parallel to the tissue surface located at different depths. Optical properties (absorption coefficient, scattering coefficient, anisotropy factor, g, and index of refraction) of different tissue constituents are chosen from the literature.

Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images.

PubMed

Khosravi, Pegah; Kazemi, Ehsan; Imielinski, Marcin; Elemento, Olivier; Hajirasouliha, Iman

2018-01-01

Pathological evaluation of tumor tissue is pivotal for diagnosis in cancer patients and automated image analysis approaches have great potential to increase precision of diagnosis and help reduce human error. In this study, we utilize several computational methods based on convolutional neural networks (CNN) and build a stand-alone pipeline to effectively classify different histopathology images across different types of cancer. In particular, we demonstrate the utility of our pipeline to discriminate between two subtypes of lung cancer, four biomarkers of bladder cancer, and five biomarkers of breast cancer. In addition, we apply our pipeline to discriminate among four immunohistochemistry (IHC) staining scores of bladder and breast cancers. Our classification pipeline includes a basic CNN architecture, Google's Inceptions with three training strategies, and an ensemble of two state-of-the-art algorithms, Inception and ResNet. Training strategies include training the last layer of Google's Inceptions, training the network from scratch, and fine-tunning the parameters for our data using two pre-trained version of Google's Inception architectures, Inception-V1 and Inception-V3. We demonstrate the power of deep learning approaches for identifying cancer subtypes, and the robustness of Google's Inceptions even in presence of extensive tumor heterogeneity. On average, our pipeline achieved accuracies of 100%, 92%, 95%, and 69% for discrimination of various cancer tissues, subtypes, biomarkers, and scores, respectively. Our pipeline and related documentation is freely available at https://github.com/ih-_lab/CNN_Smoothie. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

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.

Effects of protein-coated nanofibers on conformation of gingival fibroblast spheroids: potential utility for connective tissues regeneration.

PubMed

Kaufman, Gili; Whitescarver, Ryan; Nunes, Laiz; Palmer, Xavier-Lewis; Skrtic, Drago; Tutak, Wojtek

2017-10-09

Deep wounds in the gingiva caused by trauma or surgery require a rapid and robust healing of connective tissues. We propose utilizing gas-brushed nanofibers coated with collagen and fibrin for that purpose. Our hypotheses are that protein-coated nanofibers will: (i) attract and mobilize cells in various spatial orientations, and (ii) regulate the expression levels of specific extracellular matrix (ECM)-associated proteins, determining the initial conformational nature of dense and soft connective tissues. Gingival fibroblast monolayers and 3D spheroids were cultured on ECM substrate and covered with gas-blown poly-(DL-lactide-co-glycolide) (PLGA) nanofibers (uncoated/coated with collagen and fibrin). Cell attraction and rearrangement was followed by F-actin staining and confocal microscopy. Thicknesses of the cell layers, developed within the nanofibers, were quantified by imageJ software. The expression of collagen1α1 chain (Col1α1), fibronectin, and metalloproteinase 2 (MMP2) encoding genes was determined by quantitative reverse transcription analysis. Collagen- and fibrin- coated nanofibers induced cell migration toward fibers and supported cellular growth within the scaffolds. Both proteins affected the spatial rearrangement of fibroblasts by favoring packed cell clusters or intermittent cell spreading. These cell arrangements resembled the structural characteristic of dense and soft connective tissues, respectively. Within 3 days of incubation, fibroblast spheroids interacted with the fibers and grew robustly by increasing their thickness compared to monolayers. While the ECM key components, such as fibronectin and MMP2 encoding genes, were expressed in both protein groups, Col1α1 was predominantly expressed in bundled fibroblasts grown on collagen fibers. This enhanced expression of collagen1 is typical for dense connective tissue. Based on results of this study, our gas-blown, collagen- and fibrin-coated PLGA nanofibers are viable candidates for engineering soft and dense connective tissues with the required structural characteristics and functions needed for wound healing applications. Rapid regeneration of these layers should enhance healing of open wounds in a harsh oral environment. © 2017 IOP Publishing Ltd.

Assessment of deep tissue hyperalgesia in the groin - a method comparison of electrical vs. pressure stimulation.

PubMed

Aasvang, E K; Werner, M U; Kehlet, H

2014-09-01

Deep pain complaints are more frequent than cutaneous in post-surgical patients, and a prevalent finding in quantitative sensory testing studies. However, the preferred assessment method - pressure algometry - is indirect and tissue unspecific, hindering advances in treatment and preventive strategies. Thus, there is a need for development of methods with direct stimulation of suspected hyperalgesic tissues to identify the peripheral origin of nociceptive input. We compared the reliability of an ultrasound-guided needle stimulation protocol of electrical detection and pain thresholds to pressure algometry, by performing identical test-retest sequences 10 days apart, in deep tissues in the groin region. Electrical stimulation was performed by five up-and-down staircase series of single impulses of 0.04 ms duration, starting from 0 mA in increments of 0.2 mA until a threshold was reached and descending until sensation was lost. Method reliability was assessed by Bland-Altman plots, descriptive statistics, coefficients of variance and intraclass correlation coefficients. The electrical stimulation method was comparable to pressure algometry regarding 10 days test-retest repeatability, but with superior same-day reliability for electrical stimulation (P < 0.05). Between-subject variance rather than within-subject variance was the main source for test variation. There were no systematic differences in electrical thresholds across tissues and locations (P > 0.05). The presented tissue-specific direct deep tissue electrical stimulation technique has equal or superior reliability compared with the indirect tissue-unspecific stimulation by pressure algometry. This method may facilitate advances in mechanism based preventive and treatment strategies in acute and chronic post-surgical pain states. © 2014 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Dermal Fibroblasts from Different Layers of Pig Skin Exhibit Different Profibrotic and Morphological Characteristics.

PubMed

Zuo, Yanhai; Yu, Xiaoping; Lu, Shuliang

2016-11-01

In vitro studies of human dermal fibroblast (DF) heterogeneity have long been reported, yet in vivo studies and related research on animals are rare. The objectives of the study were to determine whether the DFs of pigs exhibit heterogeneity and to identify an animal model for the in vivo study of DF heterogeneity. The skin of three female red Duroc pigs (FRDPs) was separated into six layers, and the second and fifth layers (i.e., the superficial and deep dermis) were used in the establishment of wound models and cell cultures. To create the wound models, 54 tongue-shaped flaps were created on one side of the dorsum, and the underlying dermis was then fully replaced with the superficial or deep dermis (the superficial and deep groups, respectively). Skin samples were harvested at postoperative weeks 1, 2, and 3 for measurements of the normal and wounded skin thicknesses. Cells cultured from the superficial and deep dermis (i.e., superficial and deep DFs) were subjected to quantitative estimation of collagen and electron microscopy. The wounded skin thickness in the deep group was significantly greater than that in the superficial group. In contrast with the long deep DFs, the superficial DFs were short and exhibited microvilli-like cell surface projections. Compared with the superficial DFs, the deep DFs exhibited a greater density of rough endoplasmic reticulum and produced significantly more collagen. Similar to humans, FRDPs exhibit DF heterogeneity and should thus be a good animal model for in vivo studies of DF heterogeneity. Anat Rec, 299:1585-1599, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Deformation and reperfusion damages and their accumulation in subcutaneous tissues during loading and unloading: a theoretical modeling of deep tissue injuries.

PubMed

Mak, Arthur F T; Yu, Yanyan; Kwan, Linda P C; Sun, Lei; Tam, Eric W C

2011-11-21

Deep tissue injuries (DTI) involve damages in the subcutaneous tissues under intact skin incurred by prolonged excessive epidermal loadings. This paper presents a new theoretical model for the development of DTI, broadly based on the experimental evidence in the literatures. The model covers the loading damages implicitly inclusive of both the direct mechanical and ischemic injuries, and the additional reperfusion damages and the competing healing processes during the unloading phase. Given the damage accumulated at the end of the loading period, the relative strength of the reperfusion and the healing capacity of the involved tissues system, the model provides a description of the subsequent damage evolution during unloading. The model is used to study parametrically the scenario when reperfusion damage dominates over healing upon unloading and the opposite scenario when the loading and subsequent reperfusion damages remain small relative to the healing capacity of the tissues system. The theoretical model provides an integrated understanding of how tissue damage may further build-up paradoxically even with unloading, how long it would take for the loading and reperfusion damages in the tissues to become fully recovered, and how such loading and reperfusion damages, if not given sufficient time for recovery, may accumulate over multiple loading and unloading cycles, leading to clinical deep tissues ulceration. Copyright © 2011 Elsevier Ltd. All rights reserved.

Red and NIR light dosimetry in the human deep brain

NASA Astrophysics Data System (ADS)

Pitzschke, A.; Lovisa, B.; Seydoux, O.; Zellweger, M.; Pfleiderer, M.; Tardy, Y.; Wagnières, G.

2015-04-01

Photobiomodulation (PBM) appears promising to treat the hallmarks of Parkinson’s Disease (PD) in cellular or animal models. We measured light propagation in different areas of PD-relevant deep brain tissue during transcranial, transsphenoidal illumination (at 671 and 808 nm) of a cadaver head and modeled optical parameters of human brain tissue using Monte-Carlo simulations. Gray matter, white matter, cerebrospinal fluid, ventricles, thalamus, pons, cerebellum and skull bone were processed into a mesh of the skull (158 × 201 × 211 voxels; voxel side length: 1 mm). Optical parameters were optimized from simulated and measured fluence rate distributions. The estimated μeff for the different tissues was in all cases larger at 671 than at 808 nm, making latter a better choice for light delivery in the deep brain. Absolute values were comparable to those found in the literature or slightly smaller. The effective attenuation in the ventricles was considerably larger than literature values. Optimization yields a new set of optical parameters better reproducing the experimental data. A combination of PBM via the sphenoid sinus and oral cavity could be beneficial. A 20-fold higher efficiency of light delivery to the deep brain was achieved with ventricular instead of transcranial illumination. Our study demonstrates that it is possible to illuminate deep brain tissues transcranially, transsphenoidally and via different application routes. This opens therapeutic options for sufferers of PD or other cerebral diseases necessitating light therapy.

Musculoskeletal MRI findings of juvenile localized scleroderma.

PubMed

Eutsler, Eric P; Horton, Daniel B; Epelman, Monica; Finkel, Terri; Averill, Lauren W

2017-04-01

Juvenile localized scleroderma comprises a group of autoimmune conditions often characterized clinically by an area of skin hardening. In addition to superficial changes in the skin and subcutaneous tissues, juvenile localized scleroderma may involve the deep soft tissues, bones and joints, possibly resulting in functional impairment and pain in addition to cosmetic changes. There is literature documenting the spectrum of findings for deep involvement of localized scleroderma (fascia, muscles, tendons, bones and joints) in adults, but there is limited literature for the condition in children. We aimed to document the spectrum of musculoskeletal magnetic resonance imaging (MRI) findings of both superficial and deep juvenile localized scleroderma involvement in children and to evaluate the utility of various MRI sequences for detecting those findings. Two radiologists retrospectively evaluated 20 MRI studies of the extremities in 14 children with juvenile localized scleroderma. Each imaging sequence was also given a subjective score of 0 (not useful), 1 (somewhat useful) or 2 (most useful for detecting the findings). Deep tissue involvement was detected in 65% of the imaged extremities. Fascial thickening and enhancement were seen in 50% of imaged extremities. Axial T1, axial T1 fat-suppressed (FS) contrast-enhanced and axial fluid-sensitive sequences were rated most useful. Fascial thickening and enhancement were the most commonly encountered deep tissue findings in extremity MRIs of children with juvenile localized scleroderma. Because abnormalities of the skin, subcutaneous tissues and fascia tend to run longitudinally in an affected limb, axial T1, axial fluid-sensitive and axial T1-FS contrast-enhanced sequences should be included in the imaging protocol.

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

Impact of operative time on early joint infection and deep vein thrombosis in primary total hip arthroplasty.

PubMed

Wills, B W; Sheppard, E D; Smith, W R; Staggers, J R; Li, P; Shah, A; Lee, S R; Naranje, S M

2018-03-22

Infections and deep vein thrombosis (DVT) after total hip arthroplasty (THA) are challenging problems for both the patient and surgeon. Previous studies have identified numerous risk factors for infections and DVT after THA but have often been limited by sample size. We aimed to evaluate the effect of operative time on early postoperative infection as well as DVT rates following THA. We hypothesized that an increase in operative time would result in increased odds of acquiring an infection as well as a DVT. We conducted a retrospective analysis of prospectively collected data using the American College of Surgeons National Surgical Quality Improvement Program (NSQIP) database from 2006 to 2015 for all patients undergoing primary THA. Associations between operative time and infection or DVT were evaluated with multivariable logistic regressions controlling for demographics and several known risks factors for infection. Three different types of infections were evaluated: (1) superficial surgical site infection (SSI), an infection involving the skin or subcutaneous tissue, (2) deep SSI, an infection involving the muscle or fascial layers beneath the subcutaneous tissue, and (3) organ/space infection, an infection involving any part of the anatomy manipulated during surgery other than the incisional components. In total, 103,044 patients who underwent THA were included in our study. Our results suggested a significant association between superficial SSIs and operative time. Specifically, the adjusted odds of suffering a superficial SSI increased by 6% (CI=1.04-1.08, p<0.0001) for every 10-minute increase of operative time. When using dichotomized operative time (<90minutes or >90minutes), the adjusted odds of suffering a superficial SSI was 56% higher for patients with prolonged operative time (CI=1.05-2.32, p=0.0277). The adjusted odds of suffering a deep SSI increased by 7% for every 10-minute increase in operative time (CI=1.01-1.14, p=0.0335). No significant associations were detected between organ/space infection, wound dehiscence, or DVT and operative time either as continuous or as dichotomized. Prolonged operative times (>90min) are associated with increased rates of superficial SSIs, but not deep SSIs, organ/space infections, wound dehiscence, or DVT. III. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Depth-resolved fluorescence of biological tissue

NASA Astrophysics Data System (ADS)

Wu, Yicong; Xi, Peng; Cheung, Tak-Hong; Yim, So Fan; Yu, Mei-Yung; Qu, Jianan Y.

2005-06-01

The depth-resolved autofluorescence ofrabbit oral tissue, normal and dysplastic human ectocervical tissue within l20μm depth were investigated utilizing a confocal fluorescence spectroscopy with the excitations at 355nm and 457nm. From the topmost keratinizing layer of oral and ectocervical tissue, strong keratin fluorescence with the spectral characteristics similar to collagen was observed. The fluorescence signal from epithelial tissue between the keratinizing layer and stroma can be well resolved. Furthermore, NADH and FADfluorescence measured from the underlying non-keratinizing epithelial layer were strongly correlated to the tissue pathology. This study demonstrates that the depth-resolved fluorescence spectroscopy can reveal fine structural information on epithelial tissue and potentially provide more accurate diagnostic information for determining tissue pathology.

Measurement of absorption spectrum of deuterium oxide (D{sub 2}O) and its application to signal enhancement in multiphoton microscopy at the 1700-nm window

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

Wang, Yuxin; Wen, Wenhui; Wang, Kai

2016-01-11

1700-nm window has been demonstrated to be a promising excitation window for deep-tissue multiphoton microscopy (MPM). Long working-distance water immersion objective lenses are typically used for deep-tissue imaging. However, absorption due to immersion water at 1700 nm is still high and leads to dramatic decrease in signals. In this paper, we demonstrate measurement of absorption spectrum of deuterium oxide (D{sub 2}O) from 1200 nm to 2600 nm, covering the three low water-absorption windows potentially applicable for deep-tissue imaging (1300 nm, 1700 nm, and 2200 nm). We apply this measured result to signal enhancement in MPM at the 1700-nm window. Compared with water immersion, D{sub 2}O immersionmore » enhances signal levels in second-harmonic generation imaging, 3-photon fluorescence imaging, and third-harmonic generation imaging by 8.1, 24.8, and 24.7 times with 1662-nm excitation, in good agreement with theoretical calculation based on our absorption measurement. This suggests D{sub 2}O a promising immersion medium for deep-tissue imaging.« less

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.

Cornea Transplant

MedlinePlus

... transplants may be used that remove only certain layers of cornea tissue, or only tissue affected by ... procedure removes diseased tissue from the back corneal layers, including the endothelium, along with the Descemet membrane, ...

Multiplexed 3D FRET imaging in deep tissue of live embryos

PubMed Central

Zhao, Ming; Wan, Xiaoyang; Li, Yu; Zhou, Weibin; Peng, Leilei

2015-01-01

Current deep tissue microscopy techniques are mostly restricted to intensity mapping of fluorophores, which significantly limit their applications in investigating biochemical processes in vivo. We present a deep tissue multiplexed functional imaging method that probes multiple Förster resonant energy transfer (FRET) sensors in live embryos with high spatial resolution. The method simultaneously images fluorescence lifetimes in 3D with multiple excitation lasers. Through quantitative analysis of triple-channel intensity and lifetime images, we demonstrated that Ca2+ and cAMP levels of live embryos expressing dual FRET sensors can be monitored simultaneously at microscopic resolution. The method is compatible with a broad range of FRET sensors currently available for probing various cellular biochemical functions. It opens the door to imaging complex cellular circuitries in whole live organisms. PMID:26387920

Role of Beam Spot Size in Heating Targets at Depth.

PubMed

Ross, E Victor; Childs, James

2015-12-01

Wavelength, fluence and pulse width are primary device parameters for the treatment of skin and hair conditions. Wavelength selection is based on tissue scatter and target chromophores. Pulse width is chosen to optimize target heating. Energy absorbed by a target is determined by fluence and spot size of the light source as well as the depth of the target. We conducted an in vitro skin study and simulations to compare heating of a target at a particular depth versus spot size. Porcine skin and fat tissue were prepared and separated to form a 2mm skin layer above a 1 cm thick fat layer. A 50 μm thermocouple was placed between the layers and centered beneath a 23 x 38 mm treatment window of an 805 nm diode laser device (Vectus, Cynosure, Westford, MA). Apertures provided various incident beam spot sizes and the temperature rise of the thermocouple was measured for a fixed fluence. The 2mm deep target's temperature rise versus treatment area showed two regimes with different positive slopes. The first regime up to approximately 1 cm(2) area has a greater temperature rise versus area than that for the regime greater than 1 cm(2). The slope in the second regime is nonetheless appreciable and provides a fluence reduction factor for skin safety. The same temperature rise in a target at 2 mm depth (typical hair bulb depth in some areas) is realized by increasing the area from 1 to 4 cm(2) while reducing the fluence by half. The role of spot size and in situ beam divergence is an important consideration to determine optimum fluence settings that increase skin safety when treating deeper targets.

Photoacoustic physio-chemical analysis and its implementation in deep tissue with a catheter setup

NASA Astrophysics Data System (ADS)

Xu, Guan; Meng, Zhou-xian; Lin, Jian-die D.; Cheng, Qian; Wang, Xueding

2015-03-01

Photoacoustic (PA) measurements encode the information associated with both physical microstructures and chemical contents in biological tissues. A two-dimensional physio-chemical spectrogram (PCS) can be formulated by combining the power spectra of PA signals acquired at a series of optical wavelengths. The analysis of PCS, or namely PA physio-chemical analysis (PAPCA), enables the quantification of the relative concentrations and the spatial distributions of a variety of chemical components in the tissue. This study validated the feasibility of PAPCA in characterizing liver conditions during the progression of non-alcoholic fatty liver disease. A catheter based setup facilitating measurement in deep tissues was also tested.

Laminar and dorsoventral molecular organization of the medial entorhinal cortex revealed by large-scale anatomical analysis of gene expression.

PubMed

Ramsden, Helen L; Sürmeli, Gülşen; McDonagh, Steven G; Nolan, Matthew F

2015-01-01

Neural circuits in the medial entorhinal cortex (MEC) encode an animal's position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.

Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression

PubMed Central

Ramsden, Helen L.; Sürmeli, Gülşen; McDonagh, Steven G.; Nolan, Matthew F.

2015-01-01

Neural circuits in the medial entorhinal cortex (MEC) encode an animal’s position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations. PMID:25615592

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.

Long ranging swept-source optical coherence tomography-based angiography outperforms its spectral-domain counterpart in imaging human skin microcirculations

NASA Astrophysics Data System (ADS)

Xu, Jingjiang; Song, Shaozhen; Men, Shaojie; Wang, Ruikang K.

2017-11-01

There is an increasing demand for imaging tools in clinical dermatology that can perform in vivo wide-field morphological and functional examination from surface to deep tissue regions at various skin sites of the human body. The conventional spectral-domain optical coherence tomography-based angiography (SD-OCTA) system is difficult to meet these requirements due to its fundamental limitations of the sensitivity roll-off, imaging range as well as imaging speed. To mitigate these issues, we demonstrate a swept-source OCTA (SS-OCTA) system by employing a swept source based on a vertical cavity surface-emitting laser. A series of comparisons between SS-OCTA and SD-OCTA are conducted. Benefiting from the high system sensitivity, long imaging range, and superior roll-off performance, the SS-OCTA system is demonstrated with better performance in imaging human skin than the SD-OCTA system. We show that the SS-OCTA permits remarkable deep visualization of both structure and vasculature (up to ˜2 mm penetration) with wide field of view capability (up to 18×18 mm2), enabling a more comprehensive assessment of the morphological features as well as functional blood vessel networks from the superficial epidermal to deep dermal layers. It is expected that the advantages of the SS-OCTA system will provide a ground for clinical translation, benefiting the existing dermatological practice.

Deep-tissue two-photon imaging in brain and peripheral nerve with a compact high-pulse energy ytterbium fiber laser

NASA Astrophysics Data System (ADS)

Fontaine, Arjun K.; Kirchner, Matthew S.; Caldwell, John H.; Weir, Richard F.; Gibson, Emily A.

2018-02-01

Two-photon microscopy is a powerful tool of current scientific research, allowing optical visualization of structures below the surface of tissues. This is of particular value in neuroscience, where optically accessing regions within the brain is critical for the continued advancement in understanding of neural circuits. However, two-photon imaging at significant depths have typically used Ti:Sapphire based amplifiers that are prohibitively expensive and bulky. In this study, we demonstrate deep tissue two-photon imaging using a compact, inexpensive, turnkey operated Ytterbium fiber laser (Y-Fi, KM Labs). The laser is based on all-normal dispersion (ANDi) that provides short pulse durations and high pulse energies. Depth measurements obtained in ex vivo mouse cortex exceed those obtainable with standard two-photon microscopes using Ti:Sapphire lasers. In addition to demonstrating the capability of deep-tissue imaging in the brain, we investigated imaging depth in highly-scattering white matter with measurements in sciatic nerve showing limited optical penetration of heavily myelinated nerve tissue relative to grey matter.

In Vitro Engineering of Vascularized Tissue Surrogates

PubMed Central

Sakaguchi, Katsuhisa; Shimizu, Tatsuya; Horaguchi, Shigeto; Sekine, Hidekazu; Yamato, Masayuki; Umezu, Mitsuo; Okano, Teruo

2013-01-01

In vitro scaling up of bioengineered tissues is known to be limited by diffusion issues, specifically a lack of vasculature. Here, we report a new strategy for preserving cell viability in three-dimensional tissues using cell sheet technology and a perfusion bioreactor having collagen-based microchannels. When triple-layer cardiac cell sheets are incubated within this bioreactor, endothelial cells in the cell sheets migrate to vascularize in the collagen gel, and finally connect with the microchannels. Medium readily flows into the cell sheets through the microchannels and the newly developed capillaries, while the cardiac construct shows simultaneous beating. When additional triple-layer cell sheets are repeatedly layered, new multi-layer construct spontaneously integrates and the resulting construct becomes a vascularized thick tissue. These results confirmed our method to fabricate in vitro vascularized tissue surrogates that overcomes engineered-tissue thickness limitations. The surrogates promise new therapies for damaged organs as well as new in vitro tissue models. PMID:23419835

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.

Estimation of the absorption coefficients of two-layered media by a simple method using spatially and time-resolved reflectances

NASA Astrophysics Data System (ADS)

Shimada, M.; Sato, C.; Hoshi, Y.; Yamada, Y.

2009-08-01

Our newly developed method using spatially and time-resolved reflectances can easily estimate the absorption coefficients of each layer in a two-layered medium if the thickness of the upper layer and the reduced scattering coefficients of the two layers are known a priori. We experimentally validated this method using phantoms and examined its possibility of estimating the absorption coefficients of the tissues in human heads. In the case of a homogeneous plastic phantom (polyacetal block), the absorption coefficient estimated by our method agreed well with that obtained by a conventional method. Also, in the case of two-layered phantoms, our method successfully estimated the absorption coefficients of the two layers. Furthermore, the absorption coefficients of the extracerebral and cerebral tissue inside human foreheads were estimated under the assumption that the human heads were two-layered media. It was found that the absorption coefficients of the cerebral tissues were larger than those of the extracerebral tissues.

Predicting multicellular function through multi-layer tissue networks

PubMed Central

Zitnik, Marinka; Leskovec, Jure

2017-01-01

Abstract Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here, we present OhmNet, a hierarchy-aware unsupervised node feature learning approach for multi-layer networks. We build a multi-layer network, where each layer represents molecular interactions in a different human tissue. OhmNet then automatically learns a mapping of proteins, represented as nodes, to a neural embedding-based low-dimensional space of features. OhmNet encourages sharing of similar features among proteins with similar network neighborhoods and among proteins activated in similar tissues. The algorithm generalizes prior work, which generally ignores relationships between tissues, by modeling tissue organization with a rich multiscale tissue hierarchy. We use OhmNet to study multicellular function in a multi-layer protein interaction network of 107 human tissues. In 48 tissues with known tissue-specific cellular functions, OhmNet provides more accurate predictions of cellular function than alternative approaches, and also generates more accurate hypotheses about tissue-specific protein actions. We show that taking into account the tissue hierarchy leads to improved predictive power. Remarkably, we also demonstrate that it is possible to leverage the tissue hierarchy in order to effectively transfer cellular functions to a functionally uncharacterized tissue. Overall, OhmNet moves from flat networks to multiscale models able to predict a range of phenotypes spanning cellular subsystems. Availability and implementation: Source code and datasets are available at http://snap.stanford.edu/ohmnet. Contact: jure@cs.stanford.edu PMID:28881986

[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.

Scratching the surface: the processing of pain from deep tissues.

PubMed

Sikandar, Shafaq; Aasvang, Eske Kvanner; Dickenson, Anthony H

2016-04-01

Although most pain research focuses on skin, muscles, joints and viscerae are major sources of pain. We discuss the mechanisms of deep pains arising from somatic and visceral structures and how this can lead to widespread manifestations and chronification. We include how both altered peripheral and central sensory neurotransmission lead to deep pain states and comment on key areas such as top-down modulation where little is known. It is vital that the clinical characterization of deep pain in patients is improved to allow for back translation to preclinical models so that the missing links can be ascertained. The contribution of deeper somatic and visceral tissues to various chronic pain syndromes is common but there is much we need to know.

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.

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.

Efficacy and Pharmacological Mechanism of Pronase-Enhanced Low-Dose Antibiotics for Helicobacter pylori Eradication

PubMed Central

Liu, Kai Y.; Du, Fang C.; Fu, Qiang; Zhang, Wei J.; Sun, Hong W.; Zhang, Yi; Gan, Le L.; Yue, Zhi Y.

2014-01-01

This study examined the efficacy and pharmacological mechanism of pronase-assisted low-dose antibiotics for eradication of Helicobacter pylori. Mongolian gerbils infected with H. pylori received 7-day treatment (omeprazole, different concentrations of pronase, amoxicillin, and clarithromycin), and the efficacy was assessed using the eradication rate and the colonization of H. pylori. In Mongolian gerbils orally administered pronase, the thickness of the gastric mucous layer (GML) was examined using immunohistochemical and alcian blue staining, and the concentrations of amoxicillin in gastric tissue and serum were detected using high-performance liquid chromatography (HPLC). The eradication rates were 80.0% (12/15) in the high-pronase quadruple group (HPQG) and 86.7% (13/15) in the high-antibiotic group (HAG) (P = 1.000). The antibiotic dose in the HPQG was only 1/20 that in the HAG. Thirty minutes after oral treatment with pronase, the sticky protein of the GML was hydrolyzed, and the GML became thinner. Higher amoxicillin concentrations in both the gastric tissue and serum were observed in the pronase group than in the Am10 group. The concentration of amoxicillin in the Am10-plus-Pr108 group in gastric tissue was 3.8 times higher than in the Am10 group in 5 min. Together, these data suggest that pronase significantly reduced the dose of antibiotics used in H. pylori eradication. The pharmacological mechanism is likely pronase removal of the mucus layer, promoting chemical factor (i.e., gastric acid and pepsinogen) distribution and increasing the antibiotic concentrations in the deep GML, which acted on H. pylori collectively. Thus, pronase may enhance the level of antibiotics for eradication of H. pylori in the clinic. PMID:24687504

Method for estimating optimal spectral and energy parameters of laser irradiation in photodynamic therapy of biological tissue

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

Lisenko, S A; Kugeiko, M M

We have solved the problem of layer-by-layer laser-light dosimetry in biological tissues and of selecting an individual therapeutic dose in laser therapy. A method is proposed for real-time monitoring of the radiation density in tissue layers in vivo, concentrations of its endogenous (natural) and exogenous (specially administered) chromophores, as well as in-depth distributions of the spectrum of light action on these chromophores. As the background information use is made of the spectrum of diffuse light reflected from a patient's tissue, measured by a fibre-optic spectrophotometer. The measured spectrum is quantitatively analysed by the method of approximating functions for fluxes ofmore » light multiply scattered in tissue and by a semi-analytical method for calculating the in-depth distribution of the light flux in a multi-layered medium. We have shown the possibility of employing the developed method for monitoring photosensitizer and oxyhaemoglobin concentrations in tissue, light power absorbed by chromophores in tissue layers at different depths and laser-induced changes in the tissue morphology (vascular volume content and ratios of various forms of haemoglobin) during photodynamic therapy. (biophotonics)« less

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).

NASA light emitting diode medical applications from deep space to deep sea

NASA Astrophysics Data System (ADS)

Whelan, Harry T.; Buchmann, Ellen V.; Whelan, Noel T.; Turner, Scott G.; Cevenini, Vita; Stinson, Helen; Ignatius, Ron; Martin, Todd; Cwiklinski, Joan; Meyer, Glenn A.; Hodgson, Brian; Gould, Lisa; Kane, Mary; Chen, Gina; Caviness, James

2001-02-01

This work is supported and managed through the NASA Marshall Space Flight Center-SBIR Program. LED-technology developed for NASA plant growth experiments in space shows promise for delivering light deep into tissues of the body to promote wound healing and human tissue growth. We present the results of LED-treatment of cells grown in culture and the effects of LEDs on patients' chronic and acute wounds. LED-technology is also biologically optimal for photodynamic therapy of cancer and we discuss our successes using LEDs in conjunction with light-activated chemotherapeutic drugs. .

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.

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.

The horizontal brain slice preparation: a novel approach for visualizing and recording from all layers of the tadpole tectum.

PubMed

Hamodi, Ali S; Pratt, Kara G

2015-01-01

The Xenopus tadpole optic tectum is a multisensory processing center that receives direct visual input as well as nonvisual mechanosensory input. The tectal neurons that comprise the optic tectum are organized into layers. These neurons project their dendrites laterally into the neuropil where visual inputs target the distal region of the dendrite and nonvisual inputs target the proximal region of the same dendrite. The Xenopus tadpole tectum is a popular model to study the development of sensory circuits. However, whole cell patch-clamp electrophysiological studies of the tadpole tectum (using the whole brain or in vivo preparations) have focused solely on the deep-layer tectal neurons because only neurons of the deep layer are visible and accessible for whole cell electrophysiological recordings. As a result, whereas the development and plasticity of these deep-layer neurons has been well-studied, essentially nothing has been reported about the electrophysiology of neurons residing beyond this layer. Hence, there exists a large gap in our understanding about the functional development of the amphibian tectum as a whole. To remedy this, we developed a novel isolated brain preparation that allows visualizing and recording from all layers of the tectum. We refer to this preparation as the "horizontal brain slice preparation." Here, we describe the preparation method and illustrate how it can be used to characterize the electrophysiology of neurons across all of the layers of the tectum as well as the spatial pattern of synaptic input from the different sensory modalities. Copyright © 2015 the American Physiological Society.

[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.

Atelocollagen sponge and recombinant basic fibroblast growth factor combination therapy for resistant wounds with deep cavities.

PubMed

Nakanishi, Asako; Hakamada, Arata; Isoda, Ken-ichi; Mizutani, Hitoshi

2005-05-01

Recent advances in bioengineering have introduced materials that enhance wound healing. Even with such new tools, some deep ulcers surrounded by avascular tissues, including bone, tendon, and fascia, are resistant to various therapies and easily form deep cavities with loss of subcutaneous tissue. Atelocollagen sponges have been used as an artificial dermis to cover full-thickness skin defects. Topical recombinant human basic fibroblast growth factor has been introduced as a growth factor to induce fibroblast proliferation in skin ulcers. We applied these materials in combination in two patients with deep resistant wounds: one with a cavity reaching the mediastinum through a divided sternum and one with deep necrotic wounds caused by electric burns. These wounds did not respond to the topical basic fibroblast growth factor alone. In contrast, the combination therapy closed the wounds rapidly without further surgical treatment. This combination therapy is a potent treatment for resistant wounds with deep cavities.

The in vitro and in vivo influence of 4-META/MMA-TBB resin components on dental pulp tissues.

PubMed

Inoue, T; Miyakoshi, S; Shimono, M

2001-08-01

The purpose of this study was to qualitate the penetration of the major components of 4-META/MMA-TBB adhesive resin (4-META resin) and to characterize their influence on the in vitro and in vivo wound healing of dental pulp tissues. Fresh 4-META resin was applied to rabbit mesentery; its components penetrated the mesentery to form three of layers, depending on the amounts of monomer components in the tissue. The superficial layer was a soft-tissue hybrid layer (STHL), the intermediate layer contained small particles of polymerized 4-META resin, while the deepest layer contained unpolymerized monomer components including MMA and butanol, which were detected by gas chromatography (GC). To characterize the in vivo effects of the deepest layer, we immersed the pulp tissue in MMA or in 5% 4-META/MMA and autotransplanted it to placement beneath a rabbit kidney capsule. The MMA-immersed pulp was positive for osteocalcin and presented osteodentin formation at 7 days, as did the untreated control pulp tissue. In contrast, the 5% 4-META/MMA-immersed pulp collapsed into the cell-deficient fibrous connective tissue, with slight calcification by 7 days and less osteodentin formation at 14 days. Analysis of these data suggests that MMA does not inhibit osteogenic activity of pulp tissue, while 5% 4-META/MMA does inhibit osteogenic activity to some extent.

Photosymbiotic giant clams are transformers of solar flux.

PubMed

Holt, Amanda L; Vahidinia, Sanaz; Gagnon, Yakir Luc; Morse, Daniel E; Sweeney, Alison M

2014-12-06

'Giant' tridacnid clams have evolved a three-dimensional, spatially efficient, photodamage-preventing system for photosymbiosis. We discovered that the mantle tissue of giant clams, which harbours symbiotic nutrition-providing microalgae, contains a layer of iridescent cells called iridocytes that serve to distribute photosynthetically productive wavelengths by lateral and forward-scattering of light into the tissue while back-reflecting non-productive wavelengths with a Bragg mirror. The wavelength- and angle-dependent scattering from the iridocytes is geometrically coupled to the vertically pillared microalgae, resulting in an even re-distribution of the incoming light along the sides of the pillars, thus enabling photosynthesis deep in the tissue. There is a physical analogy between the evolved function of the clam system and an electric transformer, which changes energy flux per area in a system while conserving total energy. At incident light levels found on shallow coral reefs, this arrangement may allow algae within the clam system to both efficiently use all incident solar energy and avoid the photodamage and efficiency losses due to non-photochemical quenching that occur in the reef-building coral photosymbiosis. Both intra-tissue radiometry and multiscale optical modelling support our interpretation of the system's photophysics. This highly evolved 'three-dimensional' biophotonic system suggests a strategy for more efficient, damage-resistant photovoltaic materials and more spatially efficient solar production of algal biofuels, foods and chemicals.

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.

Developing bioproxies of past ocean ecosystem change through compound-specific stable isotope analysis of proteinaceous deep-sea corals.

NASA Astrophysics Data System (ADS)

McMahon, K.; Williams, B.; Mccarthy, M. D.; Etnoyer, P. J.

2015-12-01

Our understanding of current and future ocean conditions is framed by our ability to reconstruct past changes in ecosystem structure and function recorded in paleoarchives. One such archive, proteinaceous deep-sea corals, act as "living sediment traps" with the potential to greatly improve our ability to reconstruct long-term, high-resolution biogeochemical records of export production. Compound-specific stable isotope analysis (CSIA) of individual amino acids (AAs) in deep-sea corals has provided highly detailed new tools to reconstruct changes in both plankton community composition and sources of nitrogen. However, to realize the full potential of CSIA in deep-sea corals, it is critical to better understand the link between the biogeochemical signatures of deep-sea coral polyp tissue and diagenetically resistant proteinaceous skeletal material. We conducted the first detailed comparison of δ13C and δ15N values for individual AAs between tissue and skeleton for three deep-sea coral genera (Primnoa, Isidella, and Kulamanamana). For δ13C values, we found minimal offsets in both essential and non-essential AAs across genera, strongly supporting coral skeleton AA fingerprinting as a new tool to reconstruct plankton community structure. Similarly, there was no significant offset in source AA δ15N values between tissue and skeleton, supporting the use of Phe δ15N as a proxy for baseline nitrogen sources. However, and rather unexpectedly, we found that the d15N values of the trophic AA group were consistently 3-4‰ lighter in skeleton than polyp tissue for all three genera. We hypothesize that this may reflect a partitioning of either N flux or pathways associated with AA transamination between polyp and skeleton tissues. This offset leads to an underestimate of trophic position using current CSIA-based calculations. Overall, our work strongly supports the applicability of CSIA in proteinaceous deep-sea corals to reconstruct past changes in biogeochemical cycling and plankton community dynamics. However, it also indicates that a new correction factor will be required to reconstruct accurate records of change in plankton trophic structure.

The role of cell body density in ruminant retina mechanics assessed by atomic force and Brillouin microscopy

NASA Astrophysics Data System (ADS)

Weber, Isabell P.; Yun, Seok Hyun; Scarcelli, Giuliano; Franze, Kristian

2017-12-01

Cells in the central nervous system (CNS) respond to the stiffness of their environment. CNS tissue is mechanically highly heterogeneous, thus providing motile cells with region-specific mechanical signals. While CNS mechanics has been measured with a variety of techniques, reported values of tissue stiffness vary greatly, and the morphological structures underlying spatial changes in tissue stiffness remain poorly understood. We here exploited two complementary techniques, contact-based atomic force microscopy and contact-free Brillouin microscopy, to determine the mechanical properties of ruminant retinae, which are built up by different tissue layers. As in all vertebrate retinae, layers of high cell body densities (‘nuclear layers’) alternate with layers of low cell body densities (‘plexiform layers’). Different tissue layers varied significantly in their mechanical properties, with the photoreceptor layer being the stiffest region of the retina, and the inner plexiform layer belonging to the softest regions. As both techniques yielded similar results, our measurements allowed us to calibrate the Brillouin microscopy measurements and convert the Brillouin shift into a quantitative assessment of elastic tissue stiffness with optical resolution. Similar as in the mouse spinal cord and the developing Xenopus brain, we found a strong correlation between nuclear densities and tissue stiffness. Hence, the cellular composition of retinae appears to strongly contribute to local tissue stiffness, and Brillouin microscopy shows a great potential for the application in vivo to measure the mechanical properties of transparent tissues.

RGD-conjugated two-photon absorbing near-IR emitting fluorescent probes for tumor vascular imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Belfield, Kevin D.; Yue, Xiling; Morales, Alma R.; Githaiga, Grace W.; Woodward, Adam W.; Tang, Simon; Sawada, Junko; Komatsu, Masanobu; Liu, Xuan

2016-03-01

Observation of the activation and inhibition of angiogenesis processes is important in the progression of cancer. Application of targeting peptides, such as a small peptide that contains adjacent L-arginine (R), glycine (G) and L-aspartic acid (D) residues can afford high selectivity and deep penetration in vessel imaging. To facilitate deep tissue vasculature imaging, probes that can be excited via two-photon absorption (2PA) in the near-infrared (NIR) and subsequently emit in the NIR are essential. In this study, the enhancement of tissue image quality with RGD conjugates was investigated with new NIR-emitting pyranyl fluorophore derivatives in two-photon fluorescence microscopy. Linear and nonlinear photophysical properties of the new probes were comprehensively characterized; significantly the probes exhibited good 2PA over a broad spectral range from 700-1100 nm. Cell and tissue images were then acquired and examined, revealing deep penetration and high contrast with the new pyranyl RGD-conjugates up to 350 μm in tumor tissue.

Swept-source optical coherence tomography powered by a 1.3-μm vertical cavity surface emitting laser enables 2.3-mm-deep brain imaging in mice in vivo

NASA Astrophysics Data System (ADS)

Choi, Woo June; Wang, Ruikang K.

2015-10-01

We report noninvasive, in vivo optical imaging deep within a mouse brain by swept-source optical coherence tomography (SS-OCT), enabled by a 1.3-μm vertical cavity surface emitting laser (VCSEL). VCSEL SS-OCT offers a constant signal sensitivity of 105 dB throughout an entire depth of 4.25 mm in air, ensuring an extended usable imaging depth range of more than 2 mm in turbid biological tissue. Using this approach, we show deep brain imaging in mice with an open-skull cranial window preparation, revealing intact mouse brain anatomy from the superficial cerebral cortex to the deep hippocampus. VCSEL SS-OCT would be applicable to small animal studies for the investigation of deep tissue compartments in living brains where diseases such as dementia and tumor can take their toll.

Seeing through Musculoskeletal Tissues: Improving In Situ Imaging of Bone and the Lacunar Canalicular System through Optical Clearing

PubMed Central

Berke, Ian M.; Miola, Joseph P.; David, Michael A.; Smith, Melanie K.; Price, Christopher

2016-01-01

In situ, cells of the musculoskeletal system reside within complex and often interconnected 3-D environments. Key to better understanding how 3-D tissue and cellular environments regulate musculoskeletal physiology, homeostasis, and health is the use of robust methodologies for directly visualizing cell-cell and cell-matrix architecture in situ. However, the use of standard optical imaging techniques is often of limited utility in deep imaging of intact musculoskeletal tissues due to the highly scattering nature of biological tissues. Drawing inspiration from recent developments in the deep-tissue imaging field, we describe the application of immersion based optical clearing techniques, which utilize the principle of refractive index (RI) matching between the clearing/mounting media and tissue under observation, to improve the deep, in situ imaging of musculoskeletal tissues. To date, few optical clearing techniques have been applied specifically to musculoskeletal tissues, and a systematic comparison of the clearing ability of optical clearing agents in musculoskeletal tissues has yet to be fully demonstrated. In this study we tested the ability of eight different aqueous and non-aqueous clearing agents, with RIs ranging from 1.45 to 1.56, to optically clear murine knee joints and cortical bone. We demonstrated and quantified the ability of these optical clearing agents to clear musculoskeletal tissues and improve both macro- and micro-scale imaging of musculoskeletal tissue across several imaging modalities (stereomicroscopy, spectroscopy, and one-, and two-photon confocal microscopy) and investigational techniques (dynamic bone labeling and en bloc tissue staining). Based upon these findings we believe that optical clearing, in combination with advanced imaging techniques, has the potential to complement classical musculoskeletal analysis techniques; opening the door for improved in situ investigation and quantification of musculoskeletal tissues. PMID:26930293

Seeing through Musculoskeletal Tissues: Improving In Situ Imaging of Bone and the Lacunar Canalicular System through Optical Clearing.

PubMed

Berke, Ian M; Miola, Joseph P; David, Michael A; Smith, Melanie K; Price, Christopher

2016-01-01

In situ, cells of the musculoskeletal system reside within complex and often interconnected 3-D environments. Key to better understanding how 3-D tissue and cellular environments regulate musculoskeletal physiology, homeostasis, and health is the use of robust methodologies for directly visualizing cell-cell and cell-matrix architecture in situ. However, the use of standard optical imaging techniques is often of limited utility in deep imaging of intact musculoskeletal tissues due to the highly scattering nature of biological tissues. Drawing inspiration from recent developments in the deep-tissue imaging field, we describe the application of immersion based optical clearing techniques, which utilize the principle of refractive index (RI) matching between the clearing/mounting media and tissue under observation, to improve the deep, in situ imaging of musculoskeletal tissues. To date, few optical clearing techniques have been applied specifically to musculoskeletal tissues, and a systematic comparison of the clearing ability of optical clearing agents in musculoskeletal tissues has yet to be fully demonstrated. In this study we tested the ability of eight different aqueous and non-aqueous clearing agents, with RIs ranging from 1.45 to 1.56, to optically clear murine knee joints and cortical bone. We demonstrated and quantified the ability of these optical clearing agents to clear musculoskeletal tissues and improve both macro- and micro-scale imaging of musculoskeletal tissue across several imaging modalities (stereomicroscopy, spectroscopy, and one-, and two-photon confocal microscopy) and investigational techniques (dynamic bone labeling and en bloc tissue staining). Based upon these findings we believe that optical clearing, in combination with advanced imaging techniques, has the potential to complement classical musculoskeletal analysis techniques; opening the door for improved in situ investigation and quantification of musculoskeletal tissues.

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.

Monte Carlo modeling of time-resolved fluorescence for depth-selective interrogation of layered tissue.

PubMed

Pfefer, T Joshua; Wang, Quanzeng; Drezek, Rebekah A

2011-11-01

Computational approaches for simulation of light-tissue interactions have provided extensive insight into biophotonic procedures for diagnosis and therapy. However, few studies have addressed simulation of time-resolved fluorescence (TRF) in tissue and none have combined Monte Carlo simulations with standard TRF processing algorithms to elucidate approaches for cancer detection in layered biological tissue. In this study, we investigate how illumination-collection parameters (e.g., collection angle and source-detector separation) influence the ability to measure fluorophore lifetime and tissue layer thickness. Decay curves are simulated with a Monte Carlo TRF light propagation model. Multi-exponential iterative deconvolution is used to determine lifetimes and fractional signal contributions. The ability to detect changes in mucosal thickness is optimized by probes that selectively interrogate regions superficial to the mucosal-submucosal boundary. Optimal accuracy in simultaneous determination of lifetimes in both layers is achieved when each layer contributes 40-60% of the signal. These results indicate that depth-selective approaches to TRF have the potential to enhance disease detection in layered biological tissue and that modeling can play an important role in probe design optimization. Published by Elsevier Ireland Ltd.

Imaging deep skeletal muscle structure using a high-sensitivity ultrathin side-viewing optical coherence tomography needle probe

PubMed Central

Yang, Xiaojie; Lorenser, Dirk; McLaughlin, Robert A.; Kirk, Rodney W.; Edmond, Matthew; Simpson, M. Cather; Grounds, Miranda D.; Sampson, David D.

2013-01-01

We have developed an extremely miniaturized optical coherence tomography (OCT) needle probe (outer diameter 310 µm) with high sensitivity (108 dB) to enable minimally invasive imaging of cellular structure deep within skeletal muscle. Three-dimensional volumetric images were acquired from ex vivo mouse tissue, examining both healthy and pathological dystrophic muscle. Individual myofibers were visualized as striations in the images. Degradation of cellular structure in necrotic regions was seen as a loss of these striations. Tendon and connective tissue were also visualized. The observed structures were validated against co-registered hematoxylin and eosin (H&E) histology sections. These images of internal cellular structure of skeletal muscle acquired with an OCT needle probe demonstrate the potential of this technique to visualize structure at the microscopic level deep in biological tissue in situ. PMID:24466482

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.

Technical Note: Deep learning based MRAC using rapid ultra-short echo time imaging.

PubMed

Jang, Hyungseok; Liu, Fang; Zhao, Gengyan; Bradshaw, Tyler; McMillan, Alan B

2018-05-15

In this study, we explore the feasibility of a novel framework for MR-based attenuation correction for PET/MR imaging based on deep learning via convolutional neural networks, which enables fully automated and robust estimation of a pseudo CT image based on ultrashort echo time (UTE), fat, and water images obtained by a rapid MR acquisition. MR images for MRAC are acquired using dual echo ramped hybrid encoding (dRHE), where both UTE and out-of-phase echo images are obtained within a short single acquisition (35 sec). Tissue labeling of air, soft tissue, and bone in the UTE image is accomplished via a deep learning network that was pre-trained with T1-weighted MR images. UTE images are used as input to the network, which was trained using labels derived from co-registered CT images. The tissue labels estimated by deep learning are refined by a conditional random field based correction. The soft tissue labels are further separated into fat and water components using the two-point Dixon method. The estimated bone, air, fat, and water images are then assigned appropriate Hounsfield units, resulting in a pseudo CT image for PET attenuation correction. To evaluate the proposed MRAC method, PET/MR imaging of the head was performed on 8 human subjects, where Dice similarity coefficients of the estimated tissue labels and relative PET errors were evaluated through comparison to a registered CT image. Dice coefficients for air (within the head), soft tissue, and bone labels were 0.76±0.03, 0.96±0.006, and 0.88±0.01. In PET quantification, the proposed MRAC method produced relative PET errors less than 1% within most brain regions. The proposed MRAC method utilizing deep learning with transfer learning and an efficient dRHE acquisition enables reliable PET quantification with accurate and rapid pseudo CT generation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Generating Facial Expressions Using an Anatomically Accurate Biomechanical Model.

PubMed

Wu, Tim; Hung, Alice; Mithraratne, Kumar

2014-11-01

This paper presents a computational framework for modelling the biomechanics of human facial expressions. A detailed high-order (Cubic-Hermite) finite element model of the human head was constructed using anatomical data segmented from magnetic resonance images. The model includes a superficial soft-tissue continuum consisting of skin, the subcutaneous layer and the superficial Musculo-Aponeurotic system. Embedded within this continuum mesh, are 20 pairs of facial muscles which drive facial expressions. These muscles were treated as transversely-isotropic and their anatomical geometries and fibre orientations were accurately depicted. In order to capture the relative composition of muscles and fat, material heterogeneity was also introduced into the model. Complex contact interactions between the lips, eyelids, and between superficial soft tissue continuum and deep rigid skeletal bones were also computed. In addition, this paper investigates the impact of incorporating material heterogeneity and contact interactions, which are often neglected in similar studies. Four facial expressions were simulated using the developed model and the results were compared with surface data obtained from a 3D structured-light scanner. Predicted expressions showed good agreement with the experimental data.

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

Deep-tissue reporter-gene imaging with fluorescence and optoacoustic tomography: a performance overview.

PubMed

Deliolanis, Nikolaos C; Ale, Angelique; Morscher, Stefan; Burton, Neal C; Schaefer, Karin; Radrich, Karin; Razansky, Daniel; Ntziachristos, Vasilis

2014-10-01

A primary enabling feature of near-infrared fluorescent proteins (FPs) and fluorescent probes is the ability to visualize deeper in tissues than in the visible. The purpose of this work is to find which is the optimal visualization method that can exploit the advantages of this novel class of FPs in full-scale pre-clinical molecular imaging studies. Nude mice were stereotactically implanted with near-infrared FP expressing glioma cells to from brain tumors. The feasibility and performance metrics of FPs were compared between planar epi-illumination and trans-illumination fluorescence imaging, as well as to hybrid Fluorescence Molecular Tomography (FMT) system combined with X-ray CT and Multispectral Optoacoustic (or Photoacoustic) Tomography (MSOT). It is shown that deep-seated glioma brain tumors are possible to visualize both with fluorescence and optoacoustic imaging. Fluorescence imaging is straightforward and has good sensitivity; however, it lacks resolution. FMT-XCT can provide an improved rough resolution of ∼1 mm in deep tissue, while MSOT achieves 0.1 mm resolution in deep tissue and has comparable sensitivity. We show imaging capacity that can shift the visualization paradigm in biological discovery. The results are relevant not only to reporter gene imaging, but stand as cross-platform comparison for all methods imaging near infrared fluorescent contrast agents.

The deep muscular plexus of the pig duodenum: a histochemical and ultrastructural study with special reference to the interstitial cells.

PubMed

Henry, M; Porcher, C; Julé, Y

1998-06-10

The aim of the present study was to describe the deep muscular plexus of the pig duodenum and to characterize its cellular components. Numerous nerve varicosities have been detected in the deep muscular plexus using anti-synaptophysin antibodies. Nerve fibres were also detected here in the outer circular muscle layer, whereas no nerve fibres were observed in the inner circular muscle layer. In the deep muscular plexus, nerve fibres projected to interstitial cells which were characterized at the ultrastructural level. The interstitial cells were of two kinds: the interstitial fibroblastic-like cells (FLC) and the interstitial dense cells (IDC), both of which were interposed between nerve fibres and smooth muscle cells. The FLC were characterized by their elongated bipolar shape, the lack of basal lamina, a well-developed endoplasmic reticulum, a Golgi apparatus, and intermediate filaments. They were closely apposed to axon terminals containing small clear synaptic vesicles and/or dense-cored vesicles. They were frequently connected to each other and to smooth muscle cells of the inner and outer circular layer by desmosomes and more rarely by gap junctions. The IDC are myoid-like cells. They had a stellate appearance and were characterized by a dense cell body, numerous caveolae, and a discontinuous basal lamina. The IDC were always closely apposed to nerve fibres and were connected to smooth muscle cells by desmosomes and small gap junctions. The present results show the unique pattern of cellular organization of the deep muscular plexus of the pig small intestine. They suggest that the interstitial cells in the deep muscular plexus are involved in the integration and transmission of nervous inputs from myenteric neurons to the inner and outer circular muscle layers. The clear-cut distinction observed here between the two types of interstitial cells (fibroblastic and myoid-like) suggests that the interstitial cells of each type may also be involved in some other specific activity, which still remains to be determined.

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.

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.

Deep proton writing of high aspect ratio SU-8 micro-pillars on glass

NASA Astrophysics Data System (ADS)

Ebraert, Evert; Rwamucyo, Ben; Thienpont, Hugo; Van Erps, Jürgen

2016-12-01

Deep proton writing (DPW) is a fabrication technology developed for the rapid prototyping of polymer micro-structures. We use SU-8, a negative resist, spincoated in a layer up to 720 μm-thick in a single step on borosilicate glass, for irradiation with a collimated 12 MeV energy proton beam. Micro-pillars with a slightly conical profile are irradiated in the SU-8 layer. We determine the optimal proton fluence to be 1.02 × 104 μm-2, with which we are able to repeatably achieve micro-pillars with a top-diameter of 138 ± 1 μm and a bottom-diameter of 151 ± 3 μm. The smallest fabricated pillars have a top-diameter of 57 ± 5 μm. We achieved a root-mean-square sidewall surface roughness between 19 nm and 35 nm for the fabricated micro-pillars, measured over an area of 5 × 63.7 μm. We briefly discuss initial testing of two potential applications of the fabricated micro-pillars. Using ∼100 μm-diameter pillars as waveguides for gigascale integration optical interconnect applications, has shown a 4.7 dB improvement in optical multimode fiber-to-fiber coupling as compared to the case where an air-gap is present between the fibers at the telecom wavelength of 1550 nm. The ∼140 μm-diameter pillars were used for mold fabrication with silicone casting. The resulting mold can be used for hydrogel casting, to obtain hydrogel replicas mimicking human tissue for in vitro bio-chemical applications.

Dynamic compressive properties of bovine knee layered tissue

NASA Astrophysics Data System (ADS)

Nishida, Masahiro; Hino, Yuki; Todo, Mitsugu

2015-09-01

In Japan, the most common articular disease is knee osteoarthritis. Among many treatment methodologies, tissue engineering and regenerative medicine have recently received a lot of attention. In this field, cells and scaffolds are important, both ex vivo and in vivo. From the viewpoint of effective treatment, in addition to histological features, the compatibility of mechanical properties is also important. In this study, the dynamic and static compressive properties of bovine articular cartilage-cancellous bone layered tissue were measured using a universal testing machine and a split Hopkinson pressure bar method. The compressive behaviors of bovine articular cartilage-cancellous bone layered tissue were examined. The effects of strain rate on the maximum stress and the slope of stress-strain curves of the bovine articular cartilage-cancellous bone layered tissue were discussed.

Quantifying the determinants of decremental response in critical ventricular tachycardia substrate.

PubMed

Beheshti, Mohammadali; Nayyar, Sachin; Magtibay, Karl; Massé, Stéphane; Porta-Sanchez, Andreu; Haldar, Shouvik; Bhaskaran, Abhishek; Vigmond, Edward; Nanthakumar, Kumaraswamy

2018-05-28

Decremental response evoked with extrastimulation (DEEP) is a useful tool for determining diastolic return path of ventricular tachycardia (VT). Though a targeted VT ablation is feasible with this approach, determinants of DEEP response have not been studied OBJECTIVES: To elucidate the effects of clinically relevant factors, specifically, the proximity of the stimulation site to the arrhythmogenic scar, stimulation wave direction, number of channels open in the scar, size of the scar and number of extra stimuli on decrement and entropy of DEEP potentials. In a 3-dimensional bi-domain simulation of human ventricular tissue (TNNP cell model), an irregular subendocardial myopathic region was generated. An irregular channel of healthy tissue with five potential entry branches was shaped into the myopathic region. A bipolar electrogram was derived from two electrodes positioned in the centre of the myopathic region. Evoked delays between far-field and local Electrogram (EGM) following an extrastimulus (S1-S2, 500-350 ms) were measured as the stimulation site, channel branches, and inexcitable tissue size were altered. Stimulation adjacent to the inexcitable tissue from the side opposite to the point-of-entry produces longest DEEP delay. The DEEP delay shortens when the stimulation point is farther away from the scar, and it decreases maximally when stimulation is done from a site beside a conduction barrier. Entropy increases with S2 when stimulation site is from farther away. An unprotected channel structure with multiple side-branch openings had shorter DEEP delay compared to a protected channel structure with a paucity of additional side-branch openings and a point-of-entry on the side opposite to the pacing source. Addition of a second shorter extrastimulus did not universally lead to higher DEEP delay CONCLUSIONS: Location and direction of the wavefront in relation to scar entry and size of scar determine the degree of evoked response while the number of extrastimuli has a small additional decremental effect. Copyright © 2018 Elsevier Ltd. All rights reserved.

Characterization of the Embryogenic Tissue of the Norway Spruce Including a Transition Layer between the Tissue and the Culture Medium by Magnetic Resonance Imaging

NASA Astrophysics Data System (ADS)

Kořínek, R.; Mikulka, J.; Hřib, J.; Hudec, J.; Havel, L.; Bartušek, K.

2017-02-01

The paper describes the visualization of the cells (ESEs) and mucilage (ECMSN) in an embryogenic tissue via magnetic resonance imaging (MRI) relaxometry measurement combined with the subsequent multi-parametric segmentation. The computed relaxometry maps T1 and T2 show a thin layer (transition layer) between the culture medium and the embryogenic tissue. The ESEs, mucilage, and transition layer differ in their relaxation times T1 and T2; thus, these times can be used to characterize the individual parts within the embryogenic tissue. The observed mean values of the relaxation times T1 and T2 of the ESEs, mucilage, and transition layer are as follows: 1469 ± 324 and 53 ± 10 ms, 1784 ± 124 and 74 ± 8 ms, 929 ± 164 and 32 ± 4.7 ms, respectively. The multi-parametric segmentation exploiting the T1 and T2 relaxation times as a classifier shows the distribution of the ESEs and mucilage within the embryogenic tissue. The discussed T1 and T2 indicators can be utilized to characterize both the growth-related changes in an embryogenic tissue and the effect of biotic/abiotic stresses, thus potentially becoming a distinctive indicator of the state of any examined embryogenic tissue.

Referred pain and cutaneous responses from deep tissue electrical pain stimulation in the groin.

PubMed

Aasvang, E K; Werner, M U; Kehlet, H

2015-08-01

Persistent postherniotomy pain is located around the scar and external inguinal ring and is often described as deep rather than cutaneous, with frequent complaints of pain in adjacent areas. Whether this pain is due to local pathology or referred/projected pain is unknown, hindering mechanism-based treatment. Deep tissue electrical pain stimulation by needle electrodes in the right groin (rectus muscle, ilioinguinal/iliohypogastric nerve and perispermatic cord) was combined with assessment of referred/projected pain and the cutaneous heat pain threshold (HPT) at three prespecified areas (both groins and the lower right arm) in 19 healthy subjects. The assessment was repeated 10 days later to assess the reproducibility of individual responses. Deep electrical stimulation elicited pain at the stimulation site in all subjects, and in 15 subjects, pain from areas outside the stimulation area was reported, with 90-100% having the same response on both days, depending on the location. Deep pain stimulation significantly increased the cutaneous HPT (P<0.014). Individual HPT responses before and during deep electrical pain stimulation were significantly correlated (ρ>0.474, P≤0.040) at the two test days for the majority of test areas. Our results corroborate a systematic relationship between deep pain and changes in cutaneous nociception. The individual referred/projected pain patterns and cutaneous responses are variable, but reproducible, supporting individual differences in anatomy and sensory processing. Future studies investigating the responses to deep tissue electrical stimulation in persistent postherniotomy pain patients may advance our understanding of underlying pathophysiological mechanisms and strategies for treatment and prevention. ClinicalTrials.gov (NCT01701427). © The Author 2015. Published by Oxford University Press on behalf of the British Journal of Anaesthesia. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Induction of superficial cortical layer neurons from mouse embryonic stem cells by valproic acid.

PubMed

Juliandi, Berry; Abematsu, Masahiko; Sanosaka, Tsukasa; Tsujimura, Keita; Smith, Austin; Nakashima, Kinichi

2012-01-01

Within the developing mammalian cortex, neural progenitors first generate deep-layer neurons and subsequently more superficial-layer neurons, in an inside-out manner. It has been reported recently that mouse embryonic stem cells (mESCs) can, to some extent, recapitulate cortical development in vitro, with the sequential appearance of neurogenesis markers resembling that in the developing cortex. However, mESCs can only recapitulate early corticogenesis; superficial-layer neurons, which are normally produced in later developmental periods in vivo, are under-represented. This failure of mESCs to reproduce later corticogenesis in vitro implies the existence of crucial factor(s) that are absent or uninduced in existing culture systems. Here we show that mESCs can give rise to superficial-layer neurons efficiently when treated with valproic acid (VPA), a histone deacetylase inhibitor. VPA treatment increased the production of Cux1-positive superficial-layer neurons, and decreased that of Ctip2-positive deep-layer neurons. These results shed new light on the mechanisms of later corticogenesis. Copyright © 2011 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

Applications of rigid and flexible GRIN-endoscopes

NASA Astrophysics Data System (ADS)

Schenkl, Selma; Ehlers, Alexander; Riemann, Iris; Messerschmidt, Bernhard; Bückle, Rainer; König, Karsten

2007-02-01

Multiphoton autofluorescence imaging became an important technique for minimal invasive examination of cells in biological tissue. Rigid and flexible endoscopes based on gradient index lenses (GRIN-lenses) extend this minimalinvasive technique to deep lying cell layers, inner body and specimens, difficult to access. In the rigid endoscope, a GRIN-lens overcomes the limited depth range, given by the working distance of the microscope objective. The focus of the conventional laser scanning tomography is reproduced tens of millimeters in the specimen under study by the GRIN-lens (diameter 1.8 and 3 μm). We will present images of fluorescent beads, proteins cells and skin tissue, as well as first in vivo measurements on human skin. The autofluorescence signal stems from the endogenous fluorophore elastin and SHG from collagen. The flexible endoscope dispenses completely the need of a microscope next to the specimen of interest. The excitation laser pulses is delivered via a well-characterized photonic crystal fiber and subsequently focused by a newly designed GRIN-lens system. The fluorescence, also transferred by a fiber is detected by a PMT detector. We will show the excellent imaging qualities of a newly developed GRIN-lens system with high-resolution images of proteins, cells and plant tissue and give an out-look on multiphoton endoscopy.

Fast deep-tissue multispectral optoacoustic tomography (MSOT) for preclinical imaging of cancer and cardiovascular disease

NASA Astrophysics Data System (ADS)

Taruttis, Adrian; Razansky, Daniel; Ntziachristos, Vasilis

2012-02-01

Optoacoustic imaging has enabled the visualization of optical contrast at high resolutions in deep tissue. Our Multispectral optoacoustic tomography (MSOT) imaging results reveal internal tissue heterogeneity, where the underlying distribution of specific endogenous and exogenous sources of absorption can be resolved in detail. Technical advances in cardiac imaging allow motion-resolved multispectral measurements of the heart, opening the way for studies of cardiovascular disease. We further demonstrate the fast characterization of the pharmacokinetic profiles of lightabsorbing agents. Overall, our MSOT findings indicate new possibilities in high resolution imaging of functional and molecular parameters.

Laminar microvascular transit time distribution in the mouse somatosensory cortex revealed by Dynamic Contrast Optical Coherence Tomography

PubMed Central

Merkle, Conrad W.; Srinivasan, Vivek J.

2015-01-01

The transit time distribution of blood through the cerebral microvasculature both constrains oxygen delivery and governs the kinetics of neuroimaging signals such as blood-oxygen-level-dependent functional Magnetic Resonance Imaging (BOLD fMRI). However, in spite of its importance, capillary transit time distribution has been challenging to quantify comprehensively and efficiently at the microscopic level. Here, we introduce a method, called Dynamic Contrast Optical Coherence Tomography (DyC-OCT), based on dynamic cross-sectional OCT imaging of an intravascular tracer as it passes through the field-of-view. Quantitative transit time metrics are derived from temporal analysis of the dynamic scattering signal, closely related to tracer concentration. Since DyC-OCT does not require calibration of the optical focus, quantitative accuracy is achieved even deep in highly scattering brain tissue where the focal spot degrades. After direct validation of DyC-OCT against dilution curves measured using a fluorescent plasma label in surface pial vessels, we used DyC-OCT to investigate the transit time distribution in microvasculature across the entire depth of the mouse somatosensory cortex. Laminar trends were identified, with earlier transit times and less heterogeneity in the middle cortical layers. The early transit times in the middle cortical layers may explain, at least in part, the early BOLD fMRI onset times observed in these layers. The layer-dependencies in heterogeneity may help explain how a single vascular supply manages to deliver oxygen to individual cortical layers with diverse metabolic needs. PMID:26477654

Laminar microvascular transit time distribution in the mouse somatosensory cortex revealed by Dynamic Contrast Optical Coherence Tomography.

PubMed

Merkle, Conrad W; Srinivasan, Vivek J

2016-01-15

The transit time distribution of blood through the cerebral microvasculature both constrains oxygen delivery and governs the kinetics of neuroimaging signals such as blood-oxygen-level-dependent functional Magnetic Resonance Imaging (BOLD fMRI). However, in spite of its importance, capillary transit time distribution has been challenging to quantify comprehensively and efficiently at the microscopic level. Here, we introduce a method, called Dynamic Contrast Optical Coherence Tomography (DyC-OCT), based on dynamic cross-sectional OCT imaging of an intravascular tracer as it passes through the field-of-view. Quantitative transit time metrics are derived from temporal analysis of the dynamic scattering signal, closely related to tracer concentration. Since DyC-OCT does not require calibration of the optical focus, quantitative accuracy is achieved even deep in highly scattering brain tissue where the focal spot degrades. After direct validation of DyC-OCT against dilution curves measured using a fluorescent plasma label in surface pial vessels, we used DyC-OCT to investigate the transit time distribution in microvasculature across the entire depth of the mouse somatosensory cortex. Laminar trends were identified, with earlier transit times and less heterogeneity in the middle cortical layers. The early transit times in the middle cortical layers may explain, at least in part, the early BOLD fMRI onset times observed in these layers. The layer-dependencies in heterogeneity may help explain how a single vascular supply manages to deliver oxygen to individual cortical layers with diverse metabolic needs. Copyright © 2015 Elsevier Inc. All rights reserved.

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.

Characterization of water molecular state in in-vivo thick tissues using diffuse optical spectroscopic imaging

NASA Astrophysics Data System (ADS)

Chung, So Hyun

Structural changes in water molecules are related to physiological, anatomical and pathological properties of tissues. Near infrared (NIR) optical absorption methods are sensitive to water; however, detailed characterization of water in thick tissues is difficult to achieve because subtle spectral shifts can be obscured by multiple light scattering. In the NIR, a water absorption peak is observed around 975 nm. The precise NIR peak's shape and position are highly sensitive to water molecular disposition. A bound water index (BWI) was developed that quantifies the spectral shift and shape changes observed in tissue water absorption spectra measured by broadband diffuse optical spectroscopic imaging (DOSI). DOSI quantitatively measures light absorption and scattering spectra in cm-deep tissues and therefore reveals bound water spectral shifts. BWI as a water state index was validated by comparing broadband DOSI to MRI and a conductivity cell using bound water phantoms. Non-invasive BWI measurements of malignant and normal tissues in 18 subjects showed a significantly higher fraction of free water in malignant tissues (p<0.0001) compared to normal tissues. BWI showed potential as a prognostic index based on high correlations with tumor grade and size. An algorithm for absolute temperature measurements in deep tissues was developed based on resolving opposing effects of water vibrational frequency shifts due to macromolecular binding. DOSI measures absolute temperature with a difference of 1.1+/-0.91°C from a thermistor. Deep tissue temperature measured in forearms during cold-stress was consistent with previously reported invasively-measured deep tissue temperature. Finally, the BWI was compared to Apparent Diffusion Coefficient (ADC) of diffusion weighted MRI in 9 breast cancer patients. The BWI and ADC correlated (R=0.8, p=<0.01) and both parameters decreased with increasing bulk water content in cancer tissues. Although BWI and ADC are positively correlated in vivo, BWI appears to be more sensitive to free water in the extracellular matrix while ADC reflects increased tumor cellularity. The relationship between ADC, BWI and bulk water concentration suggests that both parameters have potential for assessing tumor histopathological grade. My results confirm the importance of water as a critical tissue component that can potentially provide unique insight into the molecular pathophysiology of cancer.

Prevention of intra-abdominal adhesion by bi-layer electrospun membrane.

PubMed

Jiang, Shichao; Wang, Wei; Yan, Hede; Fan, Cunyi

2013-06-04

The aim of this study was to compare the anti-adhesion efficacy of a bi-layer electrospun fibrous membrane consisting of hyaluronic acid-loaded poly(ε-caprolactone) (PCL) fibrous membrane as the inner layer and PCL fibrous membrane as the outer layer with a single-layer PCL electrospun fibrous membrane in a rat cecum abrasion model. The rat model utilized a cecal abrasion and abdominal wall insult surgical protocol. The bi-layer and PCL membranes were applied between the cecum and the abdominal wall, respectively. Control animals did not receive any treatment. After postoperative day 14, a visual semiquantitative grading scale was used to grade the extent of adhesion. Histological analysis was performed to reveal the features of adhesion tissues. Bi-layer membrane treated animals showed significantly lower adhesion scores than control animals (p < 0.05) and a lower adhesion score compared with the PCL membrane. Histological analysis of the bi-layer membrane treated rat rarely demonstrated tissue adhesion while that of the PCL membrane treated rat and control rat showed loose and dense adhesion tissues, respectively. Bi-layer membrane can efficiently prevent adhesion formation in abdominal cavity and showed a significantly decreased adhesion tissue formation compared with the control.

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.

Cell sheet-based tissue engineering for fabricating 3-dimensional heart tissues.

PubMed

Shimizu, Tatsuya

2014-01-01

In addition to stem cell biology, tissue engineering is an essential research field for regenerative medicine. In contrast to cell injection, bioengineered tissue transplantation minimizes cell loss and has the potential to repair tissue defects. A popular approach is scaffold-based tissue engineering, which utilizes a biodegradable polymer scaffold for seeding cells; however, new techniques of cell sheet-based tissue engineering have been developed. Cell sheets are harvested from temperature-responsive culture dishes by simply lowering the temperature. Monolayer or stacked cell sheets are transplantable directly onto damaged tissues and cell sheet transplantation has already been clinically applied. Cardiac cell sheet stacking produces pulsatile heart tissue; however, lack of vasculature limits the viable tissue thickness to 3 layers. Multistep transplantation of triple-layer cardiac cell sheets cocultured with endothelial cells has been used to form thick vascularized cardiac tissue in vivo. Furthermore, in vitro functional blood vessel formation within 3-dimensional (3D) tissues has been realized by successfully imitating in vivo conditions. Triple-layer cardiac cell sheets containing endothelial cells were layered on vascular beds and the constructs were media-perfused using novel bioreactor systems. Interestingly, cocultured endothelial cells migrate into the vascular beds and form perfusable blood vessels. An in vitro multistep procedure has also enabled the fabrication of thick, vascularized heart tissues. Cell sheet-based tissue engineering has revealed great potential to fabricate 3D cardiac tissues and should contribute to future treatment of severe heart diseases and human tissue model production.

Adaptive focus for deep tissue using diffuse backscatter

NASA Astrophysics Data System (ADS)

Kress, Jeremy; Pourrezaei, Kambiz

2014-02-01

A system integrating high density diffuse optical imaging with adaptive optics using MEMS for deep tissue interaction is presented. In this system, a laser source is scanned over a high density fiber bundle using Digital Micromirror Device (DMD) and channeled to a tissue phantom. Backscatter is then collected from the tissue phantom by a high density fiber array of different fiber type and channeled to CMOS sensor for image acquisition. Intensity focus is directly verified using a second CMOS sensor which measures intensity transmitted though the tissue phantom. A set of training patterns are displayed on the DMD and backscatter is numerically fit to the transmission intensity. After the training patterns are displayed, adaptive focus is performed using only the backscatter and fitting functions. Additionally, tissue reconstruction and prediction of interference focusing by photoacoustic and optical tomographic methods is discussed. Finally, potential NIR applications such as in-vivo adaptive neural photostimulation and cancer targeting are discussed.

Automated classification of multiphoton microscopy images of ovarian tissue using deep learning.

PubMed

Huttunen, Mikko J; Hassan, Abdurahman; McCloskey, Curtis W; Fasih, Sijyl; Upham, Jeremy; Vanderhyden, Barbara C; Boyd, Robert W; Murugkar, Sangeeta

2018-06-01

Histopathological image analysis of stained tissue slides is routinely used in tumor detection and classification. However, diagnosis requires a highly trained pathologist and can thus be time-consuming, labor-intensive, and potentially risk bias. Here, we demonstrate a potential complementary approach for diagnosis. We show that multiphoton microscopy images from unstained, reproductive tissues can be robustly classified using deep learning techniques. We fine-train four pretrained convolutional neural networks using over 200 murine tissue images based on combined second-harmonic generation and two-photon excitation fluorescence contrast, to classify the tissues either as healthy or associated with high-grade serous carcinoma with over 95% sensitivity and 97% specificity. Our approach shows promise for applications involving automated disease diagnosis. It could also be readily applied to other tissues, diseases, and related classification problems. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

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.

A six-color four-laser mobile platform for multi-spectral fluorescence imaging endoscopy

NASA Astrophysics Data System (ADS)

Black, John F.; Tate, Tyler; Keenan, Molly; Swan, Elizabeth; Utzinger, Urs; Barton, Jennifer

2015-03-01

The properties of multi-spectral fluorescence imaging using deep-UV-illumination have recently been explored using a fiber-coupled thermal source at 280 nm. The resulting images show a remarkable level of contrast thought to result from the signal being overwhelmingly generated in the uppermost few cell layers of tissue, making this approach valuable for the study of diseases that originate in the endothelial tissues of the body. With a view to extending the technique with new wavelengths, and improving beam quality for efficient small core fiber coupling we have developed a mobile self-contained tunable solid-state laser source of deep UV light. An alexandrite laser, lasing at around 750 nm is frequency doubled to produce 375 nm and then tripled to produce 250 nm light. An optical deck added to the system allows other laser sources to be incorporated into the UV beam-line and a lens system has been designed to couple these sources into a single delivery fiber with core diameters down to 50 microns. Our system incorporates five wavelengths [250 nm, 375 nm, 442 nm (HeCd), 543 nm (HeNe) and 638 nm (diode laser)] as the illumination source for a small diameter falloposcope designed for the study of the distal Fallopian tube origins of high grade serous ovarian cancer. The tunability of alexandrite offers the potential to generate other wavelengths in the 720-800, 360-400 and 240-265 nm ranges, plus other non-linear optical conversion techniques taking advantage of the high peak powers of the laser.

Impact of Tropopause Structures on Deep Convective Transport Observed during MACPEX

NASA Astrophysics Data System (ADS)

Mullendore, G. L.; Bigelbach, B. C.; Christensen, L. E.; Maddox, E.; Pinkney, K.; Wagner, S.

2016-12-01

Deep convection is the most efficient method of transporting boundary layer mass to the upper troposphere and stratosphere (UTLS). The Mid-latitude Airborne Cirrus Properties Experiment (MACPEX) was conducted during April of 2011 over the central U.S. With a focus on cirrus clouds, the campaign flights often sampled large cirrus anvils downstream from deep convection and included an extensive observational suite of chemical measurements on a high altitude aircraft. As double-tropopause structures are a common feature in the central U.S. during the springtime, the MACPEX campaign provides a good opportunity to gather cases of deep convective transport in the context of both single and double tropopause structures. Sampling of chemical plumes well downstream from convection allows for sampling in relatively quiescent conditions and analysis of irreversible transport. The analysis presented includes multiple methods to assess air mass source and possible convective processing, including back trajectories and ratios of chemical concentrations. Although missions were flown downstream of deep convection, recent processing by convection does not seem likely in all cases that high altitude carbon monoxide plumes were observed. Additionally, the impact of single and double tropopause structures on deep convective transport is shown to be strongly dependent on high stability layers.

Predator-guided sampling reveals biotic structure in the bathypelagic.

PubMed

Benoit-Bird, Kelly J; Southall, Brandon L; Moline, Mark A

2016-02-24

We targeted a habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey's distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1,200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was consistent with the general distribution patterns of foraging Cuvier's beaked whales (Ziphius cavirostris) observed in separate studies. Striking differences found in prey characteristics between regions at depth, however, did not reflect differences observed in surface layers. These differences in deep pelagic structure horizontally and relative to surface structure, absent clear physical differences, change our long-held views of this habitat as uniform. The revelation that animals deep in the water column are so spatially heterogeneous at scales from 10 m to 50 km critically affects our understanding of the processes driving predator-prey interactions, energy transfer, biogeochemical cycling, and other ecological processes in the deep sea, and the connections between the productive surface mixed layer and the deep-water column. © 2016 The Author(s).

Hubble Captures Detailed Image of Uranus Atmosphere

NASA Image and Video Library

1998-08-02

NASA Hubble Space Telescope peered deep into Uranus atmosphere to see clear and hazy layers created by a mixture of gases. Using infrared filters, Hubble captured detailed features of three layers of Uranus atmosphere.

The effects of deep convection on the concentration and size distribution of aerosol particles within the upper troposphere: A case study

NASA Astrophysics Data System (ADS)

Yin, Yan; Chen, Qian; Jin, Lianji; Chen, Baojun; Zhu, Shichao; Zhang, Xiaopei

2012-11-01

A cloud resolving model coupled with a spectral bin microphysical scheme was used to investigate the effects of deep convection on the concentration and size distribution of aerosol particles within the upper troposphere. A deep convective storm that occurred on 1 December, 2005 in Darwin, Australia was simulated, and was compared with available radar observations. The results showed that the radar echo of the storm in the developing stage was well reproduced by the model. Sensitivity tests for aerosol layers at different altitudes were conducted in order to understand how the concentration and size distribution of aerosol particles within the upper troposphere can be influenced by the vertical transport of aerosols as a result of deep convection. The results indicated that aerosols originating from the boundary layer can be more efficiently transported upward, as compared to those from the mid-troposphere, due to significantly increased vertical velocity through the reinforced homogeneous freezing of droplets. Precipitation increased when aerosol layers were lofted at different altitudes, except for the case where an aerosol layer appeared at 5.4-8.0 km, in which relatively more efficient heterogeneous ice nucleation and subsequent Wegener-Bergeron-Findeisen process resulted in more pronounced production of ice crystals, and prohibited the formation of graupel particles via accretion. Sensitivity tests revealed, at least for the cases considered, that the concentration of aerosol particles within the upper troposphere increased by a factor of 7.71, 5.36, and 5.16, respectively, when enhanced aerosol layers existed at 0-2.2 km, 2.2-5.4 km, and 5.4-8.0 km, with Aitken mode and a portion of accumulation mode (0.1-0.2μm) particles being the most susceptible to upward transport.

Refinements to SSiB with an Emphasis on Snow-Physics: Evaluation and Validation Using GSWP and Valdai Data

NASA Technical Reports Server (NTRS)

Mocko, David M.; Sud, Y. C.

2000-01-01

Refinements to the snow-physics scheme of SSiB (Simplified Simple Biosphere Model) are described and evaluated. The upgrades include a partial redesign of the conceptual architecture to better simulate the diurnal temperature of the snow surface. For a deep snowpack, there are two separate prognostic temperature snow layers - the top layer responds to diurnal fluctuations in the surface forcing, while the deep layer exhibits a slowly varying response. In addition, the use of a very deep soil temperature and a treatment of snow aging with its influence on snow density is parameterized and evaluated. The upgraded snow scheme produces better timing of snow melt in GSWP-style simulations using ISLSCP Initiative I data for 1987-1988 in the Russian Wheat Belt region. To simulate more realistic runoff in regions with high orographic variability, additional improvements are made to SSiB's soil hydrology. These improvements include an orography-based surface runoff scheme as well as interaction with a water table below SSiB's three soil layers. The addition of these parameterizations further help to simulate more realistic runoff and accompanying prognostic soil moisture fields in the GSWP-style simulations. In intercomparisons of the performance of the new snow-physics SSiB with its earlier versions using an 18-year single-site dataset from Valdai Russia, the version of SSiB described in this paper again produces the earliest onset of snow melt. Soil moisture and deep soil temperatures also compare favorably with observations.

Modal response of a computational vocal fold model with a substrate layer of adipose tissue.

PubMed

Jones, Cameron L; Achuthan, Ajit; Erath, Byron D

2015-02-01

This study demonstrates the effect of a substrate layer of adipose tissue on the modal response of the vocal folds, and hence, on the mechanics of voice production. Modal analysis is performed on the vocal fold structure with a lateral layer of adipose tissue. A finite element model is employed, and the first six mode shapes and modal frequencies are studied. The results show significant changes in modal frequencies and substantial variation in mode shapes depending on the strain rate of the adipose tissue. These findings highlight the importance of considering adipose tissue in computational vocal fold modeling.

Flood frequency matters: Why climate change degrades deep-water quality of peri-alpine lakes

NASA Astrophysics Data System (ADS)

Fink, Gabriel; Wessels, Martin; Wüest, Alfred

2016-09-01

Sediment-laden riverine floods transport large quantities of dissolved oxygen into the receiving deep layers of lakes. Hence, the water quality of deep lakes is strongly influenced by the frequency of riverine floods. Although flood frequency reflects climate conditions, the effects of climate variability on the water quality of deep lakes is largely unknown. We quantified the effects of climate variability on the potential shifts in the flood regime of the Alpine Rhine, the main catchment of Lake Constance, and determined the intrusion depths of riverine density-driven underflows and the subsequent effects on water exchange rates in the lake. A simplified hydrodynamic underflow model was developed and validated with observed river inflow and underflow events. The model was implemented to estimate underflow statistics for different river inflow scenarios. Using this approach, we integrated present and possible future flood frequencies to underflow occurrences and intrusion depths in Lake Constance. The results indicate that more floods will increase the number of underflows and the intensity of deep-water renewal - and consequently will cause higher deep-water dissolved oxygen concentrations. Vice versa, fewer floods weaken deep-water renewal and lead to lower deep-water dissolved oxygen concentrations. Meanwhile, a change from glacial nival regime (present) to a nival pluvial regime (future) is expected to decrease deep-water renewal. While flood frequencies are not expected to change noticeably for the next decades, it is most likely that increased winter discharge and decreased summer discharge will reduce the number of deep density-driven underflows by 10% and favour shallower riverine interflows in the upper hypolimnion. The renewal in the deepest layers is expected to be reduced by nearly 27%. This study underlines potential consequences of climate change on the occurrence of deep river underflows and water residence times in deep lakes.

Dermofat graft in deep nasolabial fold and facial rhytidectomy.

PubMed

Hwang, Kun; Han, Jin Yi; Kim, Dae Joong

2003-01-01

Fat and dermis or the combined tissues are used commonly in augmentation of the nasolabial fold. Guyuron obtained the dermofat graft from either the suprapubic or the groin region. The thickness of the preauricular skin was measured in seven Korean cadavers, five male and two female. We used the dermofat graft out of the preauricular skin remnant after facial rhytidectomy to augment the deep nasolabial fold in a patient. The average thickness of the epidermis was 56 +/- 12 microm, the dermis was 1820 +/- 265 microm thick, and the subcutaneous tissue was 4783 +/- 137 microm. More dense connective tissues, such as SMAS, are seen in the preauricular skin. The dermofat graft was easily obtained and prepared from the leftover preauricular skin after dissection of the lax skin in face lifting. This technique could be employed effectively and successfully to alleviate a deep nasolabial fold and concomitant facial rhytidectomy in an Asian with a thick preauricular skin.

Cellular imaging of deep organ using two-photon Bessel light-sheet nonlinear structured illumination microscopy

PubMed Central

Zhao, Ming; Zhang, Han; Li, Yu; Ashok, Amit; Liang, Rongguang; Zhou, Weibin; Peng, Leilei

2014-01-01

In vivo fluorescent cellular imaging of deep internal organs is highly challenging, because the excitation needs to penetrate through strong scattering tissue and the emission signal is degraded significantly by photon diffusion induced by tissue-scattering. We report that by combining two-photon Bessel light-sheet microscopy with nonlinear structured illumination microscopy (SIM), live samples up to 600 microns wide can be imaged by light-sheet microscopy with 500 microns penetration depth, and diffused background in deep tissue light-sheet imaging can be reduced to obtain clear images at cellular resolution in depth beyond 200 microns. We demonstrate in vivo two-color imaging of pronephric glomeruli and vasculature of zebrafish kidney, whose cellular structures located at the center of the fish body are revealed in high clarity by two-color two-photon Bessel light-sheet SIM. PMID:24876996

Reinke's edema: investigations on the role of MIB-1 and hepatocyte growth factor.

PubMed

Artico, M; Bronzetti, E; Ionta, B; Bruno, M; Greco, A; Ruoppolo, G; De Virgilio, A; Longo, L; De Vincentiis, M

2010-07-08

Reinke's edema is a benign disease of the human vocal fold, which mainly affects the sub-epithelial layer of the vocal fold. Microscopic observations show a strongly oedematous epithelium with loosened intercellular junctions, a disruption of the extracellular connections between mucosal epithelium and connective tissue, closely adherent to the thyroarytenoid muscle. Thickening of the basal layer of epithelium, known as Reinke's space, high deposition of fibronectin and chronic inflammatory infiltration it is also visible. We analyzed, together with the hepatocyte growth factor (HGF), the expression level of MIB-1 in samples harvested from patients affected by Reinke's edema, in order to define its biological role and consider it as a possible prognostic factor in the follow-up after surgical treatment. We observed a moderate expression of HGF in the lamina propria of the human vocal fold and in the basal membrane of the mucosal epithelium. Our finding suggests that this growth factor acts as an antifibrotic agent in Reinke's space and affects the fibronectin deposition in the lamina propria. MIB-1, on the contrary, showed a weak expression in the basement membrane of the mucosal epithelium and a total absence in the lamina propria deep layer, thus suggesting that only the superficial layer is actively involved in the reparatory process with a high regenerative capacity, together with a high deposition of fibronectin. The latter is necessary for the cellular connections reconstruction, after the inflammatory infiltration.

Reinke's Edema: investigations on the role of MIB-1 and hepatocyte growth factor

PubMed Central

Artico, M.; Bronzetti, E.; Ionta, B.; Bruno, M.; Greco, A.; Ruoppolo, G.; De Virgilio, A.; Longo, L.; De Vincentiis, M.

2010-01-01

Reinke's edema is a benign disease of the human vocal fold, which mainly affects the sub-epithelial layer of the vocal fold. Microscopic observations show a strongly oedematous epithelium with loosened intercellular junctions, a disruption of the extracellular connections between mucosal epithelium and connective tissue, closely adherent to the thyroarytenoid muscle. Thickening of the basal layer of epithelium, known as Reinke's space, high deposition of fibronectin and chronic inflammatory infiltration it is also visible. We analyzed, together with the hepatocyte growth factor (HGF), the expression level of MIB-1 in samples harvested from patients affected by Reinke's edema, in order to define its biological role and consider it as a possible prognostic factor in the follow-up after surgical treatment. We observed a moderate expression of HGF in the lamina propria of the human vocal fold and in the basal membrane of the mucosal epithelium. Our finding suggests that this growth factor acts as an anti - fibrotic agent in Reinke's space and affects the fibronectin deposition in the lamina propria. MIB-1, on the contrary, showed a weak expression in the basement membrane of the mucosal epithelium and a total absence in the lamina propria deep layer, thus suggesting that only the superficial layer is actively involved in the reparatory process with a high regenerative capacity, together with a high deposition of fibronectin. The latter is necessary for the cellular connections reconstruction, after the inflammatory infiltration. PMID:20819770

Observations of open-ocean deep convection in the northwestern Mediterranean Sea: Seasonal and interannual variability of mixing and deep water masses for the 2007-2013 Period

NASA Astrophysics Data System (ADS)

Houpert, L.; Durrieu de Madron, X.; Testor, P.; Bosse, A.; D'Ortenzio, F.; Bouin, M. N.; Dausse, D.; Le Goff, H.; Kunesch, S.; Labaste, M.; Coppola, L.; Mortier, L.; Raimbault, P.

2016-11-01

We present here a unique oceanographic and meteorological data set focus on the deep convection processes. Our results are essentially based on in situ data (mooring, research vessel, glider, and profiling float) collected from a multiplatform and integrated monitoring system (MOOSE: Mediterranean Ocean Observing System on Environment), which monitored continuously the northwestern Mediterranean Sea since 2007, and in particular high-frequency potential temperature, salinity, and current measurements from the mooring LION located within the convection region. From 2009 to 2013, the mixed layer depth reaches the seabed, at a depth of 2330m, in February. Then, the violent vertical mixing of the whole water column lasts between 9 and 12 days setting up the characteristics of the newly formed deep water. Each deep convection winter formed a new warmer and saltier "vintage" of deep water. These sudden inputs of salt and heat in the deep ocean are responsible for trends in salinity (3.3 ± 0.2 × 10-3/yr) and potential temperature (3.2 ± 0.5 × 10-3 C/yr) observed from 2009 to 2013 for the 600-2300 m layer. For the first time, the overlapping of the three "phases" of deep convection can be observed, with secondary vertical mixing events (2-4 days) after the beginning of the restratification phase, and the restratification/spreading phase still active at the beginning of the following deep convection event.

Quantitative Trait Locus Analysis for Deep-Sowing Germination Ability in the Maize IBM Syn10 DH Population

PubMed Central

Liu, Hongjun; Zhang, Lin; Wang, Jiechen; Li, Changsheng; Zeng, Xing; Xie, Shupeng; Zhang, Yongzhong; Liu, Sisi; Hu, Songlin; Wang, Jianhua; Lee, Michael; Lübberstedt, Thomas; Zhao, Guangwu

2017-01-01

Deep-sowing is an effective measure to ensure seeds absorbing water from deep soil layer and emerging normally in arid and semiarid regions. However, existing varieties demonstrate poor germination ability in deep soil layer and some key quantitative trait loci (QTL) or genes related to deep-sowing germination ability remain to be identified and analyzed. In this study, a high-resolution genetic map based on 280 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population which comprised 6618 bin markers was used for the QTL analysis of deep-sowing germination related traits. The results showed significant differences in germination related traits under deep-sowing condition (12.5 cm) and standard-germination condition (2 cm) between two parental lines. In total, 8, 11, 13, 15, and 18 QTL for germination rate, seedling length, mesocotyl length, plumule length, and coleoptile length were detected for the two sowing conditions, respectively. These QTL explained 2.51–7.8% of the phenotypic variance with LOD scores ranging from 2.52 to 7.13. Additionally, 32 overlapping QTL formed 11 QTL clusters on all chromosomes except for chromosome 8, indicating the minor effect genes have a pleiotropic role in regulating various traits. Furthermore, we identified six candidate genes related to deep-sowing germination ability, which were co-located in the cluster regions. The results provide a basis for molecular marker assisted breeding and functional study in deep-sowing germination ability of maize. PMID:28588594

Quantitative Trait Locus Analysis for Deep-Sowing Germination Ability in the Maize IBM Syn10 DH Population.

PubMed

Liu, Hongjun; Zhang, Lin; Wang, Jiechen; Li, Changsheng; Zeng, Xing; Xie, Shupeng; Zhang, Yongzhong; Liu, Sisi; Hu, Songlin; Wang, Jianhua; Lee, Michael; Lübberstedt, Thomas; Zhao, Guangwu

2017-01-01

Deep-sowing is an effective measure to ensure seeds absorbing water from deep soil layer and emerging normally in arid and semiarid regions. However, existing varieties demonstrate poor germination ability in deep soil layer and some key quantitative trait loci (QTL) or genes related to deep-sowing germination ability remain to be identified and analyzed. In this study, a high-resolution genetic map based on 280 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population which comprised 6618 bin markers was used for the QTL analysis of deep-sowing germination related traits. The results showed significant differences in germination related traits under deep-sowing condition (12.5 cm) and standard-germination condition (2 cm) between two parental lines. In total, 8, 11, 13, 15, and 18 QTL for germination rate, seedling length, mesocotyl length, plumule length, and coleoptile length were detected for the two sowing conditions, respectively. These QTL explained 2.51-7.8% of the phenotypic variance with LOD scores ranging from 2.52 to 7.13. Additionally, 32 overlapping QTL formed 11 QTL clusters on all chromosomes except for chromosome 8, indicating the minor effect genes have a pleiotropic role in regulating various traits. Furthermore, we identified six candidate genes related to deep-sowing germination ability, which were co-located in the cluster regions. The results provide a basis for molecular marker assisted breeding and functional study in deep-sowing germination ability of maize.

Comparison of light-transmittance in dental tissues and dental composite restorations using incremental layering build-up with varying enamel resin layer thickness

PubMed Central

2018-01-01

Objectives To evaluate and compare light-transmittance in dental tissues and dental composite restorations using the incremental double-layer technique with varying layer thickness. Materials and Methods B1-colored natural teeth slabs were compared to dental restoration build-ups with A2D and B1E-colored nanofilled, supra-nanofilled, microfilled, and microhybrid composites. The enamel layer varied from 0.3, 0.5, or 1.2 mm thick, and the dentin layer was varied to provide a standardized 3.7 mm overall sample thickness (n = 10). All increments were light-cured to 16 J/cm2 with a multi-wave LED (Valo, Ultradent). Using a spectrophotometer, the samples were irradiated by an RGB laser beam. A voltmeter recorded the light output signal to calculate the light-transmittance through the specimens. The data were analyzed using 1-way analysis of variance followed by the post hoc Tukey's test (p = 0.05). Results Mean light-transmittance observed at thicker final layers of enamel were significantly lower than those observed at thinner final layers. Within 1.2 mm final enamel resin layer (FERL) thickness, all composites were similar to the dental tissues, with exception of the nanofilled composite. However, within 0.5 mm FERL thickness, only the supra-nanofilled composite showed no difference from the dental tissues. Within 0.3 mm FERL thickness, none of the composites were similar to the dental tissues. Conclusions The supra-nanofilled composite had the most similar light-transmittance pattern when compared to the natural teeth. However, for other composites, thicker FERL have a greater chance to match the light-transmittance of natural dental tissues. PMID:29765902

Influence of water layer thickness on hard tissue ablation with pulsed CO2 laser

NASA Astrophysics Data System (ADS)

Zhang, Xianzeng; Zhan, Zhenlin; Liu, Haishan; Zhao, Haibin; Xie, Shusen; Ye, Qing

2012-03-01

The theory of hard tissue ablation reported for IR lasers is based on a process of thermomechanical interaction, which is explained by the absorption of the radiation in the water component of the tissue. The microexplosion of the water is the cause of tissue fragments being blasted from hard tissue. The aim of this study is to evaluate the influence of the interdependence of water layer thickness and incident radiant exposure on ablation performance. A total of 282 specimens of bovine shank bone were irradiated with a pulse CO2 laser. Irradiation was carried out in groups: without a water layer and with a static water layer of thickness ranging from 0.2 to 1.2 mm. Each group was subdivided into five subgroups for different radiant exposures ranging from 18 to 84 J/cm2, respectively. The incision geometry, surface morphology, and microstructure of the cut walls as well as thermal injury were examined as a function of the water layer thickness at different radiant exposures. Our results demonstrate that the additional water layer is actually a mediator of laser-tissue interaction. There exists a critical thickness of water layer for a given radiant exposure, at which the additional water layer plays multiple roles, not only acting as a cleaner to produce a clean cut but also as a coolant to prevent bone heating and reduce thermal injury, but also helping to improve the regularity of the cut shape, smooth the cut surface, and enhance ablation rate and efficiency. The results suggest that desired ablation results depend on optimal selection of both water layer thickness and radiant exposure.

Comparison of light-transmittance in dental tissues and dental composite restorations using incremental layering build-up with varying enamel resin layer thickness.

PubMed

Rocha Maia, Rodrigo; Oliveira, Dayane; D'Antonio, Tracy; Qian, Fang; Skiff, Frederick

2018-05-01

To evaluate and compare light-transmittance in dental tissues and dental composite restorations using the incremental double-layer technique with varying layer thickness. B1-colored natural teeth slabs were compared to dental restoration build-ups with A2D and B1E-colored nanofilled, supra-nanofilled, microfilled, and microhybrid composites. The enamel layer varied from 0.3, 0.5, or 1.2 mm thick, and the dentin layer was varied to provide a standardized 3.7 mm overall sample thickness ( n = 10). All increments were light-cured to 16 J/cm 2 with a multi-wave LED (Valo, Ultradent). Using a spectrophotometer, the samples were irradiated by an RGB laser beam. A voltmeter recorded the light output signal to calculate the light-transmittance through the specimens. The data were analyzed using 1-way analysis of variance followed by the post hoc Tukey's test ( p = 0.05). Mean light-transmittance observed at thicker final layers of enamel were significantly lower than those observed at thinner final layers. Within 1.2 mm final enamel resin layer (FERL) thickness, all composites were similar to the dental tissues, with exception of the nanofilled composite. However, within 0.5 mm FERL thickness, only the supra-nanofilled composite showed no difference from the dental tissues. Within 0.3 mm FERL thickness, none of the composites were similar to the dental tissues. The supra-nanofilled composite had the most similar light-transmittance pattern when compared to the natural teeth. However, for other composites, thicker FERL have a greater chance to match the light-transmittance of natural dental tissues.

Automated assessment of breast tissue density in non-contrast 3D CT images without image segmentation based on a deep CNN

NASA Astrophysics Data System (ADS)

Zhou, Xiangrong; Kano, Takuya; Koyasu, Hiromi; Li, Shuo; Zhou, Xinxin; Hara, Takeshi; Matsuo, Masayuki; Fujita, Hiroshi

2017-03-01

This paper describes a novel approach for the automatic assessment of breast density in non-contrast three-dimensional computed tomography (3D CT) images. The proposed approach trains and uses a deep convolutional neural network (CNN) from scratch to classify breast tissue density directly from CT images without segmenting the anatomical structures, which creates a bottleneck in conventional approaches. Our scheme determines breast density in a 3D breast region by decomposing the 3D region into several radial 2D-sections from the nipple, and measuring the distribution of breast tissue densities on each 2D section from different orientations. The whole scheme is designed as a compact network without the need for post-processing and provides high robustness and computational efficiency in clinical settings. We applied this scheme to a dataset of 463 non-contrast CT scans obtained from 30- to 45-year-old-women in Japan. The density of breast tissue in each CT scan was assigned to one of four categories (glandular tissue within the breast <25%, 25%-50%, 50%-75%, and >75%) by a radiologist as ground truth. We used 405 CT scans for training a deep CNN and the remaining 58 CT scans for testing the performance. The experimental results demonstrated that the findings of the proposed approach and those of the radiologist were the same in 72% of the CT scans among the training samples and 76% among the testing samples. These results demonstrate the potential use of deep CNN for assessing breast tissue density in non-contrast 3D CT images.

Sapphire implant based neuro-complex for deep-lying brain tumors phototheranostics

NASA Astrophysics Data System (ADS)

Sharova, A. S.; Maklygina, YU S.; Yusubalieva, G. M.; Shikunova, I. A.; Kurlov, V. N.; Loschenov, V. B.

2018-01-01

The neuro-complex as a combination of sapphire implant optical port and osteoplastic biomaterial "Collapan" as an Aluminum phthalocyanine nanoform photosensitizer (PS) depot was developed within the framework of this study. The main goals of such neuro-complex are to provide direct access of laser radiation to the brain tissue depth and to transfer PS directly to the pathological tissue location that will allow multiple optical phototheranostics of the deep-lying tumor region without repeated surgical intervention. The developed complex spectral-optical properties research was carried out by photodiagnostics method using the model sample: a brain tissue phantom. The optical transparency of sapphire implant allows obtaining a fluorescent signal with high accuracy, comparable to direct measurement "in contact" with the tissue.

Task-specific feature extraction and classification of fMRI volumes using a deep neural network initialized with a deep belief network: Evaluation using sensorimotor tasks

PubMed Central

Jang, Hojin; Plis, Sergey M.; Calhoun, Vince D.; Lee, Jong-Hwan

2016-01-01

Feedforward deep neural networks (DNN), artificial neural networks with multiple hidden layers, have recently demonstrated a record-breaking performance in multiple areas of applications in computer vision and speech processing. Following the success, DNNs have been applied to neuroimaging modalities including functional/structural magnetic resonance imaging (MRI) and positron-emission tomography data. However, no study has explicitly applied DNNs to 3D whole-brain fMRI volumes and thereby extracted hidden volumetric representations of fMRI that are discriminative for a task performed as the fMRI volume was acquired. Our study applied fully connected feedforward DNN to fMRI volumes collected in four sensorimotor tasks (i.e., left-hand clenching, right-hand clenching, auditory attention, and visual stimulus) undertaken by 12 healthy participants. Using a leave-one-subject-out cross-validation scheme, a restricted Boltzmann machine-based deep belief network was pretrained and used to initialize weights of the DNN. The pretrained DNN was fine-tuned while systematically controlling weight-sparsity levels across hidden layers. Optimal weight-sparsity levels were determined from a minimum validation error rate of fMRI volume classification. Minimum error rates (mean ± standard deviation; %) of 6.9 (± 3.8) were obtained from the three-layer DNN with the sparsest condition of weights across the three hidden layers. These error rates were even lower than the error rates from the single-layer network (9.4 ± 4.6) and the two-layer network (7.4 ± 4.1). The estimated DNN weights showed spatial patterns that are remarkably task-specific, particularly in the higher layers. The output values of the third hidden layer represented distinct patterns/codes of the 3D whole-brain fMRI volume and encoded the information of the tasks as evaluated from representational similarity analysis. Our reported findings show the ability of the DNN to classify a single fMRI volume based on the extraction of hidden representations of fMRI volumes associated with tasks across multiple hidden layers. Our study may be beneficial to the automatic classification/diagnosis of neuropsychiatric and neurological diseases and prediction of disease severity and recovery in (pre-) clinical settings using fMRI volumes without requiring an estimation of activation patterns or ad hoc statistical evaluation. PMID:27079534

Task-specific feature extraction and classification of fMRI volumes using a deep neural network initialized with a deep belief network: Evaluation using sensorimotor tasks.

PubMed

Jang, Hojin; Plis, Sergey M; Calhoun, Vince D; Lee, Jong-Hwan

2017-01-15

Feedforward deep neural networks (DNNs), artificial neural networks with multiple hidden layers, have recently demonstrated a record-breaking performance in multiple areas of applications in computer vision and speech processing. Following the success, DNNs have been applied to neuroimaging modalities including functional/structural magnetic resonance imaging (MRI) and positron-emission tomography data. However, no study has explicitly applied DNNs to 3D whole-brain fMRI volumes and thereby extracted hidden volumetric representations of fMRI that are discriminative for a task performed as the fMRI volume was acquired. Our study applied fully connected feedforward DNN to fMRI volumes collected in four sensorimotor tasks (i.e., left-hand clenching, right-hand clenching, auditory attention, and visual stimulus) undertaken by 12 healthy participants. Using a leave-one-subject-out cross-validation scheme, a restricted Boltzmann machine-based deep belief network was pretrained and used to initialize weights of the DNN. The pretrained DNN was fine-tuned while systematically controlling weight-sparsity levels across hidden layers. Optimal weight-sparsity levels were determined from a minimum validation error rate of fMRI volume classification. Minimum error rates (mean±standard deviation; %) of 6.9 (±3.8) were obtained from the three-layer DNN with the sparsest condition of weights across the three hidden layers. These error rates were even lower than the error rates from the single-layer network (9.4±4.6) and the two-layer network (7.4±4.1). The estimated DNN weights showed spatial patterns that are remarkably task-specific, particularly in the higher layers. The output values of the third hidden layer represented distinct patterns/codes of the 3D whole-brain fMRI volume and encoded the information of the tasks as evaluated from representational similarity analysis. Our reported findings show the ability of the DNN to classify a single fMRI volume based on the extraction of hidden representations of fMRI volumes associated with tasks across multiple hidden layers. Our study may be beneficial to the automatic classification/diagnosis of neuropsychiatric and neurological diseases and prediction of disease severity and recovery in (pre-) clinical settings using fMRI volumes without requiring an estimation of activation patterns or ad hoc statistical evaluation. Copyright © 2016 Elsevier Inc. All rights reserved.

Electronic structure properties of deep defects in hBN

NASA Astrophysics Data System (ADS)

Dev, Pratibha; Prdm Collaboration

In recent years, the search for room-temperature solid-state qubit (quantum bit) candidates has revived interest in the study of deep-defect centers in semiconductors. The charged NV-center in diamond is the best known amongst these defects. However, as a host material, diamond poses several challenges and so, increasingly, there is an interest in exploring deep defects in alternative semiconductors such as hBN. The layered structure of hBN makes it a scalable platform for quantum applications, as there is a greater potential for controlling the location of the deep defect in the 2D-matrix through careful experiments. Using density functional theory-based methods, we have studied the electronic and structural properties of several deep defects in hBN. Native defects within hBN layers are shown to have high spin ground states that should survive even at room temperature, making them interesting solid-state qubit candidates in a 2D matrix. Partnership for Reduced Dimensional Material (PRDM) is part of the NSF sponsored Partnerships for Research and Education in Materials (PREM).

Nonlinear Deep Kernel Learning for Image Annotation.

PubMed

Jiu, Mingyuan; Sahbi, Hichem

2017-02-08

Multiple kernel learning (MKL) is a widely used technique for kernel design. Its principle consists in learning, for a given support vector classifier, the most suitable convex (or sparse) linear combination of standard elementary kernels. However, these combinations are shallow and often powerless to capture the actual similarity between highly semantic data, especially for challenging classification tasks such as image annotation. In this paper, we redefine multiple kernels using deep multi-layer networks. In this new contribution, a deep multiple kernel is recursively defined as a multi-layered combination of nonlinear activation functions, each one involves a combination of several elementary or intermediate kernels, and results into a positive semi-definite deep kernel. We propose four different frameworks in order to learn the weights of these networks: supervised, unsupervised, kernel-based semisupervised and Laplacian-based semi-supervised. When plugged into support vector machines (SVMs), the resulting deep kernel networks show clear gain, compared to several shallow kernels for the task of image annotation. Extensive experiments and analysis on the challenging ImageCLEF photo annotation benchmark, the COREL5k database and the Banana dataset validate the effectiveness of the proposed method.

The Importance of Three Physical Processes in a Minimal Three-Dimensional Tropical Cyclone Model.

NASA Astrophysics Data System (ADS)

Zhu, Hongyan; Smith, Roger K.

2002-06-01

The minimal three-dimensional tropical cyclone model developed by Zhu et al. is used to explore the role of shallow convection, precipitation-cooled downdrafts, and the vertical transport of momentum by deep convection on the dynamics of tropical cyclone intensification. The model is formulated in coordinates and has three vertical levels, one characterizing a shallow boundary layer, and the other two representing the upper and lower troposphere, respectively. It has three options for treating cumulus convection on the subgrid scale and a simple scheme for the explicit release of latent heat on the grid scale.In the model, as in reality, shallow convection transports air with low moist static energy from the lower troposphere to the boundary layer, stabilizing the atmosphere not only to itself, but also to deep convection. Also it moistens and cools the lower troposphere. For realistic parameter values, the stabilization in the vortex core region is the primary effect: it reduces the deep convective mass flux and therefore the rate of heating and drying in the troposphere. This reduced heating, together with the direct cooling of the lower troposphere by shallow convection, diminishes the buoyancy in the vortex core and thereby the vortex intensification rate.The effects of precipitation-cooled downdrafts depend on the closure scheme chosen for deep convection. In the two closures in which the deep cloud mass flux depends on the degree of convective instability, the downdrafts do not change the total mass flux of air that subsides into the boundary layer, but they carry air with a lower moist static energy into this layer than does subsidence outside downdrafts. As a result they decrease the rate of intensification during the early development stage. Nevertheless, by reducing the deep convective mass flux and the drying effect of compensating subsidence, they enable grid scale saturation, and therefore rapid intensification, to occur earlier than in calculations where they are excluded. In the closure in which the deep cloud mass flux depends on the mass convergence in the boundary layer, downdrafts reduce the gestation period and increase the intensification rate.Convective momentum transport as represented in the model weakens both the primary and secondary circulations of the vortex. However, it does not significantly reduce the maximum intensity attained after the period of rapid development. The weakening of the secondary circulation impedes vortex development and significantly prolongs the gestation period.Where possible the results are compared with those found in other studies.

Distributed modeling of diffusive solute transport in peritoneal dialysis.

PubMed

Waniewski, Jacek

2002-01-01

The diffusive transport between blood and an ex-tissue medium (dialysis fluid) is evaluated using a mathematical model that takes into account the (quasicontinuous) distribution of capillaries within the tissue at various distances from the tissue surface, and includes diffusive-convective transport through the capillary wall and lymphatic absorption from the tissue. General formulas for solute penetration depth, lambda, and for the diffusive mass transport coefficient for the transport between blood and dialysis fluid, K(BD), are provided in terms of local transport coefficients for capillary wall, tissue, and lymphatic absorption. For pure diffusive transport between blood and dialysis fluid and thick tissue layers (i.e., if the solute penetration depth is much lower than the tissue thickness) these formulas yield previously known expressions. It is shown that apparent tissue layers, with widths lambdaTBL and lambdaT, respectively, may be defined according to the values of local transport parameters in such a way that K(BD) is equal to the solute clearance K(TBL) from the tissue by blood and lymph for a layer with width lambdaTBL or to the solute clearance K(T) from blood to dialysate by diffusion through the tissue layer with width lambdaT. For tissue layers with width much higher than the penetration depth: lambdaT approximately = lambdaTBL approximately = lambda. These characteristic width lengths depend on the transport parameters (and thus on the size) of solutes. Effective blood flow, which may be related to the exchange of the solute between blood and dialysate, is defined using an analogy to the extraction/absorption coefficients for blood-tissue exchange. Various approximations for the distributed model formula for diffusive mass transport coefficient (K(BD)) are possible. The appropriate range for their application is obtained from the general formula.

A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo

PubMed Central

Chu, Jun; Oh, Young-Hee; Sens, Alex; Ataie, Niloufar; Dana, Hod; Macklin, John J.; Laviv, Tal; Welf, Erik S.; Dean, Kevin M.; Zhang, Feijie; Kim, Benjamin B.; Tang, Clement Tran; Hu, Michelle; Baird, Michelle A.; Davidson, Michael W.; Kay, Mark A.; Fiolka, Reto; Yasuda, Ryohei; Kim, Douglas S.; Ng, Ho-Leung; Lin, Michael Z.

2016-01-01

Orange-red fluorescent proteins (FPs) are widely used in biomedical research for multiplexed epifluorescence microscopy with GFP-based probes, but their different excitation requirements make multiplexing with new advanced microscopy methods difficult. Separately, orange-red FPs are useful for deep-tissue imaging in mammals due to the relative tissue transmissibility of orange-red light, but their dependence on illumination limits their sensitivity as reporters in deep tissues. Here we describe CyOFP1, a bright engineered orange-red FP that is excitable by cyan light. We show that CyOFP1 enables single-excitation multiplexed imaging with GFP-based probes in single-photon and two-photon microscopy, including time-lapse imaging in light-sheet systems. CyOFP1 also serves as an efficient acceptor for resonance energy transfer from the highly catalytic blue-emitting luciferase NanoLuc. An optimized fusion of CyOFP1 and NanoLuc, called Antares, functions as a highly sensitive bioluminescent reporter in vivo, producing substantially brighter signals from deep tissues than firefly luciferase and other bioluminescent proteins. PMID:27240196

The tropical precipitation pickup threshold and clouds in a radiative convective equilibrium model: 2. Two-layer moisture

NASA Astrophysics Data System (ADS)

Igel, Matthew R.

2017-06-01

This paper complements Part 1 in which cloud processes of aggregated convection are examined in a large-domain radiative convective equilibrium simulation in order to uncover those responsible for a consistently observed, abrupt increase in mean precipitation at a column relative humidity value of approximately 77%. In Part 2, the focus is on how the transition is affected independently by total moisture above and below the base of the melting layer. When mean precipitation rates are examined as simultaneous functions of these two moisture layers, four distinct behaviors are observed. These four behaviors suggest unique, yet familiar, physical regimes in which (i) little rain is produced by infrequent clouds, (ii) shallow convection produces increasing warm rain with increasing low-level moisture, (iii) deep convection produces progressively heavier rain above the transition point with increasing total moisture, and (iv) deep stratiform cloud produces increasingly intense precipitation from melting for increasing upper level moisture. The independent thresholds separating regimes in upper and lower layer humidity are shown to result in the value of total column humidity at which a transition between clear air and deep convection, and therefore a pickup in precipitation, is possible. All four regimes force atmospheric columns toward the pickup value at 77% column humidity, but each does so through a unique set of physical processes. Layer moisture and microphysical budgets are analyzed and contrasted with column budgets.

Differential Response of Human Adipose Tissue-Derived Mesenchymal Stem Cells, Dermal Fibroblasts, and Keratinocytes to Burn Wound Exudates: Potential Role of Skin-Specific Chemokine CCL27

PubMed Central

van den Broek, Lenie J.; Kroeze, Kim L.; Waaijman, Taco; Breetveld, Melanie; Sampat-Sardjoepersad, Shakun C.; Niessen, Frank B.; Middelkoop, Esther; Scheper, Rik J.

2014-01-01

Many cell-based regenerative medicine strategies toward tissue-engineered constructs are currently being explored. Cell–cell interactions and interactions with different biomaterials are extensively investigated, whereas very few studies address how cultured cells will interact with soluble wound-healing mediators that are present within the wound bed after transplantation. The aim of this study was to determine how adipose tissue-derived mesenchymal stem cells (ASC), dermal fibroblasts, and keratinocytes will react when they come in contact with the deep cutaneous burn wound bed. Burn wound exudates isolated from deep burn wounds were found to contain many cytokines, including chemokines and growth factors related to inflammation and wound healing. Seventeen mediators were identified by ELISA (concentration range 0.0006–9 ng/mg total protein), including the skin-specific chemokine CCL27. Burn wound exudates activated both ASC and dermal fibroblasts, but not keratinocytes, to increase secretion of CXCL1, CXCL8, CCL2, and CCL20. Notably, ASC but not fibroblasts or keratinocytes showed significant increased secretion of vascular endothelial growth factor (5-fold) and interleukin-6 (253-fold), although when the cells were incorporated in bi-layered skin substitute (SS) these differences were less pronounced. A similar discrepancy between ASC and dermal fibroblast mono-cultures was observed when recombinant human-CCL27 was used instead of burn wound exudates. Although CCL27 did not stimulate the secretion of any of the wound-healing mediators by keratinocytes, these cells, in contrast to ASC or dermal fibroblasts, showed increased proliferation and migration. Taken together, these results indicate that on transplantation, keratinocytes are primarily activated to promote wound closure. In contrast, dermal fibroblasts and, in particular, ASC respond vigorously to factors present in the wound bed, leading to increased secretion of angiogenesis/granulation tissue formation factors. Our findings have implications for the choice of cell type (ASC or dermal fibroblast) to be used in regenerative medicine strategies and indicate the importance of taking into account interactions with the wound bed when developing advanced therapies for difficult-to-close cutaneous wounds. PMID:23980822

Chondrocyte Differentiation of Human Endometrial Gland-Derived MSCs in Layered Cell Sheets

PubMed Central

Shimizu, Tatsuya; Yamato, Masayuki; Umezawa, Akihiro; Okano, Teruo

2013-01-01

Recently, regenerative medicine using engineered three-dimensional (3D) tissues has been focused. In the fields of cell therapy and regenerative medicine, mesenchymal stem cells (MSCs) are attractive autologous cell sources. While, in bioengineered tissues, a 3D environment may affect the differentiation of the stem cells, little is known regarding the effect of 3D environment on cellular differentiation. In this study, MSC differentiation in in vitro 3D tissue models was assessed by human endometrial gland-derived MSCs (hEMSCs) and cell sheet technology. hEMSC sheets were layered into cell-dense 3D tissues and were cultured on porous membranes. The tissue sections revealed that chondrocyte-like cells were found within the multilayered cell sheets even at 24 h after layering. Immunostainings of chondrospecific markers were positive within those cell sheet constructs. In addition, sulfated glycosaminoglycan accumulation within the tissues increased in proportion to the numbers of layered cell sheets. The findings suggested that a high cell density and hypoxic environment in 3D tissues by layering cell sheets might accelerate a rapid differentiation of hEMSCs into chondrocytes without the help of chondro-differentiation reagents. These tissue models using cell sheets would give new insights to stem cell differentiation in 3D environment and contribute to the future application of stem cells to cartilage regenerative therapy. PMID:24348153

Deep learning based classification for head and neck cancer detection with hyperspectral imaging in an animal model

NASA Astrophysics Data System (ADS)

Ma, Ling; Lu, Guolan; Wang, Dongsheng; Wang, Xu; Chen, Zhuo Georgia; Muller, Susan; Chen, Amy; Fei, Baowei

2017-03-01

Hyperspectral imaging (HSI) is an emerging imaging modality that can provide a noninvasive tool for cancer detection and image-guided surgery. HSI acquires high-resolution images at hundreds of spectral bands, providing big data to differentiating different types of tissue. We proposed a deep learning based method for the detection of head and neck cancer with hyperspectral images. Since the deep learning algorithm can learn the feature hierarchically, the learned features are more discriminative and concise than the handcrafted features. In this study, we adopt convolutional neural networks (CNN) to learn the deep feature of pixels for classifying each pixel into tumor or normal tissue. We evaluated our proposed classification method on the dataset containing hyperspectral images from 12 tumor-bearing mice. Experimental results show that our method achieved an average accuracy of 91.36%. The preliminary study demonstrated that our deep learning method can be applied to hyperspectral images for detecting head and neck tumors in animal models.

Intermittent vibration protects aged muscle from mechanical and oxidative damage under prolonged compression.

PubMed

Wong, Sing Wan; Cheung, Brian Chun Ho; Pang, Bruce Tak Keung; Kwong, Ateline; Chung, Anna; Lee, Kenneth Ka Ho; Mak, Arthur Fut Tak

2017-04-11

Deep tissue pressure ulcers, a serious clinical challenge originating in the muscle layer, are hardly detectable at the beginning. The challenge apparently occurs in aged subjects more frequently. As the ulcer propagates to the skin surface, it becomes very difficult to manage and can lead to fatal complications. Preventive measures are thus highly desirable. Although the complex pathological mechanisms have not been fully understood, prolonged and excessive physical challenges and oxidative stress are believed to be involved in the ulcer development. Previous reports have demonstrated that oxidative stress could compromise the mechanical properties of muscle cells, making them easier to be damaged when physical challenges are introduced. In this study, we used senescence accelerated (SAMP8) mice and its control breed (SAMR1) to examine the protective effects of intermittent vibration on aged and control muscle tissues during prolonged epidermal compression under 100mmHg for 6h. Results showed that an application of 35Hz, 0.25g intermittent vibration during compression decreased the compression-induced muscle breakdown in SAMP8 mice, as indicated histologically in terms of number of interstitial nuclei. The fact that no significant difference in muscle damage could be established in the corresponding groups in SAMR1 mice suggests that SAMR1 mice could better accommodate the compression insult than SAMP8 mice. Compression-induced oxidative damage was successfully curbed using intermittent vibration in SAMP8 mice, as indicated by 8-OHdG. A possible explanation is that the anti-oxidative defense could be maintained with intermittent vibration during compression. This was supported by the expression level of PGC-1-alpha, catalase, Gpx-1 and SOD1. Our data suggested intermittent vibration could serve as a preventive measure for deep tissue ulcer, particularly in aged subjects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Double seismic zone for deep earthquakes in the izu-bonin subduction zone.

PubMed

Iidaka, T; Furukawa, Y

1994-02-25

A double seismic zone for deep earthquakes was found in the Izu-Bonin region. An analysis of SP-converted phases confirms that the deep seismic zone consists of two layers separated by approximately 20 kilometers. Numerical modeling of the thermal structure implies that the hypocenters are located along isotherms of 500 degrees to 550 degrees C, which is consistent with the hypothesis that deep earthquakes result from the phase transition of metastable olivine to a high-pressure phase in the subducting slab.

Development and application of deep convolutional neural network in target detection

NASA Astrophysics Data System (ADS)

Jiang, Xiaowei; Wang, Chunping; Fu, Qiang

2018-04-01

With the development of big data and algorithms, deep convolution neural networks with more hidden layers have more powerful feature learning and feature expression ability than traditional machine learning methods, making artificial intelligence surpass human level in many fields. This paper first reviews the development and application of deep convolutional neural networks in the field of object detection in recent years, then briefly summarizes and ponders some existing problems in the current research, and the future development of deep convolutional neural network is prospected.

The Sinking and Spreading of The Antarctic Deep Ice Shelf Water In The Ross Sea Studied By In Situ Observaions and Numerical Modeling

NASA Astrophysics Data System (ADS)

Rubino, A.; Budillon, G.; Pierini, S.; Spezie, G.

The sinking and spreading of the Deep Ice Shelf Water (DISW) in the Ross Sea are analyzed using in situ observations and the results of a nonlinear, reduced-gravity, frontal layered numerical "plume" model which is able to simulate the motion of a bottom-arrested current over realistic topography. The model is forced by prescribing the thickness of the DISW vein as well as its density structure at the southern model boundary. The ambient temperature and salinity are imposed using hydrographic data acquired by the Italian PNRA-CLIMA project. In the model water of the quiescent ambient ocean is allowed to entrain in the active deep layer due to a simple param- eterization of turbulent mixing. The importance of forcing the model with a realistic ambient density is demonstrated by carrying out a numerical simulation in which the bottom active layer is forced using an idealized ambient density. In a more realis- tic simulation the path and the density structure of the DISW vein flowing over the Challenger Basin are obtained and are found to be in good agreement with data. The evolution of the deep current beyond the continental shelf is also simulated. It provides useful information on the water flow and mixing in a region of the Ross Sea where the paucity of experimental data does not allow for a detailed description of the deep ocean dynamics.

In-situ Observations of Mid-latitude Forest Fire Plumes Deep in the Stratosphere

NASA Technical Reports Server (NTRS)

Jost, Hans-Juerg; Drdla, Katja; Stohl, Andreas; Pfister, Leonhard; Loewenstein, Max; Lopez, Jimena P.; Hudson, Paula K.; Murphy, Daniel M.; Cziczo, Daniel J.; Fromm, Michael

2004-01-01

We observed a plume of air highly enriched in carbon monoxide and particles in the stratosphere at altitudes up to 15.8 km. It can be unambiguously attributed to North American forest fires. This plume demonstrates an extratropical direct transport path from the planetary boundary layer several kilometers deep into the stratosphere, which is not fully captured by large-scale atmospheric transport models. This process indicates that the stratospheric ozone layer could be sensitive to changes in forest burning associated with climatic warming.

Comparison of the Deep Optic Nerve Head Structure between Normal-Tension Glaucoma and Nonarteritic Anterior Ischemic Optic Neuropathy.

PubMed

Lee, Eun Ji; Choi, Yun Jeong; Kim, Tae-Woo; Hwang, Jeong-Min

2016-01-01

To compare the deep optic nerve head (ONH) structure between normal-tension glaucoma (NTG) and nonarteritic anterior ischemic optic neuropathy (NAION) and also in healthy subjects as a control using enhanced depth imaging (EDI) spectral-domain optical coherence tomography (SD-OCT). This prospective cross-sectional study included 21 NAION patients who had been diagnosed as NAION at least 6 months prior to study entry, and 42 NTG patients and 42 healthy controls who were matched with NAION patients in terms of age, intraocular pressure (IOP), and optic disc area. The retinal nerve fiber layer (RNFL) thickness in the affected sector was also matched between NAION and NTG patients. The ONH was imaged using SD-OCT with the EDI technique. The anterior lamina cribrosa surface depth (LCD) and average prelaminar tissue (PT) thickness were measured in a sector of interest in each eye and compared among the three groups. In the sector-matched comparison, LCD was largest in NTG patients, followed by NAION patients, while PT was thinner in NTG patients than in NAION patients (all P < 0.001). NAION patients had a comparable LCD and a thinner PT relative to normal controls (P = 0.170 and < 0.001, respectively). The deep ONH configuration is strikingly different between NTG and NAION. The differing features provide comparative insight into the pathophysiology of the two diseases, and may be useful for differential diagnosis.

Two-layer tissue engineered urethra using oral epithelial and muscle derived cells.

PubMed

Mikami, Hiroshi; Kuwahara, Go; Nakamura, Nobuyuki; Yamato, Masayuki; Tanaka, Masatoshi; Kodama, Shohta

2012-05-01

We fabricated novel tissue engineered urethral grafts using autologously harvested oral cells. We report their viability in a canine model. Oral tissues were harvested by punch biopsy and divided into mucosal and muscle sections. Epithelial cells from mucosal sections were cultured as epithelial cell sheets. Simultaneously muscle derived cells were seeded on collagen mesh matrices to form muscle cell sheets. At 2 weeks the sheets were joined and tubularized to form 2-layer tissue engineered urethras, which were autologously grafted to surgically induced urethral defects in 10 dogs in the experimental group. Tissue engineered grafts were not applied to the induced urethral defect in control dogs. The dogs were followed 12 weeks postoperatively. Urethrogram and histological examination were done to evaluate the grafting outcome. We successfully fabricated 2-layer tissue engineered urethras in vitro and transplanted them in dogs in the experimental group. The 12-week complication-free rate was significantly higher in the experimental group than in controls. Urethrogram confirmed urethral patency without stricture in the complication-free group at 12 weeks. Histologically urethras in the transplant group showed a stratified epithelial layer overlying well differentiated submucosa. In contrast, urethras in controls showed severe fibrosis without epithelial layer formation. Two-layer tissue engineered urethras were engineered using cells harvested by minimally invasive oral punch biopsy. Results suggest that this technique can encourage regeneration of a functional urethra. Copyright © 2012 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

3D Printing of Human Tissue Mimics via Layer-by-Layer Assembly of Polymer/Hydrogel Biopapers

NASA Astrophysics Data System (ADS)

Ringeisen, Bradley

2015-03-01

The foundations of tissue engineering were built on two fundamental areas of research: cells and scaffolds. Multipotent cells and their derivatives are traditionally randomly seeded into sophisticated polymer or hydrogel scaffolds, ultimately with the goal of forming a tissue-like material through cell differentiation and cell-material interactions. One problem with this approach is that no matter how complex or biomimetic the scaffold is, the cells are still homogeneously distributed throughout this three dimensional (3D) material. Natural tissue is inherently heterogeneous on both a microscopic and macroscopic level. It also contains different types of cells in close proximity, extracellular matrix, voids, and a complex vascularized network. Recently developed 3D cell and organ printers may be able to enhance traditional tissue engineering experiments by building scaffolds layer-by-layer that are crafted to mimic the microscopic and macroscopic structure of natural tissue or organs. Over the past decade, my laboratory has developed a capillary-free, live cell printer termed biological laser printing, or BioLP. We find that printed cells do not express heat shock protein and retain >99% viability. Printed cells also incur no DNA strand fracture and preserve their ability to differentiate. Recent work has used a layer-by-layer approach, stacking sheets of hybrid polymer/hydrogel biopapers in conjunction with live cell printing to create 3D tissue structures. Our specific work is now focused on the blood-brain-barrier and air-lung interface and will be described during the presentation.

Laminar activity in the hippocampus and entorhinal cortex related to novelty and episodic encoding

PubMed Central

Maass, Anne; Schütze, Hartmut; Speck, Oliver; Yonelinas, Andrew; Tempelmann, Claus; Heinze, Hans-Jochen; Berron, David; Cardenas-Blanco, Arturo; Brodersen, Kay H.; Enno Stephan, Klaas; Düzel, Emrah

2014-01-01

The ability to form long-term memories for novel events depends on information processing within the hippocampus (HC) and entorhinal cortex (EC). The HC–EC circuitry shows a quantitative segregation of anatomical directionality into different neuronal layers. Whereas superficial EC layers mainly project to dentate gyrus (DG), CA3 and apical CA1 layers, HC output is primarily sent from pyramidal CA1 layers and subiculum to deep EC layers. Here we utilize this directionality information by measuring encoding activity within HC/EC subregions with 7 T high resolution functional magnetic resonance imaging (fMRI). Multivariate Bayes decoding within HC/EC subregions shows that processing of novel information most strongly engages the input structures (superficial EC and DG/CA2–3), whereas subsequent memory is more dependent on activation of output regions (deep EC and pyramidal CA1). This suggests that while novelty processing is strongly related to HC–EC input pathways, the memory fate of a novel stimulus depends more on HC–EC output. PMID:25424131

Combined Monte Carlo and path-integral method for simulated library of time-resolved reflectance curves from layered tissue models

NASA Astrophysics Data System (ADS)

Wilson, Robert H.; Vishwanath, Karthik; Mycek, Mary-Ann

2009-02-01

Monte Carlo (MC) simulations are considered the "gold standard" for mathematical description of photon transport in tissue, but they can require large computation times. Therefore, it is important to develop simple and efficient methods for accelerating MC simulations, especially when a large "library" of related simulations is needed. A semi-analytical method involving MC simulations and a path-integral (PI) based scaling technique generated time-resolved reflectance curves from layered tissue models. First, a zero-absorption MC simulation was run for a tissue model with fixed scattering properties in each layer. Then, a closed-form expression for the average classical path of a photon in tissue was used to determine the percentage of time that the photon spent in each layer, to create a weighted Beer-Lambert factor to scale the time-resolved reflectance of the simulated zero-absorption tissue model. This method is a unique alternative to other scaling techniques in that it does not require the path length or number of collisions of each photon to be stored during the initial simulation. Effects of various layer thicknesses and absorption and scattering coefficients on the accuracy of the method will be discussed.

An algorithm for sensing venous oxygenation using ultrasound-modulated light enhanced by microbubbles

NASA Astrophysics Data System (ADS)

Honeysett, Jack E.; Stride, Eleanor; Deng, Jing; Leung, Terence S.

2012-02-01

Near-infrared spectroscopy (NIRS) can provide an estimate of the mean oxygen saturation in tissue. This technique is limited by optical scattering, which reduces the spatial resolution of the measurement, and by absorption, which makes the measurement insensitive to oxygenation changes in larger deep blood vessels relative to that in the superficial tissue. Acousto-optic (AO) techniques which combine focused ultrasound (US) with diffuse light have been shown to improve the spatial resolution as a result of US-modulation of the light signal, however this technique still suffers from low signal-to-noise when detecting a signal from regions of high optical absorption. Combining an US contrast agent with this hybrid technique has been proposed to amplify an AO signal. Microbubbles are a clinical contrast agent used in diagnostic US for their ability to resonate in a sound field: in this work we also make use of their optical scattering properties (modelled using Mie theory). A perturbation Monte Carlo (pMC) model of light transport in a highly absorbing blood vessel containing microbubbles surrounded by tissue is used to calculate the AO signal detected on the top surface of the tissue. An algorithm based on the modified Beer-Lambert law is derived which expresses intravenous oxygen saturation in terms of an AO signal. This is used to determine the oxygen saturation in the blood vessel from a dual wavelength microbubble-contrast AO measurement. Applying this algorithm to the simulation data shows that the venous oxygen saturation is accurately recovered, and this measurement is robust to changes in the oxygenation of the superficial tissue layer.

Evaluation of the tissue reaction to a new bilayered collagen matrix in vivo and its translation to the clinic.

PubMed

Ghanaati, Shahram; Schlee, Markus; Webber, Matthew J; Willershausen, Ines; Barbeck, Mike; Balic, Ela; Görlach, Christoph; Stupp, Samuel I; Sader, Robert A; Kirkpatrick, C James

2011-02-01

This study evaluates a new collagen matrix that is designed with a bilayered structure in order to promote guided tissue regeneration and integration within the host tissue. This material induced a mild tissue reaction when assessed in a murine model and was well integrated within the host tissue, persisting in the implantation bed throughout the in vivo study. A more porous layer was rapidly infiltrated by host mesenchymal cells, while a layer designed to be a barrier allowed cell attachment and host tissue integration, but at the same time remained impermeable to invading cells for the first 30 days of the study. The tissue reaction was favorable, and unlike a typical foreign body response, did not include the presence of multinucleated giant cells, lymphocytes, or granulation tissue. In the context of translation, we show preliminary results from the clinical use of this biomaterial applied to soft tissue regeneration in the treatment of gingival tissue recession and exposed roots of human teeth. Such a condition would greatly benefit from guided tissue regeneration strategies. Our findings demonstrate that this material successfully promoted the ingrowth of gingival tissue and reversed gingival tissue recession. Of particular importance is the fact that the histological evidence from these human studies corroborates our findings in the murine model, with the barrier layer preventing unspecific tissue ingrowth, as the scaffold becomes infiltrated by mesenchymal cells from adjacent tissue into the porous layer. Also in the clinical situation no multinucleated giant cells, no granulation tissue and no evidence of a marked inflammatory response were observed. In conclusion, this bilayered matrix elicits a favorable tissue reaction, demonstrates potential as a barrier for preferential tissue ingrowth, and achieves a desirable therapeutic result when applied in humans for soft tissue regeneration.

Implication of Broadband Dispersion Measurements in Constraining Upper Mantle Velocity Structures

NASA Astrophysics Data System (ADS)

Kuponiyi, A.; Kao, H.; Cassidy, J. F.; Darbyshire, F. A.; Dosso, S. E.; Gosselin, J. M.; Spence, G.

2017-12-01

Dispersion measurements from earthquake (EQ) data are traditionally inverted to obtain 1-D shear-wave velocity models, which provide information on deep earth structures. However, in many cases, EQ-derived dispersion measurements lack short-period information, which theoretically should provide details of shallow structures. We show that in at least some cases short-period information, such as can be obtained from ambient seismic noise (ASN) processing, must be combined with EQ dispersion measurements to properly constrain deeper (e.g. upper-mantle) structures. To verify this, synthetic dispersion data are generated using hypothetical velocity models under four scenarios: EQ only (with and without deep low-velocity layers) and combined EQ and ASN data (with and without deep low-velocity layers). The now "broadband" dispersion data are inverted using a trans-dimensional Bayesian framework with the aim of recovering the initial velocity models and assessing uncertainties. Our results show that the deep low-velocity layer could only be recovered from the inversion of the combined ASN-EQ dispersion measurements. Given this result, we proceed to describe a method for obtaining reliable broadband dispersion measurements from both ASN and EQ and show examples for real data. The implication of this study in the characterization of lithospheric and upper mantle structures, such as the Lithosphere-Asthenosphere Boundary (LAB), is also discussed.

Optical coherence tomography angiography indicates associations of the retinal vascular network and disease activity in multiple sclerosis.

PubMed

Feucht, Nikolaus; Maier, Mathias; Lepennetier, Gildas; Pettenkofer, Moritz; Wetzlmair, Carmen; Daltrozzo, Tanja; Scherm, Pauline; Zimmer, Claus; Hoshi, Muna-Miriam; Hemmer, Bernhard; Korn, Thomas; Knier, Benjamin

2018-01-01

Patients with multiple sclerosis (MS) and clinically isolated syndrome (CIS) may show alterations of retinal layer architecture as measured by optical coherence tomography. Little is known about changes in the retinal vascular network during MS. To characterize retinal vessel structures in patients with MS and CIS and to test for associations with MS disease activity. In all, 42 patients with MS or CIS and 50 healthy controls underwent retinal optical coherence tomography angiography (OCT-A) with analysis of the superficial and deep vascular plexuses and the choriocapillaries. We tested OCT-A parameters for associations with retinal layer volumes, history of optic neuritis (ON), and the retrospective disease activity. Inner retinal layer volumes correlated positively with the density of both the superficial and deep vascular plexuses. Eyes of MS/CIS patients with a history of ON revealed reduced vessel densities of the superficial and deep vascular plexuses as compared to healthy controls. Higher choriocapillary vessel densities were associated with ongoing inflammatory disease activity during 24 months prior to OCT-A examination in MS and CIS patients. Optic neuritis is associated with rarefaction of the superficial and deep retinal vessels. Alterations of the choriocapillaries might be linked to disease activity in MS.

Intraspecific variation in the use of water sources by the circum-Mediterranean conifer Pinus halepensis.

PubMed

Voltas, Jordi; Lucabaugh, Devon; Chambel, Maria Regina; Ferrio, Juan Pedro

2015-12-01

The relevance of interspecific variation in the use of plant water sources has been recognized in drought-prone environments. By contrast, the characterization of intraspecific differences in water uptake patterns remains elusive, although preferential access to particular soil layers may be an important adaptive response for species along aridity gradients. Stable water isotopes were analysed in soil and xylem samples of 56 populations of the drought-avoidant conifer Pinus halepensis grown in a common garden test. We found that most populations reverted to deep soil layers as the main plant water source during seasonal summer droughts. More specifically, we detected a clear geographical differentiation among populations in water uptake patterns even under relatively mild drought conditions (early autumn), with populations originating from more arid regions taking up more water from deep soil layers. However, the preferential access to deep soil water was largely independent of aboveground growth. Our findings highlight the high plasticity and adaptive relevance of the differential access to soil water pools among Aleppo pine populations. The observed ecotypic patterns point to the adaptive relevance of resource investment in deep roots as a strategy towards securing a source of water in dry environments for P. halepensis. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Deep level defects in dilute GaAsBi alloys grown under intense UV illumination

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

Mooney, P. M.; Tarun, Marianne; Beaton, D. A.

2016-07-21

Dilute GaAs1-xBix alloys exhibiting narrow band edge photoluminescence (PL) were recently grown by molecular beam epitaxy (MBE) with the growth surface illuminated by intense UV radiation. To investigate whether the improved optical quality of these films results from a reduction in the concentration of deep level defects, p+/n and n+/p junction diodes were fabricated on both the illuminated and dark areas of several samples. Deep Level Transient Spectroscopy (DLTS) measurements show that the illuminated and dark areas of both the n- and p-type GaAs1-xBix epi-layers have similar concentrations of near mid-gap electron and hole traps, in the 1015 cm-3 range.more » Thus the improved PL spectra cannot be explained by a reduction in non-radiative recombination at deep level defects. We note that carrier freeze-out above 35 K is significantly reduced in the illuminated areas of the p-type GaAs1-xBix layers compared to the dark areas, allowing the first DLTS measurements of defect energy levels close to the valence band edge. These defect levels may account for differences in the PL spectra from the illuminated and dark areas of un-doped layers with a similar Bi fraction.« less

Deep Networks Can Resemble Human Feed-forward Vision in Invariant Object Recognition

PubMed Central

Kheradpisheh, Saeed Reza; Ghodrati, Masoud; Ganjtabesh, Mohammad; Masquelier, Timothée

2016-01-01

Deep convolutional neural networks (DCNNs) have attracted much attention recently, and have shown to be able to recognize thousands of object categories in natural image databases. Their architecture is somewhat similar to that of the human visual system: both use restricted receptive fields, and a hierarchy of layers which progressively extract more and more abstracted features. Yet it is unknown whether DCNNs match human performance at the task of view-invariant object recognition, whether they make similar errors and use similar representations for this task, and whether the answers depend on the magnitude of the viewpoint variations. To investigate these issues, we benchmarked eight state-of-the-art DCNNs, the HMAX model, and a baseline shallow model and compared their results to those of humans with backward masking. Unlike in all previous DCNN studies, we carefully controlled the magnitude of the viewpoint variations to demonstrate that shallow nets can outperform deep nets and humans when variations are weak. When facing larger variations, however, more layers were needed to match human performance and error distributions, and to have representations that are consistent with human behavior. A very deep net with 18 layers even outperformed humans at the highest variation level, using the most human-like representations. PMID:27601096

Simultaneous signal reconstruction from both superficial and deep tissue for fNIRS using depth-selective filtering method

NASA Astrophysics Data System (ADS)

Fujii, M.

2017-07-01

Two variations of a depth-selective back-projection filter for functional near-infrared spectroscopy (fNIRS) systems are introduced. The filter comprises a depth-selective algorithm that uses inverse problems applied to an optically diffusive multilayer medium. In this study, simultaneous signal reconstruction of both superficial and deep tissue from fNIRS experiments of the human forehead using a prototype of a CW-NIRS system is demonstrated.

Numerical experiments with a wind- and buoyancy-driven two-and-a-half-layer upper ocean model

NASA Astrophysics Data System (ADS)

Cherniawsky, J. Y.; Yuen, C. W.; Lin, C. A.; Mysak, L. A.

1990-09-01

We describe numerical experiments with a limited domain (15°-67°N, 65° west to east) coarse-resolution two-and-a-half-layer upper ocean model. The model consists of two active variable density layers: a Niiler and Kraus (1977) type mixed layer and a pycnocline layer, which overlays a semipassive deep ocean. The mixed layer is forced with a cosine wind stress and Haney type heat and precipitation-evaporation fluxes, which were derived from zonally averaged climatological (Levitus, 1982) surface temperatures and salinities for the North Atlantic. The second layer is forced from below with (1) Newtonian cooling to climatological temperatures and salinities at the lower boundary, (2) convective adjustment, which occurs whenever the density of the second layer is unstable with respect to climatology, and (3) mass entrainment in areas of strong upwelling, when the deep ocean ventilates through the bottom surface. The sensitivity of this model to changes in its internal (mixed layer) and external (e.g., a Newtonian coupling coefficient) parameters is investigated and compared to the results from a control experiment. We find that the model is not overly sensitive to changes in most of the parameters that were tested, albeit these results may depend to some extent on the choice of the control experiment.

The laminar structure of the common opossum masseter (Didelphis marsupialis).

PubMed

Deguchi, T; Takemura, A; Suwa, F

2001-03-01

Using three heads of the common opossum (Didelphis marsupialis), which may be considered to have a primitive mammalian form and therefore be appropriate for this study, the laminar structure of the masseter was investigated. We also attempted a comparative anatomical study of the relationships of food habits to the laminar structures of the masseter, zygomatic arch and mandibular ramus. In the common opossum masseter, a total of six layers, the primary and secondary sublayers of the superficial layer, the intermediate layer, and the primary, secondary and third sublayers of the deep layer as a proper masseter, were observed. These layers showed a typical reverse laminar structure, with the layers of tendons and muscles alternating. The maxillomandibularis and zygomaticomandibularis muscles were observed in one layer each, as an improper masseter. The laminar structure of the common opossum masseter was shown to be more similar to that of carnivorous placental animals than that of the herbivorous red kangaroo, a similar marsupial. In regard to the number of layers in the laminar structure of the masseter, the results of both this study and those of our predecessors' showed that differences in food habits affect the deep layer in the proper masseter of marsupials and placental mammals, and that of the maxillomandibularis muscle of placental mammals in the improper masseter.

Breaking the acoustic diffraction limit via nonlinear effect and thermal confinement for potential deep-tissue high-resolution imaging

PubMed Central

Yuan, Baohong; Pei, Yanbo; Kandukuri, Jayanth

2013-01-01

Our recently developed ultrasound-switchable fluorescence (USF) imaging technique showed that it was feasible to conduct high-resolution fluorescence imaging in a centimeter-deep turbid medium. Because the spatial resolution of this technique highly depends on the ultrasound-induced temperature focal size (UTFS), minimization of UTFS becomes important for further improving the spatial resolution USF technique. In this study, we found that UTFS can be significantly reduced below the diffraction-limited acoustic intensity focal size via nonlinear acoustic effects and thermal confinement by appropriately controlling ultrasound power and exposure time, which can be potentially used for deep-tissue high-resolution imaging. PMID:23479498

Evidence of nutrient partitioning in coexisting deep-sea echinoids, and seasonal dietary shifts in seasonal breeders: Perspectives from stable isotope analyses

NASA Astrophysics Data System (ADS)

Stevenson, Angela; Mitchell, Fraser J. G.

2016-02-01

The role of nutrition in echinoid growth and reproduction, as well as the mechanisms utilized to cope with food limitations in the deep sea remains under studied. We investigate echinoid feeding mechanisms within deep-sea submarine canyons in the NE Atlantic using a stable-isotope approach. Ten echinoid species were collected with a remotely operated vehicle. δ13C and δ15N stable isotope analyses (SIA) were conducted on echinoid tissues in order to investigate food sources assimilated with respect to nutrient partitioning between coexisting taxa, and seasonal dietary changes in food supply. Gut content analysis was conducted in conjunction with SIA. Echinoid taxa spanned three benthic trophic levels. This large trophic range might suggest an expansion of the trophic niches of echinoid taxa possibly to reduce interspecific competition for limited food resources. Evidence of nutrient partitioning among coexisting taxa was also found in the carbon data. Significant interspecific differences were found in the δ13C signatures of the somatic and reproductive tissues suggesting that different sources of carbon are assimilated into all tissues after the deposition of phytodetritus has taken place on the deep sea floor. However, this pattern differed for the data obtained before the deposition of phytodetritus; similar sources of carbon were assimilated into somatic tissues of different taxa, while some of these different taxa utilized significantly different sources of carbon to manufacture their reproductive tissues. While specific food sources could not be resolved from the carbon data of the present study, enriched δ15N values suggest that echinoids incorporate foods with distinctly higher δ15N values than that of POM and sediment, which could result from opportunistic feeding as well as bioerosion of the live coral framework and consequent grazing of fauna attached to the dead coral infrastructure. Seasonally deposited phytodetritus was incorporated into the reproductive tissues of the seasonal breeder, Gracilechinus alexandri, but not those of continuous breeders, Cidaroida and Echinothurioida. The material however was also found to support somatic tissue growth in cidaroids. These results suggest that seasonal breeders might utilize surface-derived phytodetritus to manufacture reproductive tissues, while continuous breeders might only utilize it for somatic tissue growth or not at all. Results for seasonal dietary shifts were compromised by poor spatial repeatability and thus require further investigation to understand better the role of phytodetritus in fuelling the growth and reproduction of deep-sea echinoids.

Shaping field for deep tissue microscopy

NASA Astrophysics Data System (ADS)

Colon, J.; Lim, H.

2015-05-01

Information capacity of a lossless image-forming system is a conserved property determined by two imaging parameters - the resolution and the field of view (FOV). Adaptive optics improves the former by manipulating the phase, or wavefront, in the pupil plane. Here we describe a homologous approach, namely adaptive field microscopy, which aims to enhance the FOV by controlling the phase, or defocus, in the focal plane. In deep tissue imaging, the useful FOV can be severely limited if the region of interest is buried in a thick sample and not perpendicular to the optic axis. One must acquire many z-scans and reconstruct by post-processing, which exposes tissue to excessive radiation and is also time consuming. We demonstrate the effective FOV can be substantially enhanced by dynamic control of the image plane. Specifically, the tilt of the image plane is continuously adjusted in situ to match the oblique orientation of the sample plane within tissue. The utility of adaptive field microscopy is tested for imaging tissue with non-planar morphology. Ocular tissue of small animals was imaged by two-photon excited fluorescence. Our results show that adaptive field microscopy can utilize the full FOV. The freedom to adjust the image plane to account for the geometrical variations of sample could be extremely useful for 3D biological imaging. Furthermore, it could facilitate rapid surveillance of cellular features within deep tissue while avoiding photo damages, making it suitable for in vivo imaging.

A computational framework for the detection of subcortical brain dysmaturation in neonatal MRI using 3D Convolutional Neural Networks.

PubMed

Ceschin, Rafael; Zahner, Alexandria; Reynolds, William; Gaesser, Jenna; Zuccoli, Giulio; Lo, Cecilia W; Gopalakrishnan, Vanathi; Panigrahy, Ashok

2018-05-21

Deep neural networks are increasingly being used in both supervised learning for classification tasks and unsupervised learning to derive complex patterns from the input data. However, the successful implementation of deep neural networks using neuroimaging datasets requires adequate sample size for training and well-defined signal intensity based structural differentiation. There is a lack of effective automated diagnostic tools for the reliable detection of brain dysmaturation in the neonatal period, related to small sample size and complex undifferentiated brain structures, despite both translational research and clinical importance. Volumetric information alone is insufficient for diagnosis. In this study, we developed a computational framework for the automated classification of brain dysmaturation from neonatal MRI, by combining a specific deep neural network implementation with neonatal structural brain segmentation as a method for both clinical pattern recognition and data-driven inference into the underlying structural morphology. We implemented three-dimensional convolution neural networks (3D-CNNs) to specifically classify dysplastic cerebelli, a subset of surface-based subcortical brain dysmaturation, in term infants born with congenital heart disease. We obtained a 0.985 ± 0. 0241-classification accuracy of subtle cerebellar dysplasia in CHD using 10-fold cross-validation. Furthermore, the hidden layer activations and class activation maps depicted regional vulnerability of the superior surface of the cerebellum, (composed of mostly the posterior lobe and the midline vermis), in regards to differentiating the dysplastic process from normal tissue. The posterior lobe and the midline vermis provide regional differentiation that is relevant to not only to the clinical diagnosis of cerebellar dysplasia, but also genetic mechanisms and neurodevelopmental outcome correlates. These findings not only contribute to the detection and classification of a subset of neonatal brain dysmaturation, but also provide insight to the pathogenesis of cerebellar dysplasia in CHD. In addition, this is one of the first examples of the application of deep learning to a neuroimaging dataset, in which the hidden layer activation revealed diagnostically and biologically relevant features about the clinical pathogenesis. The code developed for this project is open source, published under the BSD License, and designed to be generalizable to applications both within and beyond neonatal brain imaging. Copyright © 2018 Elsevier Inc. All rights reserved.

Frequency preference and attention effects across cortical depths in the human primary auditory cortex.

PubMed

De Martino, Federico; Moerel, Michelle; Ugurbil, Kamil; Goebel, Rainer; Yacoub, Essa; Formisano, Elia

2015-12-29

Columnar arrangements of neurons with similar preference have been suggested as the fundamental processing units of the cerebral cortex. Within these columnar arrangements, feed-forward information enters at middle cortical layers whereas feedback information arrives at superficial and deep layers. This interplay of feed-forward and feedback processing is at the core of perception and behavior. Here we provide in vivo evidence consistent with a columnar organization of the processing of sound frequency in the human auditory cortex. We measure submillimeter functional responses to sound frequency sweeps at high magnetic fields (7 tesla) and show that frequency preference is stable through cortical depth in primary auditory cortex. Furthermore, we demonstrate that-in this highly columnar cortex-task demands sharpen the frequency tuning in superficial cortical layers more than in middle or deep layers. These findings are pivotal to understanding mechanisms of neural information processing and flow during the active perception of sounds.

Effect of inversion layer at iron pyrite surface on photovoltaic device

NASA Astrophysics Data System (ADS)

Uchiyama, Shunsuke; Ishikawa, Yasuaki; Uraoka, Yukiharu

2018-03-01

Iron pyrite has great potential as a thin-film solar cell material because it has high optical absorption, low cost, and is earth-abundant. However, previously reported iron pyrite solar cells showed poor photovoltaic characteristics. Here, we have numerically simulated its photovoltaic characteristics and band structures by utilizing a two-dimensional (2D) device simulator, ATLAS, to evaluate the effects of an inversion layer at the surface and a high density of deep donor defect states in the bulk. We found that previous device structures did not consider the inversion layer at the surface region of iron pyrite, which made it difficult to obtain the conversion efficiency. Therefore, we remodeled the device structure and suggested that removing the inversion layer and reducing the density of deep donor defect states would lead to a high conversion efficiency of iron pyrite solar cells.

Predictive validity of granulation tissue color measured by digital image analysis for deep pressure ulcer healing: a multicenter prospective cohort study.

PubMed

Iizaka, Shinji; Kaitani, Toshiko; Sugama, Junko; Nakagami, Gojiro; Naito, Ayumi; Koyanagi, Hiroe; Konya, Chizuko; Sanada, Hiromi

2013-01-01

This multicenter prospective cohort study examined the predictive validity of granulation tissue color evaluated by digital image analysis for deep pressure ulcer healing. Ninety-one patients with deep pressure ulcers were followed for 3 weeks. From a wound photograph taken at baseline, an image representing the granulation red index (GRI) was processed in which a redder color represented higher values. We calculated the average GRI over granulation tissue and the proportion of pixels exceeding the threshold intensity of 80 for the granulation tissue surface (%GRI80) and wound surface (%wound red index 80). In the receiver operating characteristics curve analysis, most GRI parameters had adequate discriminative values for both improvement of the DESIGN-R total score and wound closure. Ulcers were categorized by the obtained cutoff points of the average GRI (≤80, >80), %GRI80 (≤55, >55-80, >80%), and %wound red index 80 (≤25, >25-50, >50%). In the linear mixed model, higher classes for all GRI parameters showed significantly greater relative improvement in overall wound severity during the 3 weeks after adjustment for patient characteristics and wound locations. Assessment of granulation tissue color by digital image analysis will be useful as an objective monitoring tool for granulation tissue quality or surrogate outcomes of pressure ulcer healing. © 2012 by the Wound Healing Society.

A multilayer scaffold design with spatial arrangement of cells to modulate esophageal tissue growth.

PubMed

Soliman, Sherif; Laurent, Julie; Kalenjian, Lena; Burnette, Kalia; Hedberg, Bert; La Francesca, Saverio

2018-05-02

Esophageal diseases may require resectioning of the damaged portion. The current standard of care requires the replacement of the esophagus with the stomach or the intestine. Such procedures have high rates of mortality and morbidity; therefore, the use of alternative conduits is needed. A tissue engineering approach that allows for the regeneration of esophageal tissues would have significant clinical application. A cell-seeded synthetic scaffold could replace the resected part of the esophagus and elicit tissue regrowth. In order to ideally recreate a functioning esophagus, its two crucial tissue layers should be induced: an epithelium on the luminal surface and a muscle layer on the exterior surface. To create a bioengineered esophagus with both tissue layers, a multilayer (ML) tubular scaffold design was considered. Luminal and exterior layers were electrospun with broad pore size to promote penetration and proliferation of mesenchymal stem cells on the lumen and smooth muscle cells on the external. These two layers would be separated by a thin layer with substantially narrower pore size intended to act as a barrier for the two cell types. This ML scaffold design was achieved via electrospinning by tuning the solution and the process parameters. Analysis of the scaffold demonstrated that this tuning enabled the production of three integrated layers with distinguishable microstructures and good mechanical integrity. In vitro validation was conducted on the separated unilayer components of the ML scaffold. The resultant proof-of-concept ML scaffold design could possibly support the spatial arrangement of cells needed to promote esophageal tissue regeneration. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2018. © 2018 Wiley Periodicals, Inc.

Acoustic properties of healthy and reconstructed cleft lip

NASA Astrophysics Data System (ADS)

Thijssen, Johan M.; van Hees, Nancy J.; Weijers, Gert G.; Huyskens, Rinske W.; Nillesen, Maartje; Katsaros, Christos; de Korte, Chris L.

2006-03-01

The feasibility of echographic imaging of the tissues in healthy lip and in reconstructed cleft lip and estimating the dimensions and the normalized echo level of these tissues is investigated. Echographic images of the upper lip were made with commercial medical ultrasound equipment, using a linear array transducer (7-11 MHz bandwidth) and a non-contact gel coupling. Tissue dimensions were measured by means of software calipers. Echo levels were calibrated and corrected for beam characteristics, gel path and tissue attenuation by using a tissue-mimicking phantom. At central position of philtrum, mean thickness (and standard deviation) of lip loose connective tissue layer, orbicularis oris muscle and dense connective layer was 4.0 (sd 0.1) mm, 2.3 (sd 0.7) mm, 2.2 (sd 0.7) mm, respectively, in healthy lip at rest. Mean (sd) echo level of muscle and dense connective tissue layer with respect to echo level of lip loose connective tissue layer was in relaxed condition: - 19.3 (sd 0.6) dB and - 10.7 (sd 4.0) dB, respectively. Echo level of loose connective tissue layer was +25.6 (sd 4.2) dB relative to phantom echo level obtained in the focus of the transducer. Color mode echo images were calculated, after adaptive filtering of the images, which show the tissues in separate colors and highlight the details of healthy lip and reconstructed cleft lip. Quantitative assessment of thickness and echo level of various lip tissues is feasible after proper calibration of the echographic equipment. Diagnostic potentials of the developed quantitative echographic techniques for non-invasive evaluation of the outcome of cleft lip reconstruction are promising.

Surface plasmon coupling for suppressing p-GaN absorption and TM-polarized emission in a deep-UV light-emitting diode.

PubMed

Kuo, Yang; Su, Chia-Ying; Hsieh, Chieh; Chang, Wen-Yen; Huang, Chu-An; Kiang, Yean-Woei; Yang, C C

2015-09-15

The radiated power enhancement (suppression) of an in- (out-of-) plane-oriented radiating dipole at a desired emission wavelength in the deep-ultraviolet (UV) range when it is coupled with a surface plasmon (SP) resonance mode induced on a nearby Al nanoparticle (NP) is demonstrated. Also, it is found that the enhanced radiated power propagates mainly in the direction from the Al NP toward the dipole. Such SP coupling behaviors can be used for suppressing the transverse-magnetic (TM)-polarized emission, enhancing the transverse-electric-polarized emission, and reducing the UV absorption of the p-GaN layer in an AlGaN-based deep-UV light-emitting diode by embedding a sphere-like Al NP in its p-AlGaN layer.

Analysis of Multiple Cytokine Polymorphisms in Individuals with Untreated Deep Carious Lesions Reveals IL1B (rs1143643) as a Susceptibility Factor for Periapical Lesion Development

PubMed Central

Dill, Alisa; Letra, Ariadne; de Souza, Letıcia Chaves; Yadlapati, Mamatha; Biguetti, Claudia Cristina; Garlet, Gustavo Pompermaier; Vieira, Alexandre R.; Silva, Renato Menezes

2017-01-01

Introduction It has been proposed that individual genetic predisposition may contribute to persistent apical periodontitis. Cytokines are associated with levels of inflammation and are involved in caries, pulpal, and periapical tissue destruction. We hypothesized that polymorphisms in cytokine genes may contribute to an individual’s increased susceptibility to apical tissue destruction in response to deep carious lesions. Methods Subjects with deep carious lesions, with or without periapical lesions (≥ 3 mm) were recruited at the University of Pittsburgh and the University of Texas at Houston. Genomic DNA samples of 316 patients were sorted into 2 groups: 136 cases with deep carious lesions and periapical lesions (cases), and 180 cases with deep carious lesions but no periapical lesions (controls). Nine single nucleotide polymorphisms in IL1B, IL6, TNF, RANK, RANKL and OPG genes were selected for genotyping. Genotypes were generated by endpoint analysis using Taqman chemistry in a real-time polymerase chain reaction instrument. Allele and genotype frequencies were compared among cases and controls using PLINK program. Ninety-three human periapical granulomas and 24 healthy periodontal ligament tissues collected post-operatively were used for mRNA expression analyses of IL1B. Results A SNP in IL1B (rs1143643) showed allelic (P=0.02) and genotypic (P=0.004) association with cases of deep caries and periapical lesions. We also observed altered transmission of IL1B marker haplotypes (P = 0.02) in these individuals. IL1B was highly expressed in granulomas (P<0.001). Conclusions Variations in IL1B may be associated with periapical lesion formation in individuals with untreated deep carious lesions. Future studies could help predict host susceptibility to developing periapical lesions. PMID:25476976

Structural changes in loaded equine tendons can be monitored by a novel spectroscopic technique

PubMed Central

Kostyuk, Oksana; Birch, Helen L; Mudera, Vivek; Brown, Robert A

2004-01-01

This study aimed to investigate the preferential collagen fibril alignment in unloaded and loaded tendons using elastic scattering spectroscopy. The device consisted of an optical probe, a pulsed light source (320–860 nm), a spectrometer and a PC. Two probes with either 2.75 mm or 300 μm source-detector separations were used to monitor deep and superficial layers, respectively. Equine superficial digital flexor tendons were subjected to ex vivo progressive tensional loading. Seven times more backscattered light was detected parallel rather than perpendicular to the tendon axis with the 2.75 mm separation probe in unloaded tendons. In contrast, using the 300 μm separation probe the plane of maximum backscatter (3-fold greater) was perpendicular to the tendon axis. There was no optical anisotropy in the cross-sectional plane of the tendon (i.e. the transversely cut tendon surface), with no structural anisotropy. During mechanical loading (9–14% strain) backscatter anisotropy increased 8.5- to 18.5-fold along the principal strain axis for 2.75 mm probe separation, but almost disappeared in the perpendicular plane (measured using the 300 μm probe separation). Optical (anisotropy) and mechanical (strain) measurements were highly correlated. We conclude that spatial anisotropy of backscattered light can be used for quantitative monitoring of collagen fibril alignment and tissue reorganization during loading, with the potential for minimally invasive real-time structural monitoring of fibrous tissues in normal, pathological or repairing tissues and in tissue engineering. PMID:14578479

Photosensitizer nanocarriers modeling for photodynamic therapy applied to dermatological diseases

NASA Astrophysics Data System (ADS)

Salas-García, I.; Fanjul-Vélez, F.; Ortega-Quijano, N.; López-Escobar, M.; Arce-Diego, J. L.

2011-02-01

Photodynamic Therapy involves the therapeutic use of photosensitizers in combination with visible light. The subsequent photochemical reactions generate reactive oxygen species which are considered the principal cytotoxic agents to induce cell death. This technique has become widely used in medicine to treat tumors and other nonmalignant diseases. However, there are several factors related to illumination or the photosensitizer that limit an optimal treatment outcome. The use of nanoparticles (NP) for PDT has been proposed as a solution to current shortcomings. In this way, there are NPs that act as carriers for photosensitizers, NPs that absorb the light and transfer the energy to the photosensitizer and NPs that are themselves photodynamically active. In dermatology, the use of topical photosensitizers produces a time dependent inhomogeneous distribution within the tumor, where the stratum corneum is the main barrier to the diffusion of the photosensitizer to the deeper layers of skin. This produces an insufficient photosensitizer accumulation in tumor tissues and therefore, a low therapeutic efficiency in the case of deep lesions. This work focuses in the use of NPs as photosensitizer carriers to improve the actual topical drug distribution in malignant skin tissues. We present a mathematical model of PS distribution in tumor tissue using NPs that takes into account parameters related to nanoparticles binding. Once the concentration profile of NPs into tissue is obtained, we use a photochemical model which allows us to calculate the temporal evolution of reactive oxygen species according to PS distribution calculated previously from NPs profile.

State of the Art: MR Imaging after Knee Cartilage Repair Surgery.

PubMed

Guermazi, Ali; Roemer, Frank W; Alizai, Hamza; Winalski, Carl S; Welsch, Goetz; Brittberg, Mats; Trattnig, Siegfried

2015-10-01

Cartilage injuries are common, especially in athletes. Because these injuries frequently affect young patients, and they have the potential to progress to osteoarthritis, treatment to alleviate symptoms and delay joint degeneration is warranted. A number of surgical techniques are available to treat focal chondral defects, including marrow stimulation, osteochondral auto- and allografting, and autologous chondrocyte implantation. Although arthroscopy is considered the standard of reference for the evaluation of cartilage before and after repair, it is invasive with associated morbidity and cannot adequately depict the deep cartilage layer and underlying bone. Magnetic resonance (MR) imaging provides unparalleled noninvasive assessment of the repair site and all other joint tissues. MR observation of cartilage repair tissue is a well-established semiquantitative scoring system for repair tissue that has primarily been used in clinical research studies. The cartilage repair osteoarthritis knee score (CROAKS) optimizes comprehensive morphologic assessment of the knee joint after cartilage repair. Furthermore, quantitative, compositional MR imaging measurements (eg, T2, T2*, T1ρ), delayed gadolinium-enhanced MR imaging of cartilage (dGEMRIC), and sodium imaging are available for biochemical assessment. These quantitative MR imaging techniques help assess collagen content and orientation, water content, and glycosaminoglycan and/or proteoglycan content both in the repair tissue as it matures and in the "native" cartilage. In this review, the authors discuss the principles of state-of-the-art morphologic and compositional MR imaging techniques for imaging of cartilage repair and their application to longitudinal studies. (©) RSNA, 2015.

Ultrastructural evaluation of multiple pass low energy versus single pass high energy radio-frequency treatment.

PubMed

Kist, David; Burns, A Jay; Sanner, Roth; Counters, Jeff; Zelickson, Brian

2006-02-01

The radio-frequency (RF) device is a system capable of volumetric heating of the mid to deep dermis and selective heating of the fibrous septa strands and fascia layer. Clinically, these effects promote dermal collagen production, and tightening of these deep subcutaneous structures. A new technique of using multiple low energy passes has been described which results in lower patient discomfort and fewer side effects. This technique has also been anecdotally described as giving more reproducible and reliable clinical results of tissue tightening and contouring. This study will compare ultrastructural changes in collagen between a single pass high energy versus up to five passes of a multiple pass lower energy treatment. Three subjects were consented and treated in the preauricular region with the RF device using single or multiple passes (three or five) in the same 1.5 cm(2) treatment area with a slight delay between passes to allow tissue cooling. Biopsies from each treatment region and a control biopsy were taken immediately, 24 hours or 6 months post treatment for electron microscopic examination of the 0-1 mm and 1-2 mm levels. Sections of tissue 1 mm x 1 mm x 80 nm were examined with an RCA EMU-4 Transmission Electron Microscope. Twenty sections from 6 blocks from each 1 mm depth were examined by 2 blinded observers. The morphology and degree of collagen change in relation to area examined was compared to the control tissue, and estimated using a quantitative scale. Ultrastructural examination of tissue showed that an increased amount of collagen fibril changes with increasing passes at energies of 97 J (three passes) and 122 J (five passes), respectively. The changes seen after five multiple passes were similar to those detected after much more painful single pass high-energy treatments. This ultrastructural study shows changes in collagen fibril morphology with an increased effect demonstrated at greater depths of the skin with multiple low-fluence passes and at lesser depths with single pass higher fluence settings. Findings suggest that similar collagen fibril alteration can occur with multiple pass low-energy treatments and single pulse high-energy treatments. The lower fluence multiple pass approach is associated with less patient discomfort, less side effects, and more consistent clinical results. Copyright 2005 Wiley-Liss, Inc.

Managing Carious Lesions: Consensus Recommendations on Carious Tissue Removal.

PubMed

Schwendicke, F; Frencken, J E; Bjørndal, L; Maltz, M; Manton, D J; Ricketts, D; Van Landuyt, K; Banerjee, A; Campus, G; Doméjean, S; Fontana, M; Leal, S; Lo, E; Machiulskiene, V; Schulte, A; Splieth, C; Zandona, A F; Innes, N P T

2016-05-01

The International Caries Consensus Collaboration undertook a consensus process and here presents clinical recommendations for carious tissue removal and managing cavitated carious lesions, including restoration, based on texture of demineralized dentine. Dentists should manage the disease dental caries and control activity of existing cavitated lesions to preserve hard tissues and retain teeth long-term. Entering the restorative cycle should be avoided as far as possible. Controlling the disease in cavitated carious lesions should be attempted using methods which are aimed at biofilm removal or control first. Only when cavitated carious lesions either are noncleansable or can no longer be sealed are restorative interventions indicated. When a restoration is indicated, the priorities are as follows: preserving healthy and remineralizable tissue, achieving a restorative seal, maintaining pulpal health, and maximizing restoration success. Carious tissue is removed purely to create conditions for long-lasting restorations. Bacterially contaminated or demineralized tissues close to the pulp do not need to be removed. In deeper lesions in teeth with sensible (vital) pulps, preserving pulpal health should be prioritized, while in shallow or moderately deep lesions, restoration longevity becomes more important. For teeth with shallow or moderately deep cavitated lesions, carious tissue removal is performed according toselective removal to firm dentine.In deep cavitated lesions in primary or permanent teeth,selective removal to soft dentineshould be performed, although in permanent teeth,stepwise removalis an option. The evidence and, therefore, these recommendations support less invasive carious lesion management, delaying entry to, and slowing down, the restorative cycle by preserving tooth tissue and retaining teeth long-term. © International & American Associations for Dental Research 2016.

High efficiency blue and white phosphorescent organic light emitting devices

NASA Astrophysics Data System (ADS)

Eom, Sang-Hyun

Organic light-emitting devices (OLEDs) have important applications in full-color flat-panel displays and as solid-state lighting sources. Achieving high efficiency deep-blue phosphorescent OLEDs (PHOLEDs) is necessary for high performance full-color displays and white light sources with a high color rendering index (CRI); however it is more challenging compared to the longer wavelength light emissions such as green and red due to the higher energy excitations for the deep-blue emitter as well as the weak photopic response of deep-blue emission. This thesis details several effective strategies to enhancing efficiencies of deep-blue PHOLEDs based on iridium(III) bis(4',6'-difluorophenylpyridinato)tetrakis(1-pyrazolyl)borate (FIr6), which are further employed to demonstrate high efficiency white OLEDs by combining the deep-blue emitter with green and red emitters. First, we have employed 1,1-bis-(di-4-tolylaminophenyl) cyclohexane (TAPC) as the hole transporting material to enhance electron and triplet exciton confinement in Fir6-based PHOLEDs, which increased external quantum efficiency up to 18 %. Second, dual-emissive-layer (D-EML) structures consisting of an N,N -dicarbazolyl-3,5-benzene (mCP) layer doped with 4 wt % FIr6 and a p-bis (triphenylsilyly)benzene (UGH2) layer doped with 25 wt % FIr6 was employed to maximize exciton generation in the emissive layer. Combined with the p-i-n device structure, high power efficiencies of (25 +/- 2) lm/W at 100 cd/m2 and (20 +/- 2) lm/W at 1000 cd/m 2 were achieved. Moreover, the peak external quantum efficiency of (20 +/- 1) % was achieved by employing tris[3-(3-pyridyl)mesityl]borane (3TPYMB) as the electron transporting material, which further improves the exciton confinement in the emissive layer. With Cs2CO3 doping in the 3TPYMB layer to greatly increase its electrical conductivity, a peak power efficiency up to (36 +/- 2) lm/W from the deep-blue PHOLED was achieved, which also maintains Commission Internationale de L'Eclairage (CIE) coordinates of (0.16, 0.28). High efficiency white PHOLEDs are also demonstrated by incorporating green and red phosphorescent emitters together with the deep-blue emitter FIr6. Similar to the FIr6-only devices, the D-EML structure with high triplet energy charge transport materials leads to a maximum external quantum efficiency of (19 +/- 1) %. Using the p-i-n device structure, a peak power efficiency of (40 +/- 2) lm/W and (36 +/- 2) lm/W at 100 cd/m2 were achieved, and the white PHOLED possesses a CRI of 79 and CIE coordinates of (0.37, 0.40). The limited light extraction from the planar-type OLEDs is also one of the remaining challenges to the OLED efficiency. Here we have developed a simple soft lithography technique to fabricate a transparent, close-packed hemispherical microlens arrays. The application of such microlens arrays to the glass surface of the large-area fluorescent OLEDs enhanced the light extraction efficiency up to (70 +/- 7)%. It is also shown that the light extraction efficiency of the OLEDs is affected by microlens contact angle, OLEDs size, and detailed layer structure of the OLEDs.

Development and characterization of non-resonant multiphoton photoacoustic spectroscopy (NMPPAS) for brain tumor margining

NASA Astrophysics Data System (ADS)

Dahal, Sudhir

During tumor removal surgery, due to the problems associated with obtaining high-resolution, real-time chemical images of where exactly the tumor ends and healthy tissue begins (tumor margining), it is often necessary to remove a much larger volume of tissue than the tumor itself. In the case of brain tumor surgery, however, it is extremely unsafe to remove excess tissue. Therefore, without an accurate image of the tumor margins, some of the tumor's finger-like projections are inevitably left behind in the surrounding parenchyma to grow again. For this reason, the development of techniques capable of providing high-resolution real-time images of tumor margins up to centimeters below the surface of a tissue is ideal for the diagnosis and treatment of tumors, as well as surgical guidance during brain tumor excision. A novel spectroscopic technique, non-resonant multiphoton photoacoustic spectroscopy (NMPPAS), is being developed with the capabilities of obtaining high-resolution subsurface chemical-based images of underlying tumors. This novel technique combines the strengths of multiphoton tissue spectroscopy and photoacoustic spectroscopy into a diagnostic methodology that will, ultimately, provide unparalleled chemical information and images to provide the state of sub-surface tissues. The NMPPAS technique employs near-infrared light (in the diagnostic window) to excite ultraviolet and/or visible light absorbing species deep below the tissue's surface. Once a multiphoton absorption event occurs, non-radiative relaxation processes generates a localized thermal expansion and subsequent acoustic wave that can be detected using a piezoelectric transducer. Since NMPPAS employs an acoustic detection modality, much deeper diagnoses can be performed than that is possible using current state of the art high-resolution chemical imaging techniques such as multiphoton fluorescence spectroscopy. NMPPAS was employed to differentiate between excised brain tumors (astrocytoma III) and healthy tissue with over 99% accuracy. NMPPAS spectral features showed evident differences between tumor and healthy tissues, and ratiometric analysis ensured that only a few wavelengths could be used for excitation instead of using numerous wavelength excitations to create spectra. This process would significantly reduce the analysis time while maintaining the same degree of accuracy. Tissue phantoms were fabricated in order to characterize the properties of NMPPAS. Scattering particles were doped into the phantoms to simulate their light scattering properties to real tissues. This allowed for better control over shape, size, reproducibility and doping in the sample while maintaining the light-tissue interaction properties of real tissue. To make NMPPAS viable for clinical applications, the technique was characterized to determine the spatial (lateral and longitudinal) resolution, depth of penetration and its ability to image in three-dimension through layers of tissue. Both resolutions were determined to be near-cellular level resolution (50-70 microm), obtained initially with the aid of the technique of multiphoton fluorescence, and later verified using NMPPAS imaging. Additionally, the maximum depth of penetration and detection was determined to be about 1.4cm, making the technique extremely suitable to margin tumors from underlying tissues in the brain. The capability of NMPPAS to detect and image layers that lie beneath other structures and blood vessels was also investigated. Three-dimensional images were obtained for the first time using NMPPAS. The images were obtained from different depths and structures were imaged through other layers of existing structures in the sample. This verified that NMPPAS was capable of detecting and imaging structures that lie embedded within the tissues. NMPPAS images of embedded structures were also obtained with the presence of hemoglobin, which is potentially the largest source of background in blood-perfused tissues, thus showing that the technique is capable of detecting and differentiating in blood-perfused samples.

Two-layer contractive encodings for learning stable nonlinear features.

PubMed

Schulz, Hannes; Cho, Kyunghyun; Raiko, Tapani; Behnke, Sven

2015-04-01

Unsupervised learning of feature hierarchies is often a good strategy to initialize deep architectures for supervised learning. Most existing deep learning methods build these feature hierarchies layer by layer in a greedy fashion using either auto-encoders or restricted Boltzmann machines. Both yield encoders which compute linear projections of input followed by a smooth thresholding function. In this work, we demonstrate that these encoders fail to find stable features when the required computation is in the exclusive-or class. To overcome this limitation, we propose a two-layer encoder which is less restricted in the type of features it can learn. The proposed encoder is regularized by an extension of previous work on contractive regularization. This proposed two-layer contractive encoder potentially poses a more difficult optimization problem, and we further propose to linearly transform hidden neurons of the encoder to make learning easier. We demonstrate the advantages of the two-layer encoders qualitatively on artificially constructed datasets as well as commonly used benchmark datasets. We also conduct experiments on a semi-supervised learning task and show the benefits of the proposed two-layer encoders trained with the linear transformation of perceptrons. Copyright © 2014 Elsevier Ltd. All rights reserved.

Traffic sign recognition based on deep convolutional neural network

NASA Astrophysics Data System (ADS)

Yin, Shi-hao; Deng, Ji-cai; Zhang, Da-wei; Du, Jing-yuan

2017-11-01

Traffic sign recognition (TSR) is an important component of automated driving systems. It is a rather challenging task to design a high-performance classifier for the TSR system. In this paper, we propose a new method for TSR system based on deep convolutional neural network. In order to enhance the expression of the network, a novel structure (dubbed block-layer below) which combines network-in-network and residual connection is designed. Our network has 10 layers with parameters (block-layer seen as a single layer): the first seven are alternate convolutional layers and block-layers, and the remaining three are fully-connected layers. We train our TSR network on the German traffic sign recognition benchmark (GTSRB) dataset. To reduce overfitting, we perform data augmentation on the training images and employ a regularization method named "dropout". The activation function we employ in our network adopts scaled exponential linear units (SELUs), which can induce self-normalizing properties. To speed up the training, we use an efficient GPU to accelerate the convolutional operation. On the test dataset of GTSRB, we achieve the accuracy rate of 99.67%, exceeding the state-of-the-art results.

The deep meridional overturning circulation in the Indian Ocean inferred from the GECCO synthesis

NASA Astrophysics Data System (ADS)

Wang, Weiqiang; Köhl, Armin; Stammer, Detlef

2012-11-01

The deep time-varying meridional overturning circulation (MOC) in the Indian Ocean in the German “Estimating the Circulation and Climate of the Ocean” consortium efforts (GECCO) ocean synthesis is being investigated. An analysis of the integrated circulation suggests that, on time average, 2.1 Sv enter the Indian Ocean in the bottom layer (>3200 m) from the south and that 12.3 Sv leave the Indian Ocean in the upper and intermediate layers (<1500 m), composed of the up-welled bottom layer inflow water, augmented by 9.6 Sv Indonesian Throughflow (ITF) water. The GECCO time-mean results differ substantially from those obtained by inverse box models, which being based on individual hydrographic sections and due to the strong seasonal cycle are susceptible to aliasing. The GECCO solution shows a large seasonal variation in its deep MOC caused by the seasonal reversal of monsoon-related wind stress forcing. The associated seasonal variations of the deep MOC range from -7 Sv in boreal winter to 3 Sv in summer. In addition, the upper and bottom transports across the 34°S section show pronounced interannual variability with roughly biennial variations superimposed by strong anomalies during each La Niña phase as well as the ITF, which mainly affect the upper layer transports. On decadal and longer timescale, the meridional overturning variability as well as long-term trends differs before and after 1980. GECCO shows a stable trend for the period 1960-1979 and substantial changes in the upper and bottom layer for the period 1980-2001. By means of an extended EOF analysis, the importance of Ekman dynamics as driving forces of the deep MOC of the Indian Ocean on the interannual timescale is highlighted. The leading modes of the zonal and meridional wind stress favour a basin-wide meridional overturning mode via Ekman upwelling or downwelling mostly in the central and eastern Indian Ocean. Moreover, tropical zonal wind stress along the equator and alongshore wind stress off the Sumatra-Java coast contribute to the evolution of the Indian Ocean dipole (IOD) events.

Sequential therapy with "vacuum sealing drainage-artificial dermis implantation-thin partial thickness skin grafting" for deep and infected wound surfaces in children.

PubMed

Yuan, X-G; Zhang, X; Fu, Y-X; Tian, X-F; Liu, Y; Xiao, J; Li, T-W; Qiu, L

2016-05-01

To evaluate the efficacy of a "vacuum sealing drainage (VSD) - artificial dermis implantation (ADI) - thin partial thickness skin grafting (TSG)" sequential therapy for deep and infected wounds in children. Fifty-three pediatric patients with deep and infected wounds were treated with sequential VSD-ADI-TSG therapy. The efficacy of this treatment was compared with that of the surgical debridement-change dressings-thin partial thickness skin grafting previously performed on 20 patients. Survival of tissue grafts, color and flexibility, subcutaneous fullness and scar formation of the graft site were examined and compared. The sequential therapy combined the advantages of the VSD treatment, in reducing tissue necrosis and infection on the wound surfaces and promoting the growth of granulation tissue, with the enhancement of grafting by artificial dermis. Compared with the 20 controls, skin grafted on the artificial dermis was more smooth and glossy, while the textures of the region were more elastic, and the scars were significantly lighter in Vancouver scale. The sequential VSD-ADI-TSG therapy is a simple and effective treatment for children with deep and infected wounds. IV. Copyright © 2016. Published by Elsevier Masson SAS.

Hourly air pollution concentrations and their important predictors over Houston, Texas using deep neural networks: case study of DISCOVER-AQ time period

NASA Astrophysics Data System (ADS)

Eslami, E.; Choi, Y.; Roy, A.

2017-12-01

Air quality forecasting carried out by chemical transport models often show significant error. This study uses a deep-learning approach over the Houston-Galveston-Brazoria (HGB) area to overcome this forecasting challenge, for the DISCOVER-AQ period (September 2013). Two approaches, deep neural network (DNN) using a Multi-Layer Perceptron (MLP) and Restricted Boltzmann Machine (RBM) were utilized. The proposed approaches analyzed input data by identifying features abstracted from its previous layer using a stepwise method. The approaches predicted hourly ozone and PM in September 2013 using several predictors of prior three days, including wind fields, temperature, relative humidity, cloud fraction, precipitation along with PM, ozone, and NOx concentrations. Model-measurement comparisons for available monitoring sites reported Indexes of Agreement (IOA) of around 0.95 for both DNN and RBM. A standard artificial neural network (ANN) (IOA=0.90) with similar architecture showed poorer performance than the deep networks, clearly demonstrating the superiority of the deep approaches. Additionally, each network (both deep and standard) performed significantly better than a previous CMAQ study, which showed an IOA of less than 0.80. The most influential input variables were identified using their associated weights, which represented the sensitivity of ozone to input parameters. The results indicate deep learning approaches can achieve more accurate ozone forecasting and identify the important input variables for ozone predictions in metropolitan areas.

Time-reversed ultrasonically encoded (TRUE) focusing for deep-tissue optogenetic modulation

NASA Astrophysics Data System (ADS)

Brake, Joshua; Ruan, Haowen; Robinson, J. Elliott; Liu, Yan; Gradinaru, Viviana; Yang, Changhuei

2018-02-01

The problem of optical scattering was long thought to fundamentally limit the depth at which light could be focused through turbid media such as fog or biological tissue. However, recent work in the field of wavefront shaping has demonstrated that by properly shaping the input light field, light can be noninvasively focused to desired locations deep inside scattering media. This has led to the development of several new techniques which have the potential to enhance the capabilities of existing optical tools in biomedicine. Unfortunately, extending these methods to living tissue has a number of challenges related to the requirements for noninvasive guidestar operation, speed, and focusing fidelity. Of existing wavefront shaping methods, time-reversed ultrasonically encoded (TRUE) focusing is well suited for applications in living tissue since it uses ultrasound as a guidestar which enables noninvasive operation and provides compatibility with optical phase conjugation for high-speed operation. In this paper, we will discuss the results of our recent work to apply TRUE focusing for optogenetic modulation, which enables enhanced optogenetic stimulation deep in tissue with a 4-fold spatial resolution improvement in 800-micron thick acute brain slices compared to conventional focusing, and summarize future directions to further extend the impact of wavefront shaping technologies in biomedicine.

Fabrication and preliminary study of a biomimetic tri-layer tubular graft based on fibers and fiber yarns for vascular tissue engineering.

PubMed

Wu, Tong; Zhang, Jialing; Wang, Yuanfei; Li, Dandan; Sun, Binbin; El-Hamshary, Hany; Yin, Meng; Mo, Xiumei

2018-01-01

Designing a biomimetic and functional tissue-engineered vascular graft has been urgently needed for repairing and regenerating defected vascular tissues. Utilizing a multi-layered vascular scaffold is commonly considered an effective way, because multi-layered scaffolds can easily simulate the structure and function of natural blood vessels. Herein, we developed a novel tri-layer tubular graft consisted of Poly(L-lactide-co-caprolactone)/collagen (PLCL/COL) fibers and Poly(lactide-co-glycolide)/silk fibroin (PLGA/SF) yarns via a three-step electrospinning method. The tri-layer vascular graft consisted of PLCL/COL aligned fibers in inner layer, PLGA/SF yarns in middle layer, and PLCL/COL random fibers in outer layer. Each layer possessed tensile mechanical strength and elongation, and the entire tubular structure provided tensile and compressive supports. Furthermore, the human umbilical vein endothelial cells (HUVECs) and smooth muscle cells (SMCs) proliferated well on the materials. Fluorescence staining images demonstrated that the axially aligned PLCL/COL fibers prearranged endothelium morphology in lumen and the circumferential oriented PLGA/SF yarns regulated SMCs organization along the single yarns. The outside PLCL/COL random fibers performed as the fixed layer to hold the entire tubular structure. The in vivo results showed that the tri-layer vascular graft supported cell infiltration, scaffold biodegradation and abundant collagen production after subcutaneous implantation for 10weeks, revealing the optimal biocompatibility and tissue regenerative capability of the tri-layer graft. Therefore, the specially designed tri-layer vascular graft will be beneficial to vascular reconstruction. Copyright © 2017. Published by Elsevier B.V.

Arctic mosses govern below-ground environment and ecosystem processes.

PubMed

Gornall, J L; Jónsdóttir, I S; Woodin, S J; Van der Wal, R

2007-10-01

Mosses dominate many northern ecosystems and their presence is integral to soil thermal and hydrological regimes which, in turn, dictate important ecological processes. Drivers, such as climate change and increasing herbivore pressure, affect the moss layer thus, assessment of the functional role of mosses in determining soil characteristics is essential. Field manipulations conducted in high arctic Spitsbergen (78 degrees N), creating shallow (3 cm), intermediate (6 cm) and deep (12 cm) moss layers over the soil surface, had an immediate impact on soil temperature in terms of both average temperatures and amplitude of fluctuations. In soil under deep moss, temperature was substantially lower and organic layer thaw occurred 4 weeks later than in other treatment plots; the growing season for vascular plants was thereby reduced by 40%. Soil moisture was also reduced under deep moss, reflecting the influence of local heterogeneity in moss depth, over and above the landscape-scale topographic control of soil moisture. Data from field and laboratory experiments show that moss-mediated effects on the soil environment influenced microbial biomass and activity, resulting in warmer and wetter soil under thinner moss layers containing more plant-available nitrogen. In arctic ecosystems, which are limited by soil temperature, growing season length and nutrient availability, spatial and temporal variation in the depth of the moss layer has significant repercussions for ecosystem function. Evidence from our mesic tundra site shows that any disturbance causing reduction in the depth of the moss layer will alleviate temperature and moisture constraints and therefore profoundly influence a wide range of ecosystem processes, including nutrient cycling and energy transfer.

[Soil moisture variation under different water and fertilization managements in apple orchard of Weibei dryland, China].

PubMed

Zhao, Zhi Yuan; Zheng, Wei; Liu, Jie; Ma, Peng Yi; Li, Zi Yan; Zhai, Bing Nian; Wang, Zhao Hui

2018-04-01

To evaluate the variations of soil moisture under different water and fertilizer treatments in apple orchard in the Weibei dryland, a field experiment was carried out in 2013-2016 at Tianjiawa Village, Baishui County, Shaanxi Province. There were three treatments, i.e., farmers traditional model (only addition of NPK chemical fertilizer, FM), extension model (swine manure and NPK chemical fertilizer combined with black plastic film in tree row space, EM), and optimized model (swine manure and NPK chemical fertilizer combined with black plastic film in tree row space and planting rape in the inter-row of apple trees, OM). The results showed that OM treatment significantly increased soil water storage capacity in 0-200 cm soil layer. Water content of 0-100 cm soil layer was increased by 5.6% and 15.3% in the dry season compared with FM and EM treatment, respectively. Moreover, the soil water relative deficit index of OM was lower than that of EM in 200-300 cm soil layer. The rainfall infiltration in the dry year could reach 300 cm depth under OM. Meanwhile, OM stabilized soil water content and efficiently alleviated the desiccation in deep soil layer. Compared with FM and EM, the 4-year average yield of OM was increased by 36.6% and 22.5%, respectively. In summary, OM could increase water use efficiency through increasing the contents of available soil water and improving the soil water condition in shallow and deep layers, which help alleviate the soil deficit in deep layer and increase yield.

Selective Activation of the Deep Layers of the Human Primary Visual Cortex by Top-Down Feedback.

PubMed

Kok, Peter; Bains, Lauren J; van Mourik, Tim; Norris, David G; de Lange, Floris P

2016-02-08

In addition to bottom-up input, the visual cortex receives large amounts of feedback from other cortical areas [1-3]. One compelling example of feedback activation of early visual neurons in the absence of bottom-up input occurs during the famous Kanizsa illusion, where a triangular shape is perceived, even in regions of the image where there is no bottom-up visual evidence for it. This illusion increases the firing activity of neurons in the primary visual cortex with a receptive field on the illusory contour [4]. Feedback signals are largely segregated from feedforward signals within each cortical area, with feedforward signals arriving in the middle layer, while top-down feedback avoids the middle layers and predominantly targets deep and superficial layers [1, 2, 5, 6]. Therefore, the feedback-mediated activity increase in V1 during the perception of illusory shapes should lead to a specific laminar activity profile that is distinct from the activity elicited by bottom-up stimulation. Here, we used fMRI at high field (7 T) to empirically test this hypothesis, by probing the cortical response to illusory figures in human V1 at different cortical depths [7-14]. We found that, whereas bottom-up stimulation activated all cortical layers, feedback activity induced by illusory figures led to a selective activation of the deep layers of V1. These results demonstrate the potential for non-invasive recordings of neural activity with laminar specificity in humans and elucidate the role of top-down signals during perceptual processing. Copyright © 2016 Elsevier Ltd. All rights reserved.

Clutter elimination for deep clinical optoacoustic imaging using localised vibration tagging (LOVIT)☆

PubMed Central

Jaeger, Michael; Bamber, Jeffrey C.; Frenz, Martin

2013-01-01

This paper investigates a novel method which allows clutter elimination in deep optoacoustic imaging. Clutter significantly limits imaging depth in clinical optoacoustic imaging, when irradiation optics and ultrasound detector are integrated in a handheld probe for flexible imaging of the human body. Strong optoacoustic transients generated at the irradiation site obscure weak signals from deep inside the tissue, either directly by propagating towards the probe, or via acoustic scattering. In this study we demonstrate that signals of interest can be distinguished from clutter by tagging them at the place of origin with localised tissue vibration induced by the acoustic radiation force in a focused ultrasonic beam. We show phantom results where this technique allowed almost full clutter elimination and thus strongly improved contrast for deep imaging. Localised vibration tagging by means of acoustic radiation force is especially promising for integration into ultrasound systems that already have implemented radiation force elastography. PMID:25302147

Near-infrared bulk optical properties of goat wound tissue and human serum: consequences for an implantable optical glucose sensor.

PubMed

Aernouts, Ben; Sharma, Sandeep; Gellynck, Karolien; Vlaminck, Lieven; Cornelissen, Maria; Saeys, Wouter

2016-10-01

Near-infrared (NIR) spectroscopy offers a promising technological platform for continuous glucose monitoring in the human body. Moreover, these measurements could be performed in vivo with an implantable single-chip based optical sensor. However, a thin tissue layer may grow in the optical path of the sensor. As most biological tissues are highly scattering, they only allow a small fraction of the collimated light to pass, significantly reducing the light throughput. To quantify the effect of a thin tissue layer in the optical path, the bulk optical properties of serum and tissue samples grown on implanted dummy sensors were characterized using double integrating sphere and unscattered transmittance measurements. The estimated bulk optical properties were then used to calculate the light attenuation through a thin tissue layer. The combination band of glucose was found to be the better option, relative to the first overtone band, as the absorptivity of glucose molecules is higher, while the reduction in unscattered transmittance due to tissue growth is less. Additionally, as the wound tissue was found to be highly scattering, the unscattered transmittance of the tissue layer is expected to be very low. Therefore, a sensor configuration which measures the diffuse transmittance and/or reflectance instead was recommended. (a) Dummy sensor; (b) explanted dummy sensor in tissue lump; (c) removal of dummy sensor from tissue lump; and (d) 900 µm slices of tissue lump. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Construction and histological analysis of a 3D human arterial wall model containing vasa vasorum using a layer-by-layer technique.

PubMed

Shima, Fumiaki; Narita, Hirokazu; Hiura, Ayami; Shimoda, Hiroshi; Akashi, Mitsuru

2017-03-01

There is considerable global demand for three-dimensional (3D) functional tissues which mimic our native organs and tissues for use as in vitro drug screening systems and in regenerative medicine. In particular, there has been an increasing number of patients who suffer from arterial diseases such as arteriosclerosis. As such, in vitro 3D arterial wall models that can evaluate the effects of novel medicines and a novel artificial graft for the treatment are required. In our previous study, we reported the rapid construction of 3D tissues by employing a layer-by-layer (LbL) technique and revealed their potential applications in the pharmaceutical fields and tissue engineering. In this study, we successfully constructed a 3D arterial wall model containing vasa vasorum by employing a LbL technique for the first time. The cells were coated with extracellular matrix nanofilms and seeded into a culture insert using a cell accumulation method. This model had a three-layered hierarchical structure: a fibroblast layer, a smooth muscle layer, and an endothelial layer, which resembled the native arterial wall. Our method could introduce vasa vasorum into a fibroblast layer in vitro and the 3D arterial wall model showed barrier function which was evaluated by immunostaining and transendothelial electrical resistance measurement. Furthermore, electron microscopy observations revealed that the vasa vasorum was composed of single-layered endothelial cells, and the endothelial tubes were surrounded by the basal lamina, which are known to promote maturation and stabilization in native blood capillaries. These models should be useful for tissue engineering, regenerative medicine, and pharmaceutical applications. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 814-823, 2017. © 2016 Wiley Periodicals, Inc.

Winter ocean-ice interactions under thin sea ice observed by IAOOS platforms during NICE2015:salty surface mixed layer and active basal melt

NASA Astrophysics Data System (ADS)

Provost, C.; Koenig, Z.; Villacieros-Robineau, N.; Sennechael, N.; Meyer, A.; Lellouche, J. M.; Garric, G.

2016-12-01

IAOOS platforms, measuring physical parameters at the atmosphere-snow-ice-ocean interface deployed as part of the N-ICE2015 campaign, provide new insights on winter conditions North of Svalbard. The three regions crossed during the drifts, the Nansen Basin, the Sofia Deep and the Svalbard northern continental slope featured distinct hydrographic properties and ice-ocean exchanges. In the Nansen Basin the quiescent warm layer was capped by a stepped halocline (60 and 110 m) and a deep thermocline (110 m). Ice was forming and the winter mixed layer salinity was larger by 0.1 g/kg than previously observed. Over the Svalbard continental slope, the Atlantic Water (AW) was very shallow (20 m from the surface) and extended offshore from the 500 m isobath by a distance of about 70 km, sank along the slope (40 m from the surface) and probably shedded eddies into the Sofia Deep. In the Sofia Deep, relatively warm waters of Atlantic origin extended from 90 m downward. Resulting from different pathways, these waters had a wide range of hydrographic characteristics. Sea-ice melt was widespread over the Svalbard continental slope and ocean-to-ice heat fluxes reached values of 400 Wm-2 (mean of 150 Wm-2 over the continentalslope). Sea-ice melt events were associated with near 12-hour fluctuations in the mixed-layer temperature and salinity corresponding to the periodicity of tides and near-inertial waves potentially generated by winter storms, large barotropic tides over steep topography and/or geostrophic adjustments.

Organization of the Tropical Convective Cloud Population by Humidity and the Critical Transition to Heavy Precipitation

NASA Astrophysics Data System (ADS)

Igel, M.

2015-12-01

The tropical atmosphere exhibits an abrupt statistical switch between non-raining and heavily raining states as column moisture increases across a wide range of length scales. Deep convection occurs at values of column humidity above the transition point and induces drying of moist columns. With a 1km resolution, large domain cloud resolving model run in RCE, what will be made clear here for the first time is how the entire tropical convective cloud population is affected by and feeds back to the pickup in heavy precipitation. Shallow convection can act to dry the low levels through weak precipitation or vertical redistribution of moisture, or to moisten toward a transition to deep convection. It is shown that not only can deep convection dehydrate the entire column, it can also dry just the lower layer through intense rain. In the latter case, deep stratiform cloud then forms to dry the upper layer through rain with anomalously high rates for its value of column humidity until both the total column moisture falls below the critical transition point and the upper levels are cloud free. Thus, all major tropical cloud types are shown to respond strongly to the same critical phase-transition point. This mutual response represents a potentially strong organizational mechanism for convection, and the frequency of and logical rules determining physical evolutions between these convective regimes will be discussed. The precise value of the point in total column moisture at which the transition to heavy precipitation occurs is shown to result from two independent thresholds in lower-layer and upper-layer integrated humidity.

Vorticity and Vertical Motions Diagnosed from Satellite Deep-Layer Temperatures. Revised

NASA Technical Reports Server (NTRS)

Spencer, Roy W.; Lapenta, William M.; Robertson, Franklin R.

1994-01-01

Spatial fields of satellite-measured deep-layer temperatures are examined in the context of quasigeostrophic theory. It is found that midtropospheric geostrophic vorticity and quasigeostrophic vertical motions can be diagnosed from microwave temperature measurements of only two deep layers. The lower- ( 1000-400 hPa) and upper- (400-50 hPa) layer temperatures are estimated from limb-corrected TIROS-N Microwave Sounding Units (MSU) channel 2 and 3 data, spatial fields of which can be used to estimate the midtropospheric thermal wind and geostrophic vorticity fields. Together with Trenberth's simplification of the quasigeostrophic omega equation, these two quantities can be then used to estimate the geostrophic vorticity advection by the thermal wind, which is related to the quasigeostrophic vertical velocity in the midtroposphere. Critical to the technique is the observation that geostrophic vorticity fields calculated from the channel 3 temperature features are very similar to those calculated from traditional, 'bottom-up' integrated height fields from radiosonde data. This suggests a lack of cyclone-scale height features near the top of the channel 3 weighting function, making the channel 3 cyclone-scale 'thickness' features approximately the same as height features near the bottom of the weighting function. Thus, the MSU data provide observational validation of the LID (level of insignificant dynamics) assumption of Hirshberg and Fritsch.

In vivo multiphoton microscopy of deep tissue with gradient index lenses

NASA Astrophysics Data System (ADS)

Levene, Michael J.; Dombeck, Daniel A.; Williams, Rebecca M.; Skoch, Jesse; Hickey, Gregory A.; Kasischke, Karl A.; Molloy, Raymond P.; Ingelsson, Martin; Stern, Edward A.; Klucken, Jochen; Bacskai, Brian J.; Zipfel, Warren R.; Hyman, Bradley T.; Webb, Watt W.

2004-06-01

Gradient index lenses enable multiphoton microscopy of deep tissues in the intact animal. In order to assess their applicability to clinical research, we present in vivo multiphoton microscopy with gradient index lenses in brain regions associated with Alzheimer's disease and Parkinson's disease in both transgenic and wild-type mice. We also demonstrate microscopy of ovary in wild type mouse using only intrinsic fluorescence and second harmonic generation, signal sources which may prove useful for both the study and diagnosis of cancer.

In vivo multiphoton microscopy beyond 1 mm in the brain

NASA Astrophysics Data System (ADS)

Miller, David R.; Medina, Flor A.; Hassan, Ahmed; Perillo, Evan P.; Hagan, Kristen; Kazmi, S. M. Shams; Zemelman, Boris V.; Dunn, Andrew K.

2017-02-01

We perform high-resolution, non-invasive, in vivo deep-tissue imaging of the mouse neocortex using multiphoton microscopy with a high repetition rate optical parametric amplifier laser source tunable between λ=1,100 and 1,400 nm. We demonstrate an imaging depth of 1,200 μm in vasculature and 1,160 μm in neurons. We also demonstrate deep-tissue imaging using Indocyanine Green (ICG), which is FDA approved and a promising route to translate multiphoton microscopy to human applications.

Deep-cascade: Cascading 3D Deep Neural Networks for Fast Anomaly Detection and Localization in Crowded Scenes.

PubMed

Sabokrou, Mohammad; Fayyaz, Mohsen; Fathy, Mahmood; Klette, Reinhard

2017-02-17

This paper proposes a fast and reliable method for anomaly detection and localization in video data showing crowded scenes. Time-efficient anomaly localization is an ongoing challenge and subject of this paper. We propose a cubicpatch- based method, characterised by a cascade of classifiers, which makes use of an advanced feature-learning approach. Our cascade of classifiers has two main stages. First, a light but deep 3D auto-encoder is used for early identification of "many" normal cubic patches. This deep network operates on small cubic patches as being the first stage, before carefully resizing remaining candidates of interest, and evaluating those at the second stage using a more complex and deeper 3D convolutional neural network (CNN). We divide the deep autoencoder and the CNN into multiple sub-stages which operate as cascaded classifiers. Shallow layers of the cascaded deep networks (designed as Gaussian classifiers, acting as weak single-class classifiers) detect "simple" normal patches such as background patches, and more complex normal patches are detected at deeper layers. It is shown that the proposed novel technique (a cascade of two cascaded classifiers) performs comparable to current top-performing detection and localization methods on standard benchmarks, but outperforms those in general with respect to required computation time.

Comparison of different histological protocols for the preservation and quantification of the intestinal mucus layer in pigs.

PubMed

Röhe, Ilen; Hüttner, Friedrich Joseph; Plendl, Johanna; Drewes, Barbara; Zentek, Jürgen

2018-02-05

The histological characterization of the intestinal mucus layer is important for many scientific experiments investigating the interaction between intestinal microbiota, mucosal immune response and intestinal mucus production. The aim of this study was to examine and compare different fixation protocols for displaying and quantifying the intestinal mucus layer in piglets and to test which histomorphological parameters may correlate with the determined mucus layer thickness. Jejunal and colonal tissue samples of weaned piglets (n=10) were either frozen in liquid nitrogen or chemically fixed using methacarn solution. The frozen tissue samples were cryosectioned and subsequently postfixed using three different postfixatives: paraformaldehyde vapor, neutrally buffered formalin solution and ethanol solution. After dehydration, methacarn fixed tissues were embedded in paraffin wax. Both sections of cryopreserved and methacarn fixed tissue samples were stained with Alcian blue (AB)-PAS followed by the microscopically determination of the mucus layer thickness. Different pH values of the Alcian Blue staining solution and two mucus layer thickness measuring methods were compared. In addition, various histomorphological parameters of methacarn fixed tissue samples were evaluated including the number of goblet cells and the mucin staining area. Cryopreservation in combination with chemical postfixation led to mucus preservation in the colon of piglets allowing mucus thickness measurements. Mucus could be only partly preserved in cryosections of the jejunum impeding any quantitative description of the mucus layer thickness. The application of different postfixations, varying pH values of the AB solution and different mucus layer measuring methods led to comparable results regarding the mucus layer thickness. Methacarn fixation proved to be unsuitable for mucus depiction as only mucus patches were found in the jejunum or a detachment of the mucus layer from the epithelium was observed in the colon. Correlation analyses revealed that the proportion of the mucin staining area per crypt area (relative mucin staining) measured in methacarn fixed tissue samples corresponded to the colonal mucus layer thickness determined in cryopreserved tissue samples. In conclusion, the results showed that cryopreservation using liquid nitrogen followed by chemical postfixation and AB-PAS staining led to a reliable mucus preservation allowing a mucus thickness determination in the colon of pigs. Moreover, the detected relative mucin staining area may serve as a suitable histomorphological parameter for the assessment of the intestinal mucus layer thickness. The findings obtained in this study can be used for the implementation of an improved standard for the histological description of the mucus layer in the colon of pigs.

Influences of spatial and temporal variability of sound scattering layers on deep diving odontocete behavior

NASA Astrophysics Data System (ADS)

Copeland, Adrienne Marie

Patchiness of prey can influence the behavior of a predator, as predicted by the optimal foraging theory which states that an animal will maximize the energy gain while minimizing energy loss. While this relationship has been studied and is relatively well understood in some terrestrial systems, the same is far from true in marine systems. It is as important to investigate this in the marine realm in order to better understand predator distribution and behavior. Micronekton, organisms from 2-20 cm, might be a key component in understanding this as it is potentially an essential link in the food web between primary producers and higher trophic levels, including cephalopods which are primary prey items of deep diving odontocetes (toothed whales). My dissertation assesses the spatial and temporal variability of micronekton in the Northwestern Hawaiian Islands (NWHI), the Main Hawaiian Islands' (MHI) Island of Hawaii, and the Gulf of Mexico (GOM). Additionally it focuses on understanding the relationship between the spatial distribution of micronekton and environmental and geographic factors, and how the spatial and temporal variability of this micronekton relates to deep diving odontocete foraging. I used both an active Simrad EK60 echosounder system to collect water column micronekton backscatter and a passive acoustic system to detect the presence of echolocation clicks from deep diving beaked, sperm, and short-finned pilot whales. My results provide insight into what might be contributing to hotspots of micronekton which formed discrete layers in all locations, a shallow scattering layer (SSL) from the surface to about 200 m and a deep scattering layer (DSL) starting at about 350 m. In both the GOM and the NWHI, the bathymetry and proximity to shore influenced the amount of micronekton backscatter with locations closer to shore and at shallower depths having higher backscatter. We found in all three locations that some species of deep diving odontocetes were searching for prey in these areas with higher micronekton backscatter. Beaked whales in the NWHI, short-finned pilot whales in the NWHI and MHI, and sperm whales in the GOM where present in areas of higher micronekton backscatter. These hotspots of backscatter may be good predictors of the distribution of some deep-diving toothed whale foragers since the hotspots potentially indicate a food web supporting the prey of the cetaceans.

New insights on the propagation of the Near Inertial Waves (NIW) governing the bottom dynamic of the Western Ionian Sea (Eastern Mediterranean Sea).

NASA Astrophysics Data System (ADS)

Lo Bue, N.; Artale, V.; Marullo, S.; Marinaro, G.; Embriaco, D.; Favali, P.; Beranzoli, L.

2017-12-01

The past general idea that the ocean-deep circulation is in quasi-stationary motion, has conditioned the observations of deep layers for a long time, excluding them from the majority of the surveys around the ocean world and influencing studies on the deep ocean processes. After the pioneering work of Munk (1966) highlighting the importance of bottom mixing processes, an underestimation of these issue has continued to persist for decades, due also to the difficulty to make reliable observations in the abyssal layers. The real awareness about the unsteady state of the abyssal layers has only risen recently and encourages us to wonder how the deep mechanisms can induce an internal instability and, consequently, affect the ocean circulation. The NIWs are characterized by a frequency near the inertial frequency f and can be generated by a variety of mechanisms, including wind, nonlinear interactions wave-shear flow and wave-topography, and geostrophic adjustments. NIWs represent one of the main high-frequency variabilities in the ocean, and they contain around half the kinetic energy observed in the oceans (Simmons et al. 2012) appearing as a prominent peak rising well above the Garrett & Munk (1975) continuum internal wave spectrum. As such, they upset the mixing processes in the upper ocean and they can interact strongly with mesoscale and sub-mesoscale motions. Likewise, NIWs likely affect the mixing of the deep ocean in ways that are just beginning to be understood. The analysis carried out on yearly time series collected by the bottom observatory SN1, the Western Ionian node of EMSO (European Multidisciplinary Seafloor and water column Observatory) Research Infrastructure, provides new important understanding on the role of the NIWs in the abyssal ocean. Also, this analysis is very useful to shed light on the possible mechanism that can trigger deep processes such as the abyssal vortex chains found by Rubino et al. (2012) in the Ionian abyssal plain of the Eastern Mediterranean (EM) basin. Finally, spectral analysis, including the Singular Spectrum Analysis (SSA) and Wavelet, allow us to explain how the NIWs can contributes to activate and increase the mixing in the bottom layers with significant impact on overall abyssal and deep circulation at local and regional scale (Mediterranean Sea).

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.

Dynamics of soil exploration by fine roots down to a depth of 10 m throughout the entire rotation in Eucalyptus grandis plantations

PubMed Central

Laclau, Jean-Paul; da Silva, Eder A.; Rodrigues Lambais, George; Bernoux, Martial; le Maire, Guerric; Stape, José L.; Bouillet, Jean-Pierre; Gonçalves, José L. de Moraes; Jourdan, Christophe; Nouvellon, Yann

2013-01-01

Although highly weathered soils cover considerable areas in tropical regions, little is known about exploration by roots in deep soil layers. Intensively managed Eucalyptus plantations are simple forest ecosystems that can provide an insight into the belowground growth strategy of fast-growing tropical trees. Fast exploration of deep soil layers by eucalypt fine roots may contribute to achieving a gross primary production that is among the highest in the world for forests. Soil exploration by fine roots down to a depth of 10 m was studied throughout the complete cycle in Eucalyptus grandis plantations managed in short rotation. Intersects of fine roots, less than 1 mm in diameter, and medium-sized roots, 1–3 mm in diameter, were counted on trench walls in a chronosequence of 1-, 2-, 3.5-, and 6-year-old plantations on a sandy soil, as well as in an adjacent 6-year-old stand growing in a clayey soil. Two soil profiles were studied down to a depth of 10 m in each stand (down to 6 m at ages 1 and 2 years) and 4 soil profiles down to 1.5–3.0 m deep. The root intersects were counted on 224 m2 of trench walls in 15 pits. Monitoring the soil water content showed that, after clear-cutting, almost all the available water stored down to a depth of 7 m was taken up by tree roots within 1.1 year of planting. The soil space was explored intensively by fine roots down to a depth of 3 m from 1 year after planting, with an increase in anisotropy in the upper layers throughout the rotation. About 60% of fine root intersects were found at a depth of more than 1 m, irrespective of stand age. The root distribution was isotropic in deep soil layers and kriged maps showed fine root clumping. A considerable volume of soil was explored by fine roots in eucalypt plantations on deep tropical soils, which might prevent water and nutrient losses by deep drainage after canopy closure and contribute to maximizing resource uses. PMID:23847645

Metasurface with interfering Fano resonance: manipulating transmission wave with high efficiency.

PubMed

Su, Zhaoxian; Song, Kun; Yin, Jianbo; Zhao, Xiaopeng

2017-06-15

We proposed a novel strategy to design a deep subwavelength metasurface with full 2π transmission phase modulation and high transmission efficiency by applying resonators with interfering Fano resonance. Theoretical investigation demonstrates that the transmission efficiency of the resonators depends on the direct transmission coefficient, direct reflection coefficient, and Q factor. When an impedance layer is added in the resonators, the direct transmission and direct reflection coefficients can be facilely manipulated so that the span of the transmission phase around the resonance frequency can be extended to 2π. As a result, we can continuously adjust the transmission phase from 0 to 2π through changing the geometric parameters of the resonators and construct a deep subwavelength metasurface with the resonators to manipulate the transmission wave with high efficiency. We also find that a layer of grating can be used as the impedance layer to change direct transmission and direct reflection in the actual design of the metasurface. The proposed strategy may provide effective guidance to design a deep subwavelength metasurface for controlling a transmitted wave with high efficiency.

Deep centers in AlGaN-based light emitting diode structures

NASA Astrophysics Data System (ADS)

Polyakov, A. Y.; Smirnov, N. B.; Govorkov, A. V.; Mil'vidskii, M. G.; Usikov, A. S.; Pushnyi, B. V.; Lundin, W. V.

1999-10-01

Deep traps were studied in GaN homojunction and AlGaN/GaN heterojunction light emitting diode (LED) p-i-n structures by means of deep levels transient spectroscopy (DLTS), admittance and electroluminescence (EL) spectra measurements. It is shown that, in homojunction LED structures, the EL spectra comes from recombination involving Mg acceptors in-diffusing into the active i-layer. This Mg in-diffusion is strongly suppressed in heterostructures with the upper p-type layer containing about 5% of Al. As a result the main peak in the EL spectra of heterostructures is shifted toward higher energy compared to homojunctions. Joint doping of the i-layer with Zn and Si allows to shift the main EL peak to longer wavelength. The dominant electron traps observed in the studied LED structures had ionization energies of 0.55 and 0.85 eV. The dominant hole traps had apparent ionization energies of 0.85 and 0.4 eV. The latter traps were shown to be metastable and it is argued that they could be at least in part responsible for the persistent photoconductivity observed in p-GaN.

Residual Deep Convolutional Neural Network Predicts MGMT Methylation Status.

PubMed

Korfiatis, Panagiotis; Kline, Timothy L; Lachance, Daniel H; Parney, Ian F; Buckner, Jan C; Erickson, Bradley J

2017-10-01

Predicting methylation of the O6-methylguanine methyltransferase (MGMT) gene status utilizing MRI imaging is of high importance since it is a predictor of response and prognosis in brain tumors. In this study, we compare three different residual deep neural network (ResNet) architectures to evaluate their ability in predicting MGMT methylation status without the need for a distinct tumor segmentation step. We found that the ResNet50 (50 layers) architecture was the best performing model, achieving an accuracy of 94.90% (+/- 3.92%) for the test set (classification of a slice as no tumor, methylated MGMT, or non-methylated). ResNet34 (34 layers) achieved 80.72% (+/- 13.61%) while ResNet18 (18 layers) accuracy was 76.75% (+/- 20.67%). ResNet50 performance was statistically significantly better than both ResNet18 and ResNet34 architectures (p < 0.001). We report a method that alleviates the need of extensive preprocessing and acts as a proof of concept that deep neural architectures can be used to predict molecular biomarkers from routine medical images.

A Weighted Deep Representation Learning Model for Imbalanced Fault Diagnosis in Cyber-Physical Systems.

PubMed

Wu, Zhenyu; Guo, Yang; Lin, Wenfang; Yu, Shuyang; Ji, Yang

2018-04-05

Predictive maintenance plays an important role in modern Cyber-Physical Systems (CPSs) and data-driven methods have been a worthwhile direction for Prognostics Health Management (PHM). However, two main challenges have significant influences on the traditional fault diagnostic models: one is that extracting hand-crafted features from multi-dimensional sensors with internal dependencies depends too much on expertise knowledge; the other is that imbalance pervasively exists among faulty and normal samples. As deep learning models have proved to be good methods for automatic feature extraction, the objective of this paper is to study an optimized deep learning model for imbalanced fault diagnosis for CPSs. Thus, this paper proposes a weighted Long Recurrent Convolutional LSTM model with sampling policy (wLRCL-D) to deal with these challenges. The model consists of 2-layer CNNs, 2-layer inner LSTMs and 2-Layer outer LSTMs, with under-sampling policy and weighted cost-sensitive loss function. Experiments are conducted on PHM 2015 challenge datasets, and the results show that wLRCL-D outperforms other baseline methods.

A New Deep Learning Model for Fault Diagnosis with Good Anti-Noise and Domain Adaptation Ability on Raw Vibration Signals

PubMed Central

Zhang, Wei; Peng, Gaoliang; Li, Chuanhao; Chen, Yuanhang; Zhang, Zhujun

2017-01-01

Intelligent fault diagnosis techniques have replaced time-consuming and unreliable human analysis, increasing the efficiency of fault diagnosis. Deep learning models can improve the accuracy of intelligent fault diagnosis with the help of their multilayer nonlinear mapping ability. This paper proposes a novel method named Deep Convolutional Neural Networks with Wide First-layer Kernels (WDCNN). The proposed method uses raw vibration signals as input (data augmentation is used to generate more inputs), and uses the wide kernels in the first convolutional layer for extracting features and suppressing high frequency noise. Small convolutional kernels in the preceding layers are used for multilayer nonlinear mapping. AdaBN is implemented to improve the domain adaptation ability of the model. The proposed model addresses the problem that currently, the accuracy of CNN applied to fault diagnosis is not very high. WDCNN can not only achieve 100% classification accuracy on normal signals, but also outperform the state-of-the-art DNN model which is based on frequency features under different working load and noisy environment conditions. PMID:28241451

A deep-sea sediment transport storm

NASA Astrophysics Data System (ADS)

Gross, Thomas F.; Williams, A. J.; Newell, A. R. M.

1988-02-01

Photographs taken of the sea bottom since the 1960s suggest that sediments at great depth may be actively resuspended and redistributed1. Further, it has been suspected that active resus-pension/transport may be required to maintain elevated concentrations of particles in deep-sea nepheloid layers. But currents with sufficient energy to erode the bottom, and to maintain the particles in suspension, have not been observed concurrently with large concentrations of particles in the deep nepheloid layer2-4. The high-energy benthic boundary-layer experiment (HEBBLE) was designed to test the hypothesis that bed modifications can result from local erosion and deposition as modelled by simple one-dimensional local forcing mechanics5. We observed several 'storms' of high kinetic energy and near-bed flow associated with large concentrations of suspended sediment during the year-long deployments of moored instruments at the HEBBLE study site. These observations, at 4,880 m off the Nova Scotian Rise in the north-west Atlantic, indicate that large episodic events may suspend bottom sediments in areas well removed from coastal and shelf sources.

A Weighted Deep Representation Learning Model for Imbalanced Fault Diagnosis in Cyber-Physical Systems

PubMed Central

Guo, Yang; Lin, Wenfang; Yu, Shuyang; Ji, Yang

2018-01-01

Predictive maintenance plays an important role in modern Cyber-Physical Systems (CPSs) and data-driven methods have been a worthwhile direction for Prognostics Health Management (PHM). However, two main challenges have significant influences on the traditional fault diagnostic models: one is that extracting hand-crafted features from multi-dimensional sensors with internal dependencies depends too much on expertise knowledge; the other is that imbalance pervasively exists among faulty and normal samples. As deep learning models have proved to be good methods for automatic feature extraction, the objective of this paper is to study an optimized deep learning model for imbalanced fault diagnosis for CPSs. Thus, this paper proposes a weighted Long Recurrent Convolutional LSTM model with sampling policy (wLRCL-D) to deal with these challenges. The model consists of 2-layer CNNs, 2-layer inner LSTMs and 2-Layer outer LSTMs, with under-sampling policy and weighted cost-sensitive loss function. Experiments are conducted on PHM 2015 challenge datasets, and the results show that wLRCL-D outperforms other baseline methods. PMID:29621131

Studying the distribution of deep Raman spectroscopy signals using liquid tissue phantoms with varying optical properties.

PubMed

Vardaki, Martha Z; Gardner, Benjamin; Stone, Nicholas; Matousek, Pavel

2015-08-07

In this study we employed large volume liquid tissue phantoms, consisting of a scattering agent (Intralipid), an absorption agent (Indian ink) and a synthesized calcification powder (calcium hydroxyapatite (HAP)) similar to that found in cancerous tissues (e.g. breast and prostate), to simulate human tissues. We studied experimentally the magnitude and origin of Raman signals in a transmission Raman geometry as a function of optical properties of the medium and the location of calcifications within the phantom. The goal was to inform the development of future noninvasive cancer screening applications in vivo. The results provide insight into light propagation and Raman scattering distribution in deep Raman measurements, exploring also the effect of the variation of relative absorbance of laser and Raman photons within the phantoms. Most notably when modeling breast and prostate tissues it follows that maximum signals is obtained from the front and back faces of the tissue with the central region contributing less to the measured spectrum.

Focusing light through biological tissue and tissue-mimicking phantoms up to 9.6 cm in thickness with digital optical phase conjugation

NASA Astrophysics Data System (ADS)

Shen, Yuecheng; Liu, Yan; Ma, Cheng; Wang, Lihong V.

2016-08-01

Optical phase conjugation (OPC)-based wavefront shaping techniques focus light through or within scattering media, which is critically important for deep-tissue optical imaging, manipulation, and therapy. However, to date, the sample thickness in OPC experiments has been limited to only a few millimeters. Here, by using a laser with a long coherence length and an optimized digital OPC system that can safely deliver more light power, we focused 532-nm light through tissue-mimicking phantoms up to 9.6 cm thick, as well as through ex vivo chicken breast tissue up to 2.5 cm thick. Our results demonstrate that OPC can be achieved even when photons have experienced on average 1000 scattering events. The demonstrated penetration of nearly 10 cm (˜100 transport mean free paths) has never been achieved before by any optical focusing technique, and it shows the promise of OPC for deep-tissue noninvasive optical imaging, manipulation, and therapy.

Specialized probes based on hydroxyapatite calcium for heart tissues research by atomic force microscopy

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

Zhukov, Mikhail, E-mail: cloudjyk@yandex.ru; Golubok, Alexander; Institute for Analytical Instrumentation, Russian Academy of Sciences

The new specialized AFM-probes with hydroxyapatite structures for atomic force microscopy of heart tissues calcification were created and studied. A process of probe fabrication is demonstrated. The adhesive forces between specialized hydroxyapatite probe and endothelium/subendothelial layers were investigated. It was found that the adhesion forces are significantly higher for the subendothelial layers. We consider that it is connected with the formation and localization of hydroxyapatite in the area of subendothelial layers of heart tissues. In addition, the roughness analysis and structure visualization of the endothelial surface of the heart tissue were carried out. The results show high efficiency of createdmore » specialized probes at study a calcinations process of the aortic heart tissues.« less

Volume Ice Radiolysis in the Outer Solar System

NASA Technical Reports Server (NTRS)

Cooper, John F.; Cooper, Paul D.

2006-01-01

The primary energy flux of charged particle components of the heliospheric and magnetospheric environments of the solar system is primarily carried by highly penetrating energetic particles. Although laboratory experiments on production of organics and oxidants typically only address effects on very thin surface layers, energy deposition occurs on surfaces of icy bodies of the outer solar system to meters in depth. Time scales for significant radiolytic deposition vary from thousands of years at millimeter depths on Europa to billions of years in the meters-deep regolith of Kuiper Belt Objects. Radioisotope decay (e.g., K-40) also contributes to volume radiolysis as the only energy source at much greater depths. Radiolytic oxygen is a potential resource for life within Europa and a partial source of oxygen for Saturn's magnetosphere and Titan's upper atmosphere. Interactions of very high energy cosmic rays with ices at Titan's surface may provide one of the few sources of oxidants in that highly reducing environment. The red colors of low-inclination classical Kuiper Belt Objects at 40-50 AU, and Centaur objects originating from this same population, may arise from volume radiolysis of deep ice layers below more refractory radiation crusts eroded away by surface sputtering and micrometeoroid impacts. A variety of techniques are potentially available to measure volume radiolysis products and have been proposed for study as part of the new Space Physics of Life initiative at NASA Goddard Space Flight Center. The technique of Electron Paramagnetic Resonance (EPR) has been used in medical studies to measure oxidant production in irradiated human tissue for cancer treatment. Other potential techniques include optical absorption spectroscopy and standard wet chemical analysis. These and other potential techniques are briefly reviewed for applicability to problems in solar system ice radiolysis and astrobiology.

Rock Abrasion Tool Exhibits the Deep Red Pigment of Mars

NASA Image and Video Library

2006-07-21

This image shows the round, metallic working end of the rock abrasion tool at the end of a metallic cylinder. The flat grinding face, attached brush, and much of the smooth, metallic exterior of cylinder are covered with a deep reddish-brown layer of dust

Dissipation in the deep interiors of Ganymede and Europa

NASA Astrophysics Data System (ADS)

Hussmann, Hauke; Shoji, Daigo; Steinbruegge, Gregor; Stark, Alexander; Sohl, Frank

2017-04-01

Jupiter's satellites are subject to strong tidal forces which result in variations of the gravitational potential and deformations of the satellites' surfaces on the diurnal tidal cycle. Tidal flexing in the deep interiors can be a significant heat source for the satellites' thermal-orbital evolution. Whereas typical structure models of Europa consist of a core, a silicate mantle, an ocean and an outer ice-I shell [1], pressures inside Ganymede are sufficient for high-pressure ice phases to occur between the silicate mantle and the ocean [2]. With current data it is unknown whether the deep interiors (i.e., Europa's silicate shell and Ganymede's silicate mantle and/or high-pressure ice layer) are dissipative. Other possibilities would be that the dissipation rates are in general very low (unlikely at least for Europa due to recent observations) or that dissipative processes are mainly occurring in the ice-I shell and/or ocean. Thus, for evaluations of the heating state of these satellites, it is important to measure the magnitude of the interior dissipation. However, observation of the interior layers such as high-pressure ice layers is more challenging than that of the surface ice-I layer. Here we suggest a method to constrain the dissipation states of the deep interiors of Ganymede and Europa by altimetry and gravity measurements from an orbiting or multi-flyby spacecraft. Tidal variations are generally described by the Love numbers k2 and h2 for the tide-induced potential variation due to internal mass redistribution and the radial surface displacement, respectively. The phase-lags of these complex numbers contain information about the rheological and dissipative states of the satellites. For the satellites we assume a decoupling of the outer ice-shell from the deep interior by a liquid subsurface water ocean. We show that, in this case, the phase-lag difference between the lags of k2 and h2 can provide information on the rheological and thermal state of the deep interiors if the viscosities of the deeper layers are small (the phase-lag difference is almost independent of the dissipation in the surface layer). In case of Ganymede, phase-lag differences can reach values of a few degrees for high-pressure ice viscosities of 1e13-1e14 Pa s (around the lower boundary at its melting temperature) and would indicate a highly dissipative state of the deep interior. In this case, in contrast to the phase lags itself, the phase-lag difference is dominated by dissipation in the high-pressure ice layer rather than dissipation within the ice-I shell. These phase lags would be detectable from spacecraft in orbit around the satellite [3]. For Europa the phase-lag difference could reach values exceeding 20 deg if the silicate mantle contains melt and phase-lag measurements could help distinguish between (1) a hot dissipative (melt-containing) silicate mantle which would in thermal equilibrium correspond to a very thin outer ice-I shell and (2) a cold deep interior implying that dissipation would mainly occur in a thick (several tens of km) outer ice-I shell. These measurements are highly relevant for ESA's Jupiter Icy Moons Explorer (JUICE) and NASA's Europa Multiple Flyby Mission, both targeted for the Jupiter system. References: [1] Schubert, G., F. Sohl and H. Hussmann 2009. Interior of Europa. In: Europa, (R.T. Pappalardo, W.B. McKinnon, K. Khurana, Eds.), University of Arizona Press, pp. 353 - 368. [2] Schubert G., J. D. Anderson, T. Spohn, and W. B. McKinnon 2004. Interior composition, structure, and dynamics of the Galilean satellites. In: F. Bagenal, T. E. Dowling, and W. B. McKinnon (eds.) Jupiter. The Planet, Satellites, and Magnetosphere, pp. 281-306. Cambridge University Press. [3] Hussmann, H., D. Shoji, G. Steinbrügge, A. Stark, F. Sohl 2016. Constraints on dissipation in the deep interiors of Ganymede and Europa from tidal phase-lags. Cel. Mech. Dyn. Astr. 126, 131 - 144.

In vivo optical coherence tomography in endoscopic diagnostics of bladder disease

NASA Astrophysics Data System (ADS)

Daniltchenko, Dmitri; Lankenau, Eva; Konig, Frank; Shay, Brian; Huettmann, Gereon; Sachs, Markus D.; Schnorr, Dietmar; Loening, Stefan A.

2004-07-01

Purpose: OCT is a new imaging method which produces a 3 mm wide x 2.5 mm deep 2D picture with a resolution of 15 μm. Materials and Methods: We utilised the Tomograph Sirius 713, developed at the Medical Laser Centre in cooperation with 4-Optics AG, Lubeck, Germany. This apparatus uses a special Super-Luminescence-Diode (SLD) that produces light within the near infrared wavelength, with a central wavelength of 1300 nm and spectral width of 45 nm. The coherence length is reduced to 15 μm. The light is introduced into a fibreglass optic which is a couple of meters long and is easy to handle. To measure the depth of invasion and position of urothelial bladder tumours, the fibreglass optic is attached to a regular endoscope (Wolf, Knittlingen, Germany) via a OCT adapter. That way, in parallel to the regular endoscopic view of the bladder mucosa with or without pathologic findings, an OCT picture of the superficial as well as the deeper muscle layers is visible online. OCT was used to obtaine 275 images from the bladder of 30 patients. Results: OCT of normal bladder mucosa produces an image with a cross section of up to 2.5 mm. It is possible to distinguish transitional epithelium, lamina propria, smooth muscles and capillaries. In cystitis the thickness of the mucosa is constant, but the distinction between the different layers is blurred. In squamous metaplasia there is thickening of the epithelial layer, with preservation of lamination of the lower layers. In transitional cell carcinoma there is a complete loss of the regular layered structure. Thus, the border between tumour and normal bladder tissue can be easily distinguished. Conclusions: This method can provide valuable information on tumour invasion and extension in real time and therefore influence therapeutic strategies

Cervical Cancer Stage IA

MedlinePlus

... of the cervix and vagina. An inset shows cancer in the cervix that is up to 5 mm deep, but ... microscope is found in the tissues of the cervix. In stage IA1, the cancer is not more than 3 millimeters deep and ...

Retinal Structure of Birds of Prey Revealed by Ultra-High Resolution Spectral-Domain Optical Coherence Tomography

PubMed Central

Ruggeri, Marco; Major, James C.; McKeown, Craig; Knighton, Robert W.; Puliafito, Carmen A.

2010-01-01

Purpose. To reveal three-dimensional (3-D) information about the retinal structures of birds of prey in vivo. Methods. An ultra-high resolution spectral-domain optical coherence tomography (SD-OCT) system was built for in vivo imaging of retinas of birds of prey. The calibrated imaging depth and axial resolution of the system were 3.1 mm and 2.8 μm (in tissue), respectively. 3-D segmentation was performed for calculation of the retinal nerve fiber layer (RNFL) map. Results. High-resolution OCT images were obtained of the retinas of four species of birds of prey: two diurnal hawks (Buteo platypterus and Buteo brachyurus) and two nocturnal owls (Bubo virginianus and Strix varia). These images showed the detailed retinal anatomy, including the retinal layers and the structure of the deep and shallow foveae. The calculated thickness map showed the RNFL distribution. Traumatic injury to one bird's retina was also successfully imaged. Conclusions. Ultra-high resolution SD-OCT provides unprecedented high-quality 2-D and 3-D in vivo visualization of the retinal structures of birds of prey. SD-OCT is a powerful imaging tool for vision research in birds of prey. PMID:20554605

Synthetic, multi-layer, self-oscillating vocal fold model fabrication.

PubMed

Murray, Preston R; Thomson, Scott L

2011-12-02

Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders. Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes). Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry, clinical instrument development, laryngeal aerodynamics, vocal fold contact pressure, and subglottal acoustics (a more comprehensive list can be found in Kniesburges et al.) Existing synthetic vocal fold models, however, have either been homogenous (one-layer models) or have been fabricated using two materials of differing stiffness (two-layer models). This approach does not allow for representation of the actual multi-layer structure of the human vocal folds that plays a central role in governing vocal fold flow-induced vibratory response. Consequently, one- and two-layer synthetic vocal fold models have exhibited disadvantages such as higher onset pressures than what are typical for human phonation (onset pressure is the minimum lung pressure required to initiate vibration), unnaturally large inferior-superior motion, and lack of a "mucosal wave" (a vertically-traveling wave that is characteristic of healthy human vocal fold vibration). In this paper, fabrication of a model with multiple layers of differing material properties is described. The model layers simulate the multi-layer structure of the human vocal folds, including epithelium, superficial lamina propria (SLP), intermediate and deep lamina propria (i.e., ligament; a fiber is included for anterior-posterior stiffness), and muscle (i.e., body) layers. Results are included that show that the model exhibits improved vibratory characteristics over prior one- and two-layer synthetic models, including onset pressure closer to human onset pressure, reduced inferior-superior motion, and evidence of a mucosal wave.