Rapid and efficient differentiation of Yersinia species using high-resolution melting analysis.

PubMed

Souza, Roberto A; Frazão, Miliane R; Almeida, Alzira M P; Falcão, Juliana P

2015-08-01

The primary goal of clinical microbiology is the accurate identification of the causative agent of the disease. Here, we describe a method for differentiation between Yersinia species using PCR-HRMA. The results revealed species-specific melting profiles. The herein developed assay can be used as an effective method to differentiate Yersinia species. Copyright © 2015 Elsevier B.V. All rights reserved.

Enhancement of slope efficiency and output power in GaN-based vertical-cavity surface-emitting lasers with a SiO2-buried lateral index guide

NASA Astrophysics Data System (ADS)

Kuramoto, Masaru; Kobayashi, Seiichiro; Akagi, Takanobu; Tazawa, Komei; Tanaka, Kazufumi; Saito, Tatsuma; Takeuchi, Tetsuya

2018-03-01

We have achieved a high output power of 6 mW from a 441 nm GaN-based vertical-cavity surface-emitting laser (VCSEL) under continuous wave (CW) operation, by reducing both the internal loss and the reflectivity of the front cavity mirror. A preliminary analysis of the internal loss revealed an enormously high transverse radiation loss in a conventional GaN-based VCSEL without lateral optical confinement (LOC). Introducing an LOC structure enhanced the slope efficiency by a factor of 4.7, with a further improvement to a factor of 6.7 upon reducing the front mirror reflectivity. The result was a slope efficiency of 0.87 W/A and an external differential quantum efficiency of 32% under pulsed operation. A flip-chip-bonded VCSEL also exhibited a high slope efficiency of 0.64 W/A and an external differential quantum efficiency of 23% for the front-side output under CW operation. The reflectivity of the cavity mirror was adjusted by varying the number of AlInN/GaN distributed Bragg reflector pairs from 46 to 42, corresponding to reflectivity values from 99.8% to 99.5%. These results demonstrate that a combination of internal loss reduction and cavity mirror control is a very effective way of obtaining a high output GaN-based VCSEL.

Differential results integrated with continuous and discrete gravity measurements between nearby stations

NASA Astrophysics Data System (ADS)

Xu, Weimin; Chen, Shi; Lu, Hongyan

2016-04-01

Integrated gravity is an efficient way in studying spatial and temporal characteristics of the dynamics and tectonics. Differential measurements based on the continuous and discrete gravity observations shows highly competitive in terms of both efficiency and precision with single result. The differential continuous gravity variation between the nearby stations, which is based on the observation of Scintrex g-Phone relative gravimeters in every single station. It is combined with the repeated mobile relative measurements or absolute results to study the regional integrated gravity changes. Firstly we preprocess the continuous records by Tsoft software, and calculate the theoretical earth tides and ocean tides by "MT80TW" program through high precision tidal parameters from "WPARICET". The atmospheric loading effects and complex drift are strictly considered in the procedure. Through above steps we get the continuous gravity in every station and we can calculate the continuous gravity variation between nearby stations, which is called the differential continuous gravity changes. Then the differential results between related stations is calculated based on the repeated gravity measurements, which are carried out once or twice every year surrounding the gravity stations. Hence we get the discrete gravity results between the nearby stations. Finally, the continuous and discrete gravity results are combined in the same related stations, including the absolute gravity results if necessary, to get the regional integrated gravity changes. This differential gravity results is more accurate and effective in dynamical monitoring, regional hydrologic effects studying, tectonic activity and other geodynamical researches. The time-frequency characteristics of continuous gravity results are discussed to insure the accuracy and efficiency in the procedure.

A novel composite adaptive flap controller design by a high-efficient modified differential evolution identification approach.

PubMed

Li, Nailu; Mu, Anle; Yang, Xiyun; Magar, Kaman T; Liu, Chao

2018-05-01

The optimal tuning of adaptive flap controller can improve adaptive flap control performance on uncertain operating environments, but the optimization process is usually time-consuming and it is difficult to design proper optimal tuning strategy for the flap control system (FCS). To solve this problem, a novel adaptive flap controller is designed based on a high-efficient differential evolution (DE) identification technique and composite adaptive internal model control (CAIMC) strategy. The optimal tuning can be easily obtained by DE identified inverse of the FCS via CAIMC structure. To achieve fast tuning, a high-efficient modified adaptive DE algorithm is proposed with new mutant operator and varying range adaptive mechanism for the FCS identification. A tradeoff between optimized adaptive flap control and low computation cost is successfully achieved by proposed controller. Simulation results show the robustness of proposed method and its superiority to conventional adaptive IMC (AIMC) flap controller and the CAIMC flap controllers using other DE algorithms on various uncertain operating conditions. The high computation efficiency of proposed controller is also verified based on the computation time on those operating cases. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Efficient and Controlled Generation of 2D and 3D Bile Duct Tissue from Human Pluripotent Stem Cell-Derived Spheroids.

PubMed

Tian, Lipeng; Deshmukh, Abhijeet; Ye, Zhaohui; Jang, Yoon-Young

2016-08-01

While in vitro liver tissue engineering has been increasingly studied during the last several years, presently engineered liver tissues lack the bile duct system. The lack of bile drainage not only hinders essential digestive functions of the liver, but also leads to accumulation of bile that is toxic to hepatocytes and known to cause liver cirrhosis. Clearly, generation of bile duct tissue is essential for engineering functional and healthy liver. Differentiation of human induced pluripotent stem cells (iPSCs) to bile duct tissue requires long and/or complex culture conditions, and has been inefficient so far. Towards generating a fully functional liver containing biliary system, we have developed defined and controlled conditions for efficient 2D and 3D bile duct epithelial tissue generation. A marker for multipotent liver progenitor in both adult human liver and ductal plate in human fetal liver, EpCAM, is highly expressed in hepatic spheroids generated from human iPSCs. The EpCAM high hepatic spheroids can, not only efficiently generate a monolayer of biliary epithelial cells (cholangiocytes), in a 2D differentiation condition, but also form functional ductal structures in a 3D condition. Importantly, this EpCAM high spheroid based biliary tissue generation is significantly faster than other existing methods and does not require cell sorting. In addition, we show that a knock-in CK7 reporter human iPSC line generated by CRISPR/Cas9 genome editing technology greatly facilitates the analysis of biliary differentiation. This new ductal differentiation method will provide a more efficient method of obtaining bile duct cells and tissues, which may facilitate engineering of complete and functional liver tissue in the future.

Robust and Highly-Efficient Differentiation of Functional Monocytic Cells from Human Pluripotent Stem Cells under Serum- and Feeder Cell-Free Conditions

PubMed Central

Yanagimachi, Masakatsu D.; Niwa, Akira; Tanaka, Takayuki; Honda-Ozaki, Fumiko; Nishimoto, Seiko; Murata, Yuuki; Yasumi, Takahiro; Ito, Jun; Tomida, Shota; Oshima, Koichi; Asaka, Isao; Goto, Hiroaki; Heike, Toshio; Nakahata, Tatsutoshi; Saito, Megumu K.

2013-01-01

Monocytic lineage cells (monocytes, macrophages and dendritic cells) play important roles in immune responses and are involved in various pathological conditions. The development of monocytic cells from human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) is of particular interest because it provides an unlimited cell source for clinical application and basic research on disease pathology. Although the methods for monocytic cell differentiation from ESCs/iPSCs using embryonic body or feeder co-culture systems have already been established, these methods depend on the use of xenogeneic materials and, therefore, have a relatively poor-reproducibility. Here, we established a robust and highly-efficient method to differentiate functional monocytic cells from ESCs/iPSCs under serum- and feeder cell-free conditions. This method produced 1.3×106±0.3×106 floating monocytes from approximately 30 clusters of ESCs/iPSCs 5–6 times per course of differentiation. Such monocytes could be differentiated into functional macrophages and dendritic cells. This method should be useful for regenerative medicine, disease-specific iPSC studies and drug discovery. PMID:23573196

High Efficient Differentiation of Functional Hepatocytes from Porcine Induced Pluripotent Stem Cells

PubMed Central

Ao, Ying; Mich-Basso, Jocelyn Danielle; Lin, Bo; Yang, Lei

2014-01-01

Hepatocyte transplantation is considered to be a promising therapy for patients with liver diseases. Induced pluripotent stem cells (iPSCs) provide an unlimited source for the generation of functional hepatocytes. In this study, we generated iPSCs from porcine ear fibroblasts (PEFs) by overexpressing Sox2, Klf4, Oct4, and c-Myc (SKOM), and developed a novel strategy for the efficient differentiation of hepatocyte-like cells from porcine iPSCs by following the processes of early liver development. The differentiated cells displayed the phenotypes of hepatocytes, exhibited classic hepatocyte-associated bio-functions, such as LDL uptake, glycogen storage and urea secretion, as well as possessed the metabolic activities of cytochrome P-450 (CYP) 3A and 2C. Furthermore, we compared the hepatocyte differentiation efficacy of our protocol with another published method, and the results demonstrated that our differentiation strategy could significantly improve the generation of morphological and functional hepatocyte-like cells from porcine iPSCs. In conclusion, this study establishes an efficient method for in vitro generation of functional hepatocytes from porcine iPSCs, which could represent a promising cell source for preclinical testing of cell-based therapeutics for liver failure and for pharmacological applications. PMID:24949734

Mathematical model for prediction of efficiency indicators of educational activity in high school

NASA Astrophysics Data System (ADS)

Tikhonova, O. M.; Kushnikov, V. A.; Fominykh, D. S.; Rezchikov, A. F.; Ivashchenko, V. A.; Bogomolov, A. S.; Filimonyuk, L. Yu; Dolinina, O. N.; Kushnikov, O. V.; Shulga, T. E.; Tverdokhlebov, V. A.

2018-05-01

The quality of high school is a current problem all over the world. The paper presents the system dedicated to predicting the accreditation indicators of technical universities based on J. Forrester mechanism of system dynamics. The mathematical model is developed for prediction of efficiency indicators of the educational activity and is based on the apparatus of nonlinear differential equations.

Production of erythrocytes from directly isolated or Delta1 Notch ligand expanded CD34+ hematopoietic progenitor cells: process characterization, monitoring and implications for manufacture.

PubMed

Glen, Katie E; Workman, Victoria L; Ahmed, Forhad; Ratcliffe, Elizabeth; Stacey, Adrian J; Thomas, Robert J

2013-09-01

Economic ex vivo manufacture of erythrocytes at 10(12) cell doses requires an efficiently controlled bio-process capable of extensive proliferation and high terminal density. High-resolution characterization of the process would identify production strategies for increased efficiency, monitoring and control. CD34(+) cord blood cells or equivalent cells that had been pre-expanded for 7 days with Delta1 Notch ligand were placed in erythroid expansion and differentiation conditions in a micro-scale ambr suspension bioreactor. Multiple culture parameters were varied, and phenotype markers and metabolites measured to identify conserved trends and robust monitoring markers. The cells exhibited a bi-modal erythroid differentiation pattern with an erythroid marker peak after 2 weeks and 3 weeks of culture; differentiation was comparatively weighted toward the second peak in Delta1 pre-expanded cells. Both differentiation events were strengthened by omission of stem cell factor and dexamethasone. The cumulative cell proliferation and death, or directly measured CD45 expression, enabled monitoring of proliferative rate of the cells. The metabolic activities of the cultures (glucose, glutamine and ammonia consumption or production) were highly variable but exhibited systematic change synchronized with the change in differentiation state. Erythroid differentiation chronology is partly determined by the heterogeneous CD34(+) progenitor compartment with implications for input control; Delta1 ligand-mediated progenitor culture can alter differentiation profile with control benefits for engineering production strategy. Differentiation correlated changes in cytokine response, markers and metabolic state will enable scientifically designed monitoring and timing of manufacturing process steps. Copyright © 2013 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Single-cell RNA sequencing reveals metallothionein heterogeneity during hESC differentiation to definitive endoderm.

PubMed

Lu, Junjie; Baccei, Anna; Lummertz da Rocha, Edroaldo; Guillermier, Christelle; McManus, Sean; Finney, Lydia A; Zhang, Cheng; Steinhauser, Matthew L; Li, Hu; Lerou, Paul H

2018-04-01

Differentiation of human pluripotent stem cells towards definitive endoderm (DE) is the critical first step for generating cells comprising organs such as the gut, liver, pancreas and lung. This in-vitro differentiation process generates a heterogeneous population with a proportion of cells failing to differentiate properly and maintaining expression of pluripotency factors such as Oct4. RNA sequencing of single cells collected at four time points during a 4-day DE differentiation identified high expression of metallothionein genes in the residual Oct4-positive cells that failed to differentiate to DE. Using X-ray fluorescence microscopy and multi-isotope mass spectrometry, we discovered that high intracellular zinc level corresponds with persistent Oct4 expression and failure to differentiate. This study improves our understanding of the cellular heterogeneity during in-vitro directed differentiation and provides a valuable resource to improve DE differentiation efficiency. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Study on efficiency droop in InGaN/GaN light-emitting diodes based on differential carrier lifetime analysis

NASA Astrophysics Data System (ADS)

Meng, Xiao; Wang, Lai; Hao, Zhibiao; Luo, Yi; Sun, Changzheng; Han, Yanjun; Xiong, Bing; Wang, Jian; Li, Hongtao

2016-01-01

Efficiency droop is currently one of the most popular research problems for GaN-based light-emitting diodes (LEDs). In this work, a differential carrier lifetime measurement system is optimized to accurately determine carrier lifetimes (τ) of blue and green LEDs under different injection current (I). By fitting the τ-I curves and the efficiency droop curves of the LEDs according to the ABC carrier rate equation model, the impact of Auger recombination and carrier leakage on efficiency droop can be characterized simultaneously. For the samples used in this work, it is found that the experimental τ-I curves cannot be described by Auger recombination alone. Instead, satisfactory fitting results are obtained by taking both carrier leakage and carriers delocalization into account, which implies carrier leakage plays a more significant role in efficiency droop at high injection level.

Proteomic analysis indicates that mitochondrial energy metabolism in skeletal muscle tissue is negatively correlated with feed efficiency in pigs

NASA Astrophysics Data System (ADS)

Fu, Liangliang; Xu, Yueyuan; Hou, Ye; Qi, Xiaolong; Zhou, Lian; Liu, Huiying; Luan, Yu; Jing, Lu; Miao, Yuanxin; Zhao, Shuhong; Liu, Huazhen; Li, Xinyun

2017-03-01

Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE is essential for trait improvement. In this study, the skeletal muscle proteome of high-FE and low-FE pigs were investigated by the iTRAQ approach. A total of 1780 proteins were identified, among which 124 proteins were differentially expressed between the high- and low-FE pigs, with 74 up-regulated and 50 down-regulated in the high-FE pigs. Ten randomly selected differentially expressed proteins (DEPs) were validated by Western blotting and quantitative PCR (qPCR). Gene ontology (GO) analysis showed that all the 25 DEPs located in mitochondria were down-regulated in the high-FE pigs. Furthermore, the glucose-pyruvate-tricarboxylic acid (TCA)-oxidative phosphorylation energy metabolism signaling pathway was found to differ between high- and low-FE pigs. The key enzymes involved in the conversion of glucose to pyruvate were up-regulated in the high-FE pigs. Thus, our results suggested mitochondrial energy metabolism in the skeletal muscle tissue was negatively correlated with FE in pigs, and glucose utilization to generate ATP was more efficient in the skeletal muscle tissue of high-FE pigs. This study offered new targets and pathways for improvement of FE in pigs.

Proteomic analysis indicates that mitochondrial energy metabolism in skeletal muscle tissue is negatively correlated with feed efficiency in pigs

PubMed Central

Fu, Liangliang; Xu, Yueyuan; Hou, Ye; Qi, Xiaolong; Zhou, Lian; Liu, Huiying; Luan, Yu; Jing, Lu; Miao, Yuanxin; Zhao, Shuhong; Liu, Huazhen; Li, Xinyun

2017-01-01

Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE is essential for trait improvement. In this study, the skeletal muscle proteome of high-FE and low-FE pigs were investigated by the iTRAQ approach. A total of 1780 proteins were identified, among which 124 proteins were differentially expressed between the high- and low-FE pigs, with 74 up-regulated and 50 down-regulated in the high-FE pigs. Ten randomly selected differentially expressed proteins (DEPs) were validated by Western blotting and quantitative PCR (qPCR). Gene ontology (GO) analysis showed that all the 25 DEPs located in mitochondria were down-regulated in the high-FE pigs. Furthermore, the glucose-pyruvate-tricarboxylic acid (TCA)-oxidative phosphorylation energy metabolism signaling pathway was found to differ between high- and low-FE pigs. The key enzymes involved in the conversion of glucose to pyruvate were up-regulated in the high-FE pigs. Thus, our results suggested mitochondrial energy metabolism in the skeletal muscle tissue was negatively correlated with FE in pigs, and glucose utilization to generate ATP was more efficient in the skeletal muscle tissue of high-FE pigs. This study offered new targets and pathways for improvement of FE in pigs. PMID:28345649

Derivation of highly purified cardiomyocytes from human induced pluripotent stem cells using small molecule-modulated differentiation and subsequent glucose starvation.

PubMed

Sharma, Arun; Li, Guang; Rajarajan, Kuppusamy; Hamaguchi, Ryoko; Burridge, Paul W; Wu, Sean M

2015-03-18

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have become an important cell source to address the lack of primary cardiomyocytes available for basic research and translational applications. To differentiate hiPSCs into cardiomyocytes, various protocols including embryoid body (EB)-based differentiation and growth factor induction have been developed. However, these protocols are inefficient and highly variable in their ability to generate purified cardiomyocytes. Recently, a small molecule-based protocol utilizing modulation of Wnt/β-Catenin signaling was shown to promote cardiac differentiation with high efficiency. With this protocol, greater than 50%-60% of differentiated cells were cardiac troponin-positive cardiomyocytes were consistently observed. To further increase cardiomyocyte purity, the differentiated cells were subjected to glucose starvation to specifically eliminate non-cardiomyocytes based on the metabolic differences between cardiomyocytes and non-cardiomyocytes. Using this selection strategy, we consistently obtained a greater than 30% increase in the ratio of cardiomyocytes to non-cardiomyocytes in a population of differentiated cells. These highly purified cardiomyocytes should enhance the reliability of results from human iPSC-based in vitro disease modeling studies and drug screening assays.

2-Micron Laser Transmitter for Coherent CO2 DIAL Measurement

NASA Technical Reports Server (NTRS)

Singh, Upendra N.; Bai, Yingxin; Yu, Jirong

2009-01-01

Carbon dioxide (CO2) has been recognized as one of the most important greenhouse gases. It is essential for the study of global warming to accurately measure the CO2 concentration in the atmosphere and continuously record its variation. A high repetition rate, highly efficient, Q-switched 2-micron laser system as the transmitter of a coherent differential absorption lidar for CO2 measurement has been developed in NASA Langley Research Center. This laser system is capable of making a vertical profiling of CO2 from ground and column measurement of CO2 from air and space-borne platform. The transmitter is a master-slave laser system. The master laser operates in a single frequency, either on-line or off-line of a selected CO2 absorption line. The slave laser is a Q-switched ring-cavity Ho:YLF laser which is pumped by a Tm:fiber laser. The repetition rate can be adjusted from a few hundred Hz to 10 kHz. The injection seeding success rate is from 99.4% to 99.95%. For 1 kHz operation, the output pulse energy is 5.5mJ with the pulse length of 50 ns. The optical-to-optical efficiency is 39% when the pump power is 14.5W. A Ho:YLF laser operating in the range of 2.05 micrometers can be tuned over several characteristic lines of CO2 absorption. Experimentally, a diode pumped Ho:Tm:YLF laser has been successfully used as the transmitter of coherent differential absorption lidar for the measurement of CO2 with a repetition rate of 5 Hz and pulse energy of 75 mJ. For coherent detection, high repetition rate is required for speckle averaging to obtain highly precise measurements. However, a diode pumped Ho:Tm:YLF laser can not operate in high repetition rate due to the large heat loading and up-conversion. A Tm:fiber laser pumped Ho:YLF laser with low heat loading can operate in high repetition rate. A theoretical model has been established to simulate the performance of Tm:fiber laser pumped Ho:YLF lasers. For continuous wave (CW) operation, high pump intensity with small beam size is suitable for high efficiency. For Q-switched operation, the optimal energy extraction relies on the pump intensity, pump volume, and pump duration which is inversely proportion to the repetition rate. CW and Q-switched Ho:YLF lasers with different linear cavity configurations have been designed and demonstrated for a 30 W Tm:fiber pump laser. The CW Ho laser slope efficiency and optical-to-optical efficiencies reach 65% and 55%, respectively. The pulsed laser efficiency depends on the repetition rate. For 1 kHz operation, the optical-to-optical efficiency is 39% when the pump power is 14.5W. Currently, the injection seeding success rate is between 99.4% and 99.95%. After a ten thousand pulses, the standard deviation of the laser frequency jitter is about 3 MHz. It meets the requirements of highly precise CO2 concentration measurement. In conclusion, an injection seeded, high repetition rate, Q-switched Ho:YLF laser has been developed for a coherent CO2 differential absorption lidar. This master-slave laser system has high optical-to-optical efficiency and seeding success rate. It can potentially meet the requirements of the coherent detection of CO2 concentration by a differential absorption lidar technique.

CD71(high) population represents primitive erythroblasts derived from mouse embryonic stem cells.

PubMed

Chao, Ruihua; Gong, Xueping; Wang, Libo; Wang, Pengxiang; Wang, Yuan

2015-01-01

The CD71/Ter119 combination has been widely used to reflect dynamic maturation of erythrocytes in vivo. However, because CD71 is expressed on all proliferating cells, it is unclear whether it can be utilized as an erythrocyte-specific marker during differentiation of embryonic stem cells (ESCs). In this study, we revealed that a population expressing high level of CD71 (CD71(high)) during mouse ESC differentiation represented an in vitro counterpart of yolk sac-derived primitive erythroblasts (EryPs) isolated at 8.5days post coitum. In addition, these CD71(high) cells went through "maturational globin switching" and enucleated during terminal differentiation in vitro that were similar to the yolk sac-derived EryPs in vivo. We further demonstrated that the formation of CD71(high) population was regulated differentially by key factors including Scl, HoxB4, Eaf1, and Klf1. Taken together, our study provides a technical advance that allows efficient segregation of EryPs from differentiated ESCs in vitro for further understanding molecular regulation during primitive erythropoiesis. Copyright © 2014. Published by Elsevier B.V.

Comparison of neutron spectra measured with three sizes of organic liquid scintillators using differentiation analysis

NASA Technical Reports Server (NTRS)

Shook, D. F.; Pierce, C. R.

1972-01-01

Proton recoil distributions were obtained by using organic liquid scintillators of different size. The measured distributions are converted to neutron spectra by differentiation analysis for comparison to the unfolded spectra of the largest scintillator. The approximations involved in the differentiation analysis are indicated to have small effects on the precision of neutron spectra measured with the smaller scintillators but introduce significant error for the largest scintillator. In the case of the smallest cylindrical scintillator, nominally 1.2 by 1.3 cm, the efficiency is shown to be insensitive to multiple scattering and to the angular distribution to the incident flux. These characteristics of the smaller scintillator make possible its use to measure scalar flux spectra within media high efficiency is not required.

A High Proliferation Rate is Critical for Reproducible and Standardized Embryoid Body Formation from Laminin-521-Based Human Pluripotent Stem Cell Cultures.

PubMed

Dziedzicka, Dominika; Markouli, Christina; Barbé, Lise; Spits, Claudia; Sermon, Karen; Geens, Mieke

2016-12-01

When aiming for homogenous embryoid body (EB) differentiation, the use of equal-sized EBs is required to avoid a size-induced differentiation bias. In this study we developed an efficient and standardized EB formation protocol for human pluripotent stem cells (hPSC) cultured in a laminin-521-based xeno-free system. As the cell proliferation rate of the cells growing on laminin-521 strongly affected the efficiency of aggregate formation, we found that recently passaged cells, as well as the addition of ROCK inhibitor, were essential for reproducible EB formation from hPSC single-cell suspensions. EBs could be obtained in a variety of differentiation media, in 96-well round-bottom plates and in hanging drops. Gene expression studies on differentially sized EBs from three individual human embryonic stem cell lines demonstrated that the medium used for differentiation influenced the differentiation outcome to a much greater extent than the number of cells used for the initial EB formation. Our findings give a new insight into factors that influence the EB formation and differentiation process. This optimized method allows us to easily manipulate EB formation and provide an excellent starting point for downstream EB-based differentiation protocols.

Induction of mice adult bone marrow mesenchymal stem cells into functional motor neuron-like cells.

PubMed

Abdullah, Rafal H; Yaseen, Nahi Y; Salih, Shahlaa M; Al-Juboory, Ahmad Adnan; Hassan, Ayman; Al-Shammari, Ahmed Majeed

2016-11-01

The differentiation of mesenchymal stem cells (MSC) into acetylcholine secreted motor neuron-like cells, followed by elongation of the cell axon, is a promising treatment for spinal cord injury and motor neuron cell dysfunction in mammals. Differentiation is induced through a pre-induction step using Beta- mercaptoethanol (BME) followed by four days of induction with retinoic acid and sonic hedgehog. This process results in a very efficient differentiation of BM-MSCs into motor neuron-like cells. Immunocytochemistry showed that these treated cells had specific motor neural markers: microtubule associated protein-2 and acetylcholine transferase. The ability of these cells to function as motor neuron cells was assessed by measuring acetylcholine levels in a culture media during differentiation. High-performance liquid chromatography (HPLC) showed that the differentiated cells were functional. Motor neuron axon elongation was then induced by adding different concentrations of a nerve growth factor (NGF) to the differentiation media. Using a collagen matrix to mimic the natural condition of neural cells in a three-dimensional model showed that the MSCs were successfully differentiated into motor neuron-like cells. This process can efficiently differentiate MSCs into functional motor neurons that can be used for autologous nervous system therapy and especially for treating spinal cord injuries. Copyright © 2016 Elsevier B.V. All rights reserved.

A Wireless Fiber Photometry System Based on a High-Precision CMOS Biosensor With Embedded Continuous-Time Modulation.

PubMed

Khiarak, Mehdi Noormohammadi; Martianova, Ekaterina; Bories, Cyril; Martel, Sylvain; Proulx, Christophe D; De Koninck, Yves; Gosselin, Benoit

2018-06-01

Fluorescence biophotometry measurements require wide dynamic range (DR) and high-sensitivity laboratory apparatus. Indeed, it is often very challenging to accurately resolve the small fluorescence variations in presence of noise and high-background tissue autofluorescence. There is a great need for smaller detectors combining high linearity, high sensitivity, and high-energy efficiency. This paper presents a new biophotometry sensor merging two individual building blocks, namely a low-noise sensing front-end and a order continuous-time modulator (CTSDM), into a single module for enabling high-sensitivity and high energy-efficiency photo-sensing. In particular, a differential CMOS photodetector associated with a differential capacitive transimpedance amplifier-based sensing front-end is merged with an incremental order 1-bit CTSDM to achieve a large DR, low hardware complexity, and high-energy efficiency. The sensor leverages a hardware sharing strategy to simplify the implementation and reduce power consumption. The proposed CMOS biosensor is integrated within a miniature wireless head mountable prototype for enabling biophotometry with a single implantable fiber in the brain of live mice. The proposed biophotometry sensor is implemented in a 0.18- CMOS technology, consuming from a 1.8- supply voltage, while achieving a peak dynamic range of over a 50- input bandwidth, a sensitivity of 24 mV/nW, and a minimum detectable current of 2.46- at a 20- sampling rate.

[Validation of Differential Extraction Kit in forensic sexual assault cases].

PubMed

Wu, Dan; Cao, Yu; Xu, Yan; He, Bai-Fang; Bi, Gang; Zhou, Huai-Gu

2009-12-01

To evaluate the validity of Differential Extraction Kit in isolating spermatozoa and epithelial cell DNA from mixture samples. Selective lysis of spermatid and epithelial cells combined with paramagnetic particle method were applied to extract the DNA from the mock samples under controlled conditions and forensic case samples, and template DNA were analyzed by STR genotype method. This Differential Extraction Kit is efficient to obtain high quality spermatid and epithelial cell DNA from the mixture samples with different proportion of sperm to epithelial cell. The Differential Extraction Kit can be applied in DNA extraction for mixed stain from forensic sexual assault samples.

An automated high throughput screening-compatible assay to identify regulators of stem cell neural differentiation.

PubMed

Casalino, Laura; Magnani, Dario; De Falco, Sandro; Filosa, Stefania; Minchiotti, Gabriella; Patriarca, Eduardo J; De Cesare, Dario

2012-03-01

The use of Embryonic Stem Cells (ESCs) holds considerable promise both for drug discovery programs and the treatment of degenerative disorders in regenerative medicine approaches. Nevertheless, the successful use of ESCs is still limited by the lack of efficient control of ESC self-renewal and differentiation capabilities. In this context, the possibility to modulate ESC biological properties and to obtain homogenous populations of correctly specified cells will help developing physiologically relevant screens, designed for the identification of stem cell modulators. Here, we developed a high throughput screening-suitable ESC neural differentiation assay by exploiting the Cell(maker) robotic platform and demonstrated that neural progenies can be generated from ESCs in complete automation, with high standards of accuracy and reliability. Moreover, we performed a pilot screening providing proof of concept that this assay allows the identification of regulators of ESC neural differentiation in full automation.

High-efficiency generation of induced pluripotent mesenchymal stem cells from human dermal fibroblasts using recombinant proteins.

PubMed

Chen, Fanfan; Zhang, Guoqiang; Yu, Ling; Feng, Yanye; Li, Xianghui; Zhang, Zhijun; Wang, Yongting; Sun, Dapeng; Pradhan, Sriharsa

2016-07-30

Induced pluripotent mesenchymal stem cells (iPMSCs) are novel candidates for drug screening, regenerative medicine, and cell therapy. However, introduction of transcription factor encoding genes for induced pluripotent stem cell (iPSC) generation which could be used to generate mesenchymal stem cells is accompanied by the risk of insertional mutations in the target cell genome. We demonstrate a novel method using an inactivated viral particle to package and deliver four purified recombinant Yamanaka transcription factors (Sox2, Oct4, Klf4, and c-Myc) resulting in reprogramming of human primary fibroblasts. Whole genome bisulfite sequencing was used to analyze genome-wide CpG methylation of human iPMSCs. Western blot, quantitative PCR, immunofluorescence, and in-vitro differentiation were used to assess the pluripotency of iPMSCs. The resulting reprogrammed fibroblasts show high-level expression of stem cell markers. The human fibroblast-derived iPMSC genome showed gains in DNA methylation in low to medium methylated regions and concurrent loss of methylation in previously hypermethylated regions. Most of the differentially methylated regions are close to transcription start sites and many of these genes are pluripotent pathway associated. We found that DNA methylation of these genes is regulated by the four iPSC transcription factors, which functions as an epigenetic switch during somatic reprogramming as reported previously. These iPMSCs successfully differentiate into three embryonic germ layer cells, both in vitro and in vivo. Following multipotency induction in our study, the delivered transcription factors were degraded, leading to an improved efficiency of subsequent programmed differentiation. Recombinant transcription factor based reprogramming and derivatization of iPMSC offers a novel high-efficiency approach for regenerative medicine from patient-derived cells.

Constant-Differential-Pressure Two-Fluid Accumulator

NASA Technical Reports Server (NTRS)

Piecuch, Benjamin; Dalton, Luke T.

2010-01-01

A two-fluid accumulator has been designed, built, and demonstrated to provide an acceptably close approximation to constant differential static pressure between two fluids over the full ranges of (1) accumulator stroke, (2) rates of flow of the fluids, and (3) common static pressure applied to the fluids. Prior differential- pressure two-fluid accumulators are generally not capable of maintaining acceptably close approximations to constant differential pressures. The inadequacies of a typical prior differential-pressure two-fluid accumulator can be summarized as follows: The static differential pressure is governed by the intrinsic spring rate (essentially, the stiffness) of an accumulator tank. The spring rate can be tailored through selection of the tank-wall thickness, selection of the number and/or shape of accumulator convolutions, and/or selection of accumulator material(s). Reliance on the intrinsic spring rate of the tank results in three severe limitations: (1) The spring rate and the expulsion efficiency tend to be inversely proportional to each other: that is to say, as the stiffness (and thus the differential pressure) is increased, the range of motion of the accumulator is reduced. (2) As the applied common static pressure increases, the differential pressure tends to decrease. An additional disadvantage, which may or may not be considered limiting, depending on the specific application, is that an increase in stiffness entails an increase in weight. (3) The additional weight required by a low expulsion efficiency accumulator eliminates the advantage given to such gas storage systems. The high expulsion efficiency provided by this two-fluid accumulator allows for a lightweight, tightly packaged system, which can be used in conjunction with a fuel cell-based system.

An improved protocol that induces human embryonic stem cells to differentiate into neural cells in vitro.

PubMed

Zhou, Jun-Mei; Chu, Jian-Xin; Chen, Xue-Jin

2008-01-01

Human embryonic stem (ES) cells have the capacity for self-renewal and are able to differentiate into any cell type. However, obtaining high-efficient neural differentiation from human ES cells remains a challenge. This study describes an improved 4-stage protocol to induce a human ES cell line derived from a Chinese population to differentiate into neural cells. At the first stage, embryonic bodies (EBs) were formed in a chemically-defined neural inducing medium rather than in traditional serum or serum-replacement medium. At the second stage, rosette-like structures were formed. At the third stage, the rosette-like structures were manually selected rather than enzymatically digested to form floating neurospheres. At the fourth stage, the neurospheres were further differentiated into neurons. The results show that, at the second stage, the rate of the formation of rosette-like structures from EBs induced by noggin was 88+/-6.32%, higher than that of retinoic acid 55+/-5.27%. Immunocytochemistry staining was used to confirm the neural identity of the cells. These results show a major improvement in obtaining efficient neural differentiation of human ES cells.

Efficient production of erythroid, megakaryocytic and myeloid cells, using single cell-derived iPSC colony differentiation.

PubMed

Hansen, Marten; Varga, Eszter; Aarts, Cathelijn; Wust, Tatjana; Kuijpers, Taco; von Lindern, Marieke; van den Akker, Emile

2018-04-28

Hematopoietic differentiation of human induced pluripotent stem cells (iPSCs) provide opportunities not only for fundamental research and disease modelling/drug testing but also for large-scale production of blood effector cells for future clinical application. Although there are multiple ways to differentiate human iPSCs towards hematopoietic lineages, there is a need to develop reproducible and robust protocols. Here we introduce an efficient way to produce three major blood cell types using a standardized differentiation protocol that starts with a single hematopoietic initiation step. This system is feeder-free, avoids EB-formation, starts with a hematopoietic initiation step based on a novel single cell-derived iPSC colony differentiation and produces multi-potential progenitors within 8-10 days. Followed by lineage-specific growth factor supplementation these cells can be matured into well characterized erythroid, megakaryocytic and myeloid cells with high-purity, without transcription factor overexpression or any kind of pre-purification step. This standardized differentiation system provides a simple platform to produce specific blood cells in a reproducible manner for hematopoietic development studies, disease modelling, drug testing and the potential for future therapeutic applications. Copyright © 2018. Published by Elsevier B.V.

Differentiation therapy revisited.

PubMed

de Thé, Hugues

2018-02-01

The concept of differentiation therapy emerged from the fact that hormones or cytokines may promote differentiation ex vivo, thereby irreversibly changing the phenotype of cancer cells. Its hallmark success has been the treatment of acute promyelocytic leukaemia (APL), a condition that is now highly curable by the combination of retinoic acid (RA) and arsenic. Recently, drugs that trigger differentiation in a variety of primary tumour cells have been identified, suggesting that they are clinically useful. This Opinion article analyses the basis for the clinical successes of RA or arsenic in APL by assessing the respective roles of terminal maturation and loss of self-renewal. By reviewing other successful examples of drug-induced tumour cell differentiation, novel approaches to transform differentiating drugs into more efficient therapies are proposed.

Doping-enhanced radiative efficiency enables lasing in unpassivated GaAs nanowires

PubMed Central

Burgess, Tim; Saxena, Dhruv; Mokkapati, Sudha; Li, Zhe; Hall, Christopher R.; Davis, Jeffrey A.; Wang, Yuda; Smith, Leigh M.; Fu, Lan; Caroff, Philippe; Tan, Hark Hoe; Jagadish, Chennupati

2016-01-01

Nanolasers hold promise for applications including integrated photonics, on-chip optical interconnects and optical sensing. Key to the realization of current cavity designs is the use of nanomaterials combining high gain with high radiative efficiency. Until now, efforts to enhance the performance of semiconductor nanomaterials have focused on reducing the rate of non-radiative recombination through improvements to material quality and complex passivation schemes. Here we employ controlled impurity doping to increase the rate of radiative recombination. This unique approach enables us to improve the radiative efficiency of unpassivated GaAs nanowires by a factor of several hundred times while also increasing differential gain and reducing the transparency carrier density. In this way, we demonstrate lasing from a nanomaterial that combines high radiative efficiency with a picosecond carrier lifetime ready for high speed applications. PMID:27311597

Dielectric metasurfaces solve differential and integro-differential equations.

PubMed

Abdollahramezani, Sajjad; Chizari, Ata; Dorche, Ali Eshaghian; Jamali, Mohammad Vahid; Salehi, Jawad A

2017-04-01

Leveraging subwavelength resonant nanostructures, plasmonic metasurfaces have recently attracted much attention as a breakthrough concept for engineering optical waves both spatially and spectrally. However, inherent ohmic losses concomitant with low coupling efficiencies pose fundamental impediments over their practical applications. Not only can all-dielectric metasurfaces tackle such substantial drawbacks, but also their CMOS-compatible configurations support both Mie resonances that are invariant to the incident angle. Here, we report on a transmittive metasurface comprising arrayed silicon nanodisks embedded in a homogeneous dielectric medium to manipulate phase and amplitude of incident light locally and almost independently. By taking advantage of the interplay between the electric/magnetic resonances and employing general concepts of spatial Fourier transformation, a highly efficient metadevice is proposed to perform mathematical operations including solution of ordinary differential and integro-differential equations with constant coefficients. Our findings further substantiate dielectric metasurfaces as promising candidates for miniaturized, two-dimensional, and planar optical analog computing systems that are much thinner than their conventional lens-based counterparts.

Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data.

PubMed

Liu, Zhenqiu; Sun, Fengzhu; Braun, Jonathan; McGovern, Dermot P B; Piantadosi, Steven

2015-04-01

Identifying disease associated taxa and constructing networks for bacteria interactions are two important tasks usually studied separately. In reality, differentiation of disease associated taxa and correlation among taxa may affect each other. One genus can be differentiated because it is highly correlated with another highly differentiated one. In addition, network structures may vary under different clinical conditions. Permutation tests are commonly used to detect differences between networks in distinct phenotypes, and they are time-consuming. In this manuscript, we propose a multilevel regularized regression method to simultaneously identify taxa and construct networks. We also extend the framework to allow construction of a common network and differentiated network together. An efficient algorithm with dual formulation is developed to deal with the large-scale n ≪ m problem with a large number of taxa (m) and a small number of samples (n) efficiently. The proposed method is regularized with a general Lp (p ∈ [0, 2]) penalty and models the effects of taxa abundance differentiation and correlation jointly. We demonstrate that it can identify both true and biologically significant genera and network structures. Software MLRR in MATLAB is available at http://biostatistics.csmc.edu/mlrr/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Differential detection in quadrature-quadrature phase shift keying (Q2PSK) systems

NASA Astrophysics Data System (ADS)

El-Ghandour, Osama M.; Saha, Debabrata

1991-05-01

A generalized quadrature-quadrature phase shift keying (Q2PSK) signaling format is considered for differential encoding and differential detection. Performance in the presence of additive white Gaussian noise (AWGN) is analyzed. Symbol error rate is found to be approximately twice the symbol error rate in a quaternary DPSK system operating at the same Eb/N0. However, the bandwidth efficiency of differential Q2PSK is substantially higher than that of quaternary DPSK. When the error is due to AWGN, the ratio of double error rate to single error rate can be very high, and the ratio may approach zero at high SNR. To improve error rate, differential detection through maximum-likelihood decoding based on multiple or N symbol observations is considered. If N and SNR are large this decoding gives a 3-dB advantage in error rate over conventional N = 2 differential detection, fully recovering the energy loss (as compared to coherent detection) if the observation is extended to a large number of symbol durations.

Highly efficient methods to obtain homogeneous dorsal neural progenitor cells from human and mouse embryonic stem cells and induced pluripotent stem cells.

PubMed

Zhang, Meixiang; Ngo, Justine; Pirozzi, Filomena; Sun, Ying-Pu; Wynshaw-Boris, Anthony

2018-03-15

Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have been widely used to generate cellular models harboring specific disease-related genotypes. Of particular importance are ESC and iPSC applications capable of producing dorsal telencephalic neural progenitor cells (NPCs) that are representative of the cerebral cortex and overcome the challenges of maintaining a homogeneous population of cortical progenitors over several passages in vitro. While previous studies were able to derive NPCs from pluripotent cell types, the fraction of dorsal NPCs in this population is small and decreases over several passages. Here, we present three protocols that are highly efficient in differentiating mouse and human ESCs, as well as human iPSCs, into a homogeneous and stable population of dorsal NPCs. These protocols will be useful for modeling cerebral cortical neurological and neurodegenerative disorders in both mouse and human as well as for high-throughput drug screening for therapeutic development. We optimized three different strategies for generating dorsal telencephalic NPCs from mouse and human pluripotent cell types through single or double inhibition of bone morphogenetic protein (BMP) and/or SMAD pathways. Mouse and human pluripotent cells were aggregated to form embryoid bodies in suspension and were treated with dorsomorphin alone (BMP inhibition) or combined with SB431542 (double BMP/SMAD inhibition) during neural induction. Neural rosettes were then selected from plated embryoid bodies to purify the population of dorsal NPCs. We tested the expression of key dorsal NPC markers as well as nonectodermal markers to confirm the efficiency of our three methods in comparison to published and commercial protocols. Single and double inhibition of BMP and/or SMAD during neural induction led to the efficient differentiation of dorsal NPCs, based on the high percentage of PAX6-positive cells and the NPC gene expression profile. There were no statistically significant differences in the variation of PAX6 and SOX1-positive NPCs between the two human pluripotent cell-derived methods; therefore, both methods are suitable for producing stable dorsal NPCs. When further differentiated into mature neurons, NPCs gave rise to a population of almost exclusively forebrain cortical neurons, confirming the dorsal fate commitment of the progenitors. The methods described in this study show improvements over previously published studies and are highly efficient at differentiating human and mouse pluripotent cell types into dorsal PAX6-positive NPCs and eventually into forebrain cortical neurons.

Terahertz Quantum Cascade Structures Using Step Wells And Longitudinal Optical-Phonon Scattering

DTIC Science & Technology

2009-06-01

emit many photons, which allows for differential quantum efficiencies greater than unity and hence higher power output. QCLs have been successfully...maintained. The step in the well allows for high injection efficiency due to the spatial separation of the wavefunctions. A step quantum well, in which at...III.D.34), the photon density is determined to be ( )thiphotonphoton IILeAn − Γ = ητ (III.D.35) where the internal quantum efficiency

Using the MCNP Taylor series perturbation feature (efficiently) for shielding problems

NASA Astrophysics Data System (ADS)

Favorite, Jeffrey

2017-09-01

The Taylor series or differential operator perturbation method, implemented in MCNP and invoked using the PERT card, can be used for efficient parameter studies in shielding problems. This paper shows how only two PERT cards are needed to generate an entire parameter study, including statistical uncertainty estimates (an additional three PERT cards can be used to give exact statistical uncertainties). One realistic example problem involves a detailed helium-3 neutron detector model and its efficiency as a function of the density of its high-density polyethylene moderator. The MCNP differential operator perturbation capability is extremely accurate for this problem. A second problem involves the density of the polyethylene reflector of the BeRP ball and is an example of first-order sensitivity analysis using the PERT capability. A third problem is an analytic verification of the PERT capability.

Rapid and efficient CRISPR/Cas9 gene inactivation in human neurons during human pluripotent stem cell differentiation and direct reprogramming.

PubMed

Rubio, Alicia; Luoni, Mirko; Giannelli, Serena G; Radice, Isabella; Iannielli, Angelo; Cancellieri, Cinzia; Di Berardino, Claudia; Regalia, Giulia; Lazzari, Giovanna; Menegon, Andrea; Taverna, Stefano; Broccoli, Vania

2016-11-18

The CRISPR/Cas9 system is a rapid and customizable tool for gene editing in mammalian cells. In particular, this approach has widely opened new opportunities for genetic studies in neurological disease. Human neurons can be differentiated in vitro from hPSC (human Pluripotent Stem Cells), hNPCs (human Neural Precursor Cells) or even directly reprogrammed from fibroblasts. Here, we described a new platform which enables, rapid and efficient CRISPR/Cas9-mediated genome targeting simultaneously with three different paradigms for in vitro generation of neurons. This system was employed to inactivate two genes associated with neurological disorder (TSC2 and KCNQ2) and achieved up to 85% efficiency of gene targeting in the differentiated cells. In particular, we devised a protocol that, combining the expression of the CRISPR components with neurogenic factors, generated functional human neurons highly enriched for the desired genome modification in only 5 weeks. This new approach is easy, fast and that does not require the generation of stable isogenic clones, practice that is time consuming and for some genes not feasible.

Polydopamine-mediated surface modification of scaffold materials for human neural stem cell engineering.

PubMed

Yang, Kisuk; Lee, Jung Seung; Kim, Jin; Lee, Yu Bin; Shin, Heungsoo; Um, Soong Ho; Kim, Jeong Beom; Park, Kook In; Lee, Haeshin; Cho, Seung-Woo

2012-10-01

Surface modification of tissue engineering scaffolds and substrates is required for improving the efficacy of stem cell therapy by generating physicochemical stimulation promoting proliferation and differentiation of stem cells. However, typical surface modification methods including chemical conjugation or physical absorption have several limitations such as multistep, complicated procedures, surface denaturation, batch-to-batch inconsistencies, and low surface conjugation efficiency. In this study, we report a mussel-inspired, biomimetic approach to surface modification for efficient and reliable manipulation of human neural stem cell (NSC) differentiation and proliferation. Our study demonstrates that polydopamine coating facilitates highly efficient, simple immobilization of neurotrophic growth factors and adhesion peptides onto polymer substrates. The growth factor or peptide-immobilized substrates greatly enhance differentiation and proliferation of human NSCs (human fetal brain-derived NSCs and human induced pluripotent stem cell-derived NSCs) at a level comparable or greater than currently available animal-derived coating materials (Matrigel) with safety issues. Therefore, polydopamine-mediated surface modification can provide a versatile platform technology for developing chemically defined, safe, functional substrates and scaffolds for therapeutic applications of human NSCs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Multiple-try differential evolution adaptive Metropolis for efficient solution of highly parameterized models

NASA Astrophysics Data System (ADS)

Eric, L.; Vrugt, J. A.

2010-12-01

Spatially distributed hydrologic models potentially contain hundreds of parameters that need to be derived by calibration against a historical record of input-output data. The quality of this calibration strongly determines the predictive capability of the model and thus its usefulness for science-based decision making and forecasting. Unfortunately, high-dimensional optimization problems are typically difficult to solve. Here we present our recent developments to the Differential Evolution Adaptive Metropolis (DREAM) algorithm (Vrugt et al., 2009) to warrant efficient solution of high-dimensional parameter estimation problems. The algorithm samples from an archive of past states (Ter Braak and Vrugt, 2008), and uses multiple-try Metropolis sampling (Liu et al., 2000) to decrease the required burn-in time for each individual chain and increase efficiency of posterior sampling. This approach is hereafter referred to as MT-DREAM. We present results for 2 synthetic mathematical case studies, and 2 real-world examples involving from 10 to 240 parameters. Results for those cases show that our multiple-try sampler, MT-DREAM, can consistently find better solutions than other Bayesian MCMC methods. Moreover, MT-DREAM is admirably suited to be implemented and ran on a parallel machine and is therefore a powerful method for posterior inference.

20180311 - Differential Gene Expression and Concentration-Response Modeling Workflow for High-Throughput Transcriptomic (HTTr) Data: Results From MCF7 Cells (SOT)

EPA Science Inventory

Increasing efficiency and declining cost of generating whole transcriptome profiles has made high-throughput transcriptomics a practical option for chemical bioactivity screening. The resulting data output provides information on the expression of thousands of genes and is amenab...

Differential Gene Expression and Concentration-Response Modeling Workflow for High-Throughput Transcriptomic (HTTr) Data: Results From MCF7 Cells

EPA Science Inventory

Increasing efficiency and declining cost of generating whole transcriptome profiles has made high-throughput transcriptomics a practical option for chemical bioactivity screening. The resulting data output provides information on the expression of thousands of genes and is amenab...

High Repetition Rate and Frequency Stabilized Ho:YLF Laser for CO2 Differential Absorption Lidar

NASA Technical Reports Server (NTRS)

Bai, Yingxin; Yu, Jirong; Petros, M.; Petzar, Pau; Trieu, Bo; Lee, Hyung; Singh, U.

2009-01-01

High repetition rate operation of an injection seeded Ho:YLF laser has been demonstrated. For 1 kHz operation, the output pulse energy reaches 5.8mJ and the optical-to-optical efficiency is 39% when the pump power is 14.5W.

A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits.

PubMed

Shiraishi, Emi; Maeda, Kazuhiro; Kurata, Hiroyuki

2009-02-01

Numerical simulation of differential equation systems plays a major role in the understanding of how metabolic network models generate particular cellular functions. On the other hand, the classical and technical problems for stiff differential equations still remain to be solved, while many elegant algorithms have been presented. To relax the stiffness problem, we propose new practical methods: the gradual update of differential-algebraic equations based on gradual application of the steady-state approximation to stiff differential equations, and the gradual update of the initial values in differential-algebraic equations. These empirical methods show a high efficiency for simulating the steady-state solutions for the stiff differential equations that existing solvers alone cannot solve. They are effective in extending the applicability of dynamic simulation to biochemical network models.

Spectral methods in time for a class of parabolic partial differential equations

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

Ierley, G.; Spencer, B.; Worthing, R.

1992-09-01

In this paper, we introduce a fully spectral solution for the partial differential equation u[sub t] + uu[sub x] + vu[sub xx] + [mu]u[sub xxx] + [lambda]u[sub xxxx] = O. For periodic boundary conditions in space, the use of a Fourier expansion in x admits of a particularly efficient algorithm with respect to expansion of the time dependence in a Chebyshev series. Boundary conditions other than periodic may still be treated with reasonable, though lesser, efficiency. for all cases, very high accuracy is attainable at moderate computational cost relative to the expense of variable order finite difference methods in time.more » 14 refs., 9 figs.« less

More efficient repair of DNA double-strand breaks in skeletal muscle stem cells compared to their committed progeny.

PubMed

Vahidi Ferdousi, Leyla; Rocheteau, Pierre; Chayot, Romain; Montagne, Benjamin; Chaker, Zayna; Flamant, Patricia; Tajbakhsh, Shahragim; Ricchetti, Miria

2014-11-01

The loss of genome integrity in adult stem cells results in accelerated tissue aging and is possibly cancerogenic. Adult stem cells in different tissues appear to react robustly to DNA damage. We report that adult skeletal stem (satellite) cells do not primarily respond to radiation-induced DNA double-strand breaks (DSBs) via differentiation and exhibit less apoptosis compared to other myogenic cells. Satellite cells repair these DNA lesions more efficiently than their committed progeny. Importantly, non-proliferating satellite cells and post-mitotic nuclei in the fiber exhibit dramatically distinct repair efficiencies. Altogether, reduction of the repair capacity appears to be more a function of differentiation than of the proliferation status of the muscle cell. Notably, satellite cells retain a high efficiency of DSB repair also when isolated from the natural niche. Finally, we show that repair of DSB substrates is not only very efficient but, surprisingly, also very accurate in satellite cells and that accurate repair depends on the key non-homologous end-joining factor DNA-PKcs. Copyright © 2014. Published by Elsevier B.V.

Vertical cavity surface-emitting semiconductor lasers with injection laser pumping

NASA Astrophysics Data System (ADS)

McDaniel, D. L., Jr.; McInerney, J. G.; Raja, M. Y. A.; Schaus, C. F.; Brueck, S. R. J.

1990-05-01

Continuous-wave GaAs/GaAlAs edge-emitting diode lasers were used to pump GaAs/AlGaAs and InGaAs/AlGaAs vertical cavity surface-emitting lasers (VCSELs) with resonant periodic gain (RPG) at room temperature. Pump threshold as low as 11 mW, output powers as high as 27 mW at 850 nm, and external differential quantum efficiencies of about 70 percent were observed in GaAs/AlGaAs surface -emitters; spectral brightness 22 times that of the pump laser was also observed. Output powers as high as 85 mW at 950 nm and differential quantum efficiencies of up to 58 percent were recorded for the InGaAs surface-emitting laser. This is the highest quasi-CW output power ever reported for any RPG VCSEL, and the first time such a device has been pumped using an injection laser diode.

Highly efficient pseudomorphic InGaAs/GaAs/AlGaAs single quantum well lasers for monolithic integration

NASA Technical Reports Server (NTRS)

Larsson, A.; Cody, J.; Forouhar, S.; Lang, R. J.

1990-01-01

Highly efficient ridge waveguide pseudomorphic single quantum well lasers, emitting at 980 nm, have been fabricated from an In(0.2)Ga(0.8)As/GaAs/AlGaAs graded-index separate confinement heterostructure grown by molecular beam epitaxy. The laterial index guiding provided by the ridge reduces the anomalously large lateral loss of optical power found in gain-guided structures, thereby reducing the internal loss by more than 50 percent. The low threshold current (7.6 mA) and high differential quantum efficiency (79 percent) obtained under continuous operation as well as the transparency of the GaAs substrate to the emitted radiation render these lasers attractive for Ga-As-based optoelectronic integration.

Strained-layer InGaAs/GaAs/AlGaAs single quantum well lasers with high internal quantum efficiency

NASA Technical Reports Server (NTRS)

Larsson, Anders; Cody, Jeffrey; Lang, Robert J.

1989-01-01

Low threshold current density strained-layer In(0.2)Ga(0.8)As/GaAs/AlGaAs single quantum well lasers, emitting at 980 nm, have been grown by molecular beam epitaxy. Contrary to what has been reported for broad-area lasers with pseudomorphic InGaAs active layers grown by metalorganic chemical vapor deposition, these layers exhibit a high internal quantum efficiency (about 90 percent). The maximum external differential quantum efficiency is 70 percent, limited by an anomalously high internal loss possibly caused by a large lateral spreading of the optical mode. In addition, experimental results supporting the theoretically predicted strain-induced reduction of the valence-band nonparabolicity and density of states are presented.

Discontinuous Spectral Difference Method for Conservation Laws on Unstructured Grids

NASA Technical Reports Server (NTRS)

Liu, Yen; Vinokur, Marcel; Wang, Z. J.

2004-01-01

A new, high-order, conservative, and efficient method for conservation laws on unstructured grids is developed. The concept of discontinuous and high-order local representations to achieve conservation and high accuracy is utilized in a manner similar to the Discontinuous Galerkin (DG) and the Spectral Volume (SV) methods, but while these methods are based on the integrated forms of the equations, the new method is based on the differential form to attain a simpler formulation and higher efficiency. A discussion on the Discontinuous Spectral Difference (SD) Method, locations of the unknowns and flux points and numerical results are also presented.

Reduced basis ANOVA methods for partial differential equations with high-dimensional random inputs

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

Liao, Qifeng, E-mail: liaoqf@shanghaitech.edu.cn; Lin, Guang, E-mail: guanglin@purdue.edu

2016-07-15

In this paper we present a reduced basis ANOVA approach for partial deferential equations (PDEs) with random inputs. The ANOVA method combined with stochastic collocation methods provides model reduction in high-dimensional parameter space through decomposing high-dimensional inputs into unions of low-dimensional inputs. In this work, to further reduce the computational cost, we investigate spatial low-rank structures in the ANOVA-collocation method, and develop efficient spatial model reduction techniques using hierarchically generated reduced bases. We present a general mathematical framework of the methodology, validate its accuracy and demonstrate its efficiency with numerical experiments.

High-resolution melting analysis (HRM) for differentiation of four major Taeniidae species in dogs Taenia hydatigena, Taenia multiceps, Taenia ovis, and Echinococcus granulosus sensu stricto.

PubMed

Dehghani, Mansoureh; Mohammadi, Mohammad Ali; Rostami, Sima; Shamsaddini, Saeedeh; Mirbadie, Seyed Reza; Harandi, Majid Fasihi

2016-07-01

Tapeworms of the genus Taenia include several species of important parasites with considerable medical and veterinary significance. Accurate identification of these species in dogs is the prerequisite of any prevention and control program. Here, we have applied an efficient method for differentiating four major Taeniid species in dogs, i.e., Taenia hydatigena, T. multiceps, T. ovis, and Echinococcus granulosus sensu stricto. High-resolution melting (HRM) analysis is simpler, less expensive, and faster technique than conventional DNA-based assays and enables us to detect PCR amplicons in a closed system. Metacestode samples were collected from local abattoirs from sheep. All the isolates had already been identified by PCR-sequencing, and their sequence data were deposited in the GenBank. Real-time PCR coupled with HRM analysis targeting mitochondrial cox1 and ITS1 genes was used to differentiate taeniid species. Distinct melting curves were obtained from ITS1 region enabling accurate differentiation of three Taenia species and E. granulosus in dogs. The HRM curves of Taenia species and E .granulosus were clearly separated at Tm of 85 to 87 °C. In addition, double-pick melting curves were produced in mixed infections. Cox1 melting curves were not decisive enough to distinguish four taeniids. In this work, the efficiency of HRM analysis to differentiate four major taeniid species in dogs has been demonstrated using ITS1 gene.

DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data.

PubMed

Gaspar, John M; Hart, Ronald P

2017-11-29

DNA methylation is an epigenetic modification that is studied at a single-base resolution with bisulfite treatment followed by high-throughput sequencing. After alignment of the sequence reads to a reference genome, methylation counts are analyzed to determine genomic regions that are differentially methylated between two or more biological conditions. Even though a variety of software packages is available for different aspects of the bioinformatics analysis, they often produce results that are biased or require excessive computational requirements. DMRfinder is a novel computational pipeline that identifies differentially methylated regions efficiently. Following alignment, DMRfinder extracts methylation counts and performs a modified single-linkage clustering of methylation sites into genomic regions. It then compares methylation levels using beta-binomial hierarchical modeling and Wald tests. Among its innovative attributes are the analyses of novel methylation sites and methylation linkage, as well as the simultaneous statistical analysis of multiple sample groups. To demonstrate its efficiency, DMRfinder is benchmarked against other computational approaches using a large published dataset. Contrasting two replicates of the same sample yielded minimal genomic regions with DMRfinder, whereas two alternative software packages reported a substantial number of false positives. Further analyses of biological samples revealed fundamental differences between DMRfinder and another software package, despite the fact that they utilize the same underlying statistical basis. For each step, DMRfinder completed the analysis in a fraction of the time required by other software. Among the computational approaches for identifying differentially methylated regions from high-throughput bisulfite sequencing datasets, DMRfinder is the first that integrates all the post-alignment steps in a single package. Compared to other software, DMRfinder is extremely efficient and unbiased in this process. DMRfinder is free and open-source software, available on GitHub ( github.com/jsh58/DMRfinder ); it is written in Python and R, and is supported on Linux.

Increased expressions of genes and proteins involved in mitochondrial oxidation and antioxidant pathway in adipose tissue of pigs selected for a low residual feed intake.

PubMed

Louveau, I; Vincent, A; Tacher, S; Gilbert, H; Gondret, F

2016-12-01

Adipose tissue is a primary sensor for nutrient availability and regulates many functions including feed intake and energy homeostasis. This study was undertaken to determine the molecular responses of adipose tissue to differences in feed intake and feed efficiency. Subcutaneous adipose tissue was collected from two lines of pigs divergently selected for residual feed intake (RFI), a measure of feed efficiency defined as the difference between actual and expected feed intake, and from a subset of high-RFI pigs that were feed-restricted at the level of the voluntary feed intake of low-RFI pigs during the growing-finishing period. Transcriptomics analyses indicated that the number of genes that were differentially expressed ( < 0.01) between low- and high-RFI pigs ( = 8 per group at each stage) in adipose tissue was much lower when pigs were considered at 19 kg (postweaning) than at 115 kg BW (market weight). Extended investigations were performed at 115 kg BW to compare low-RFI ( = 8), high-RFI ( = 8), and feed-restricted high-RFI ( = 8) pigs. They included in silico pathway analyses of the differentially expressed (DE) genes ( < 0.01) and a complementary proteomic investigation to list adipose proteins with a differential abundance ( < 0.10). Only 23% of the DE genes were affected by both RFI and feed restriction. This indicates that the responses of adipose tissue to RFI difference shared only some common mechanisms with feed intake modulation, notably the regulation of cell cycle (including ) and transferase activity pathway. Two carboxylesterase genes (, ) involved in lipolysis, were among the most overexpressed genes in the low-RFI pigs; they were also affected by feed restriction within the high-RFI line. About 60% of the molecular changes between low- and high-RFI pigs were specific to genetic divergence in feed efficiency, independently of feed intake. Different genes and proteins known to be associated with mitochondrial oxidative metabolism were overexpressed in adipose tissue of low-RFI pigs compared with high-RFI pigs; other proteins participating in the generation of energy were also affected by feed restriction within the high-RFI line. Finally, mitochondrial antioxidant genes were upregulated in low-RFI pigs vs. high-RFI pigs. Altogether, increased oxidative and antioxidant processes in adipose tissue might be associated with improved feed efficiency.

Ex vivo electroporation of retinal cells: a novel, high efficiency method for functional studies in primary retinal cultures

PubMed Central

Vergara, Maria Natalia; Gutierrez, Christian; O’Brien, David R.; Canto-Soler, Maria Valeria

2013-01-01

Primary retinal cultures constitute valuable tools not only for basic research on retinal cell development and physiology, but also for the identification of factors or drugs that promote cell survival and differentiation. In order to take full advantage of the benefits of this system it is imperative to develop efficient and reliable techniques for the manipulation of gene expression. However, achieving appropriate transfection efficiencies in these cultures has remained challenging. The purpose of this work was to develop and optimize a technique that would allow the transfection of chick retinal cells with high efficiency and reproducibility for multiple applications. We developed an ex vivo electroporation method applied to dissociated retinal cell cultures that offers a significant improvement over other currently available transfection techniques, increasing efficiency by five-fold. In this method, eyes were enucleated, devoid of RPE, and electroporated with GFP-encoding plasmids using custom-made electrodes. Electroporated retinas were then dissociated into single cells and plated in low density conditions, to be analyzed after 4 days of incubation. Parameters such as voltage and number of electric pulses, as well as plasmid concentration and developmental stage of the animal were optimized for efficiency. The characteristics of the cultures were assessed by morphology and immunocytochemistry, and cell viability was determined by ethidium homodimer staining. Cell imaging and counting was performed using an automated high-throughput system. This procedure resulted in transfection efficiencies in the order of 22–25 % of cultured cells, encompassing both photoreceptors and non-photoreceptor neurons, and without affecting normal cell survival and differentiation. Finally, the feasibility of the technique for cell-autonomous studies of gene function in a biologically relevant context was tested by carrying out gain and loss-of-function experiments for the transcription factor PAX6. Electroporation of a plasmid construct expressing PAX6 resulted in a marked upregulation in the expression levels of this protein that could be measured in the whole culture as well as cell-intrinsically. This was accompanied by a significant decrease in the percentage of cells differentiating as photoreceptors among the transfected population. Conversely, electroporation of an RNAi construct targeting PAX6 resulted in a significant decrease in the levels of this protein, with a concomitant increase in the proportion of photoreceptors. Taken together these results provide strong proof-of-principle of the suitability of this technique for genetic studies in retinal cultures. The combination of the high transfection efficiency obtained by this method with automated high-throughput cell analysis supplies the scientific community with a powerful system for performing functional studies in a cell-autonomous manner. PMID:23370269

Ex vivo electroporation of retinal cells: a novel, high efficiency method for functional studies in primary retinal cultures.

PubMed

Vergara, M Natalia; Gutierrez, Christian; O'Brien, David R; Canto-Soler, M Valeria

2013-04-01

Primary retinal cultures constitute valuable tools not only for basic research on retinal cell development and physiology, but also for the identification of factors or drugs that promote cell survival and differentiation. In order to take full advantage of the benefits of this system it is imperative to develop efficient and reliable techniques for the manipulation of gene expression. However, achieving appropriate transfection efficiencies in these cultures has remained challenging. The purpose of this work was to develop and optimize a technique that would allow the transfection of chick retinal cells with high efficiency and reproducibility for multiple applications. We developed an ex vivo electroporation method applied to dissociated retinal cell cultures that offers a significant improvement over other currently available transfection techniques, increasing efficiency by five-fold. In this method, eyes were enucleated, devoid of RPE, and electroporated with GFP-encoding plasmids using custom-made electrodes. Electroporated retinas were then dissociated into single cells and plated in low density conditions, to be analyzed after 4 days of incubation. Parameters such as voltage and number of electric pulses, as well as plasmid concentration and developmental stage of the animal were optimized for efficiency. The characteristics of the cultures were assessed by morphology and immunocytochemistry, and cell viability was determined by ethidium homodimer staining. Cell imaging and counting was performed using an automated high-throughput system. This procedure resulted in transfection efficiencies in the order of 22-25% of cultured cells, encompassing both photoreceptors and non-photoreceptor neurons, and without affecting normal cell survival and differentiation. Finally, the feasibility of the technique for cell-autonomous studies of gene function in a biologically relevant context was tested by carrying out gain and loss-of-function experiments for the transcription factor PAX6. Electroporation of a plasmid construct expressing PAX6 resulted in a marked upregulation in the expression levels of this protein that could be measured in the whole culture as well as cell-intrinsically. This was accompanied by a significant decrease in the percentage of cells differentiating as photoreceptors among the transfected population. Conversely, electroporation of an RNAi construct targeting PAX6 resulted in a significant decrease in the levels of this protein, with a concomitant increase in the proportion of photoreceptors. Taken together these results provide strong proof-of-principle of the suitability of this technique for genetic studies in retinal cultures. The combination of the high transfection efficiency obtained by this method with automated high-throughput cell analysis supplies the scientific community with a powerful system for performing functional studies in a cell-autonomous manner. Copyright © 2013 Elsevier Ltd. All rights reserved.

Laser diode bars based on AlGaAs/GaAs quantum-well heterostructures with an efficiency up to 70%

NASA Astrophysics Data System (ADS)

Ladugin, M. A.; Marmalyuk, A. A.; Padalitsa, A. A.; Bagaev, T. A.; Andreev, A. Yu.; Telegin, K. Yu.; Lobintsov, A. V.; Davydova, E. I.; Sapozhnikov, S. M.; Danilov, A. I.; Podkopaev, A. V.; Ivanova, E. B.; Simakov, V. A.

2017-05-01

The results of the development and fabrication of laser diode bars (λ = 800 - 810 nm) based on AlGaAs/GaAs quantum-well heterostructures with a high efficiency are presented. An increase in the internal quantum and external differential efficiencies together with a decrease in the working voltage and the series resistance allowed us to improve the output parameters of the semiconductor laser under quasi-cw pumping. The output power of the laser diode bars with a 5-mm transverse length reached 210 W, and the efficiency was ~70%.

High-Throughput Screening Assay for Embryoid Body Differentiation of Human Embryonic Stem Cells

PubMed Central

Outten, Joel T.; Gadue, Paul; French, Deborah L.; Diamond, Scott L.

2012-01-01

Serum-free human pluripotent stem cell media offer the potential to develop reproducible clinically applicable differentiation strategies and protocols. The vast array of possible growth factor and cytokine combinations for media formulations makes differentiation protocol optimization both labor and cost-intensive. This unit describes a 96-well plate, 4-color flow cytometry-based screening assay to optimize pluripotent stem cell differentiation protocols. We provide conditions both to differentiate human embryonic stem cells (hESCs) to the three primary germ layers, ectoderm, endoderm, and mesoderm, and to utilize flow cytometry to distinguish between them. This assay exhibits low inter-well variability and can be utilized to efficiently screen a variety of media formulations, reducing cost, incubator space, and labor. Protocols can be adapted to a variety of differentiation stages and lineages. PMID:22415836

Development of a Pulsed 2-micron Laser Transmitter for CO2 Sensing from Space

NASA Technical Reports Server (NTRS)

Singh, Upendra N.; Yu, Jirong; Bai, Yingxin; Petros, Mulugeta; Menzies, Robert T.

2011-01-01

NASA Langley Research Center (LaRC), in collaboration with NASA Jet Propulsion Laboratory (JPL), is engaged in the development and demonstration of a highly efficient, versatile, 2-micron pulsed laser that can be used in a pulsed Differential Absorption Lidar (DIAL)/Integrated Path Differential Absorption (IPDA) instrument to make precise, high-resolution CO2 measurements to investigate sources, sinks, and fluxes of CO2. This laser transmitter will feature performance characteristics needed for an ASCENDS system that will be capable of delivering the CO2 measurement precision required by the Earth Science Decadal Survey (DS).

Differentiated cells are more efficient than adult stem cells for cloning by somatic cell nuclear transfer.

PubMed

Sung, Li-Ying; Gao, Shaorong; Shen, Hongmei; Yu, Hui; Song, Yifang; Smith, Sadie L; Chang, Ching-Chien; Inoue, Kimiko; Kuo, Lynn; Lian, Jin; Li, Ao; Tian, X Cindy; Tuck, David P; Weissman, Sherman M; Yang, Xiangzhong; Cheng, Tao

2006-11-01

Since the creation of Dolly via somatic cell nuclear transfer (SCNT), more than a dozen species of mammals have been cloned using this technology. One hypothesis for the limited success of cloning via SCNT (1%-5%) is that the clones are likely to be derived from adult stem cells. Support for this hypothesis comes from the findings that the reproductive cloning efficiency for embryonic stem cells is five to ten times higher than that for somatic cells as donors and that cloned pups cannot be produced directly from cloned embryos derived from differentiated B and T cells or neuronal cells. The question remains as to whether SCNT-derived animal clones can be derived from truly differentiated somatic cells. We tested this hypothesis with mouse hematopoietic cells at different differentiation stages: hematopoietic stem cells, progenitor cells and granulocytes. We found that cloning efficiency increases over the differentiation hierarchy, and terminally differentiated postmitotic granulocytes yield cloned pups with the greatest cloning efficiency.

Focal plane infrared readout circuit

NASA Technical Reports Server (NTRS)

Pain, Bedabrata (Inventor)

2002-01-01

An infrared imager, such as a spectrometer, includes multiple infrared photodetectors and readout circuits for reading out signals from the photodetectors. Each readout circuit includes a buffered direct injection input circuit including a differential amplifier with active feedback provided through an injection transistor. The differential amplifier includes a pair of input transistors, a pair of cascode transistors and a current mirror load. Photocurrent from a photodetector can be injected onto an integration capacitor in the readout circuit with high injection efficiency at high speed. A high speed, low noise, wide dynamic range linear infrared multiplexer array for reading out infrared detectors with large capacitances can be achieved even when short exposure times are used. The effect of image lag can be reduced.

High sensitivity spectroscopic and thermal characterization of cooling efficiency for optical refrigeration materials

NASA Astrophysics Data System (ADS)

Melgaard, Seth D.; Seletskiy, Denis V.; Di Lieto, Alberto; Tonelli, Mauro; Sheik-Bahae, Mansoor

2012-03-01

Since recent demonstration of cryogenic optical refrigeration, a need for reliable characterization tools of cooling performance of different materials is in high demand. We present our experimental apparatus that allows for temperature and wavelength dependent characterization of the materials' cooling efficiency and is based on highly sensitive spectral differencing technique or two-band differential spectral metrology (2B-DSM). First characterization of a 5% w.t. ytterbium-doped YLF crystal showed quantitative agreement with the current laser cooling model, as well as measured a minimum achievable temperature (MAT) at 110 K. Other materials and ion concentrations are also investigated and reported here.

Differential theory of learning for efficient neural network pattern recognition

NASA Astrophysics Data System (ADS)

Hampshire, John B., II; Vijaya Kumar, Bhagavatula

1993-09-01

We describe a new theory of differential learning by which a broad family of pattern classifiers (including many well-known neural network paradigms) can learn stochastic concepts efficiently. We describe the relationship between a classifier's ability to generate well to unseen test examples and the efficiency of the strategy by which it learns. We list a series of proofs that differential learning is efficient in its information and computational resource requirements, whereas traditional probabilistic learning strategies are not. The proofs are illustrated by a simple example that lends itself to closed-form analysis. We conclude with an optical character recognition task for which three different types of differentially generated classifiers generalize significantly better than their probabilistically generated counterparts.

Differential theory of learning for efficient neural network pattern recognition

NASA Astrophysics Data System (ADS)

Hampshire, John B., II; Vijaya Kumar, Bhagavatula

1993-08-01

We describe a new theory of differential learning by which a broad family of pattern classifiers (including many well-known neural network paradigms) can learn stochastic concepts efficiently. We describe the relationship between a classifier's ability to generalize well to unseen test examples and the efficiency of the strategy by which it learns. We list a series of proofs that differential learning is efficient in its information and computational resource requirements, whereas traditional probabilistic learning strategies are not. The proofs are illustrated by a simple example that lends itself to closed-form analysis. We conclude with an optical character recognition task for which three different types of differentially generated classifiers generalize significantly better than their probabilistically generated counterparts.

Derivation, expansion and differentiation of induced pluripotent stem cells in continuous suspension cultures

PubMed Central

Fluri, David A.; Tonge, Peter D.; Song, Hannah; Baptista, Ricardo P.; Shakiba, Nika; Shukla, Shreya; Clarke, Geoffrey; Nagy, Andras; Zandstra, Peter W.

2016-01-01

We demonstrate derivation of induced pluripotent stem cells (iPSCs) from terminally differentiated mouse cells in serum- and feeder-free stirred suspension cultures. Temporal analysis of global gene expression revealed high correlations between cells reprogrammed in suspension and cells reprogrammed in adhesion-dependent conditions. Suspension (S) reprogrammed iPSCs (SiPSCs) could be differentiated into all three germ layers in vitro and contributed to chimeric embryos in vivo. SiPSC generation allowed for efficient selection of reprogramming factor expressing cells based on their differential survival and proliferation in suspension. Seamless integration of SiPSC reprogramming and directed differentiation enabled the scalable production of functionally and phenotypically defined cardiac cells in a continuous single cell- and small aggregate-based process. This method is an important step towards the development of a robust PSC generation, expansion and differentiation technology. PMID:22447133

RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation

PubMed Central

Fuchs, Gilad; Shema, Efrat; Vesterman, Rita; Kotler, Eran; Wolchinsky, Zohar; Wilder, Sylvia; Golomb, Lior; Pribluda, Ariel; Zhang, Feng; Haj-Yahya, Mahmood; Feldmesser, Ester; Brik, Ashraf; Yu, Xiaochun; Hanna, Jacob; Aberdam, Daniel; Domany, Eytan; Oren, Moshe

2012-01-01

Summary Embryonic stem cells (ESC) maintain high genomic plasticity, essential for their capacity to enter diverse differentiation pathways. Post-transcriptional modifications of chromatin histones play a pivotal role in maintaining this plasticity. We now report that one such modification, monoubiquitylation of histone H2B on lysine 120 (H2Bub1), catalyzed by the E3 ligase RNF20, increases during ESC differentiation and is required for efficient execution of this process. This increase is particularly important for the transcriptional induction of relatively long genes during ESC differentiation. Furthermore, we identify the deubiquitinase USP44 as a negative regulator of H2B ubiquitylation, whose downregulation during ESC differentiation contributes to the increase in H2Bub1. Our findings suggest that optimal ESC differentiation requires dynamic changes in H2B ubiquitylation patterns, which must occur in a timely and well-coordinated manner. PMID:22681888

Knockdown of SLC41A1 magnesium transporter promotes mineralization and attenuates magnesium inhibition during osteogenesis of mesenchymal stromal cells.

PubMed

Tsao, Yu-Tzu; Shih, Ya-Yi; Liu, Yu-An; Liu, Yi-Shiuan; Lee, Oscar K

2017-02-21

Magnesium is essential for numerous physiological functions. Magnesium exists mostly in bone and the amount is dynamically regulated by skeletal remodeling. Accelerating bone mass loss occurs when magnesium intake is insufficient; whereas high magnesium could lead to mineralization defects. However, the underlying magnesium regulatory mechanisms remain elusive. In the present study, we investigated the effects of high extracellular magnesium concentration on osteogenic differentiation of mesenchymal stromal/stem cells (MSCs) and the role of magnesium transporter SLC41A1 in the mineralization process. Murine MSCs derived from the bone marrow of BALB/c mouse or commercially purchased human MSCs were treated with osteogenic induction medium containing 5.8 mM magnesium chloride and the osteogenic differentiation efficiency was compared with that of MSCs in normal differentiation medium containing 0.8 mM magnesium chloride by cell morphology, gene expression profile of osteogenic markers, and Alizarin Red staining. Slc41a1 gene knockdown in MSCs was performed by siRNA transfection using Lipofectamine RNAiMAX, and the differentiation efficiency of siRNA-treated MSCs was also assessed. High concentration of extracellular magnesium ion inhibited mineralization during osteogenic differentiation of MSCs. Early osteogenic marker genes including osterix, alkaline phosphatase, and type I collagen were significantly downregulated in MSCs under high concentration of magnesium, whereas late marker genes such as osteopontin, osteocalcin, and bone morphogenetic protein 2 were upregulated with statistical significance compared with those in normal differentiation medium containing 0.8 mM magnesium. siRNA treatment targeting SLC41A1 magnesium transporter, a member of the solute carrier family with a predominant Mg 2+ efflux system, accelerated the mineralization process and ameliorated the inhibition of mineralization caused by high concentration of magnesium. High concentration of magnesium significantly upregulated Dkk1 gene expression and the upregulation was attenuated after the Slc41a1 gene was knocked down. Immunofluorescent staining showed that Slc41a1 gene knockdown promoted the translocation of phosphorylated β-catenin into nuclei. In addition, secreted MGP protein was elevated after Slc41a1 was knocked down. High concentration of extracellular magnesium modulates gene expression of MSCs during osteogenic differentiation and inhibits the mineralization process. Additionally, we identified magnesium transporter SLC41A1 that regulates the interaction of magnesium and MSCs during osteogenic differentiation. Wnt signaling is suggested to be involved in SLC41A1-mediated regulation. Tissue-specific SLC41A1 could be a potential treatment for bone mass loss; in addition, caution should be taken regarding the role of magnesium in osteoporosis and the design of magnesium alloys for implantation.

The landscape of sex-differential transcriptome and its consequent selection in human adults.

PubMed

Gershoni, Moran; Pietrokovski, Shmuel

2017-02-07

The prevalence of several human morbid phenotypes is sometimes much higher than intuitively expected. This can directly arise from the presence of two sexes, male and female, in one species. Men and women have almost identical genomes but are distinctly dimorphic, with dissimilar disease susceptibilities. Sexually dimorphic traits mainly result from differential expression of genes present in both sexes. Such genes can be subject to different, and even opposing, selection constraints in the two sexes. This can impact human evolution by differential selection on mutations with dissimilar effects on the two sexes. We comprehensively mapped human sex-differential genetic architecture across 53 tissues. Analyzing available RNA-sequencing data from 544 adults revealed thousands of genes differentially expressed in the reproductive tracts and tissues common to both sexes. Sex-differential genes are related to various biological systems, and suggest new insights into the pathophysiology of diverse human diseases. We also identified a significant association between sex-specific gene transcription and reduced selection efficiency and accumulation of deleterious mutations, which might affect the prevalence of different traits and diseases. Interestingly, many of the sex-specific genes that also undergo reduced selection efficiency are essential for successful reproduction in men or women. This seeming paradox might partially explain the high incidence of human infertility. This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease.

Runge-Kutta Methods for Linear Ordinary Differential Equations

NASA Technical Reports Server (NTRS)

Zingg, David W.; Chisholm, Todd T.

1997-01-01

Three new Runge-Kutta methods are presented for numerical integration of systems of linear inhomogeneous ordinary differential equations (ODES) with constant coefficients. Such ODEs arise in the numerical solution of the partial differential equations governing linear wave phenomena. The restriction to linear ODEs with constant coefficients reduces the number of conditions which the coefficients of the Runge-Kutta method must satisfy. This freedom is used to develop methods which are more efficient than conventional Runge-Kutta methods. A fourth-order method is presented which uses only two memory locations per dependent variable, while the classical fourth-order Runge-Kutta method uses three. This method is an excellent choice for simulations of linear wave phenomena if memory is a primary concern. In addition, fifth- and sixth-order methods are presented which require five and six stages, respectively, one fewer than their conventional counterparts, and are therefore more efficient. These methods are an excellent option for use with high-order spatial discretizations.

Efficient femtosecond driven SOX 17 delivery into mouse embryonic stem cells: differentiation studies

NASA Astrophysics Data System (ADS)

Thobakgale, Lebogang; Manoto, Sello Lebohang; Lemboumba, Satuurnin Ombinda; Maaza, Malik; Mthunzi-Kufa, Patience

2017-02-01

Embryonic stem cells have great promise in regenerative medicine because of their ability to self-renew and differentiate into various cell types. Delivery of therapeutic genes into cells has already been achieved using of chemical agents and viral vectors with high transfection efficiencies. However, these methods have also been documented as toxic and in the latter case they can cause latent cell infections. In this study we use femtosecond laser pulses to optically deliver genetic material in mouse embryonic stem cells. Femtosecond laser pulses in contrast to the conventional approach, minimises the risk of unwanted side effects because photons are used to create transient pores on the membrane which allow free entry of molecules with no need for delivery agents. Using an Olympus microscope, fluorescence imaging of the samples post irradiation was performed and decreased expression of stage specific embryonic antigen one (SSEA-1) consistent with on-going cellular differentiation was observed. Our results also show that femtosecond laser pulses were effective in delivering SOX 17 plasmid DNA (pSOX17) which resulted in the differentiation of mouse embryonic stem cells into endoderm cells. We thus concluded that laser transfection of stem cells for the purpose of differentiation, holds potential for applications in tissue engineering as a method of generating new cell lines.

The differentiation and isolation of mouse embryonic stem cells toward hepatocytes using galactose-carrying substrata.

PubMed

Meng, Qingyuan; Haque, Amranul; Hexig, Bayar; Akaike, Toshihiro

2012-02-01

A simple culture system to achieve the differentiation of embryonic stem (ES) cells toward hepatocytes with high efficiency is crucial in providing a cell source for the medical application. In this study, we report the effect of a matrix-dependent enrichment of ES cell-derived hepatocytes using immobilized poly(N-p-vinylbenzyl-4-O-β-D-galactopyranosyl-D-gluconamide) (PVLA) with E-cadherin-IgG Fc (E-cad-Fc) as a galactose-carrying substratum. PVLA and E-cad-Fc were confirmed to be stably co-adsorbed onto polystyrene surface by quartz crystal microbalance (QCM). We showed that the E-cad-Fc/PVLA hybrid substratum was efficient in culturing primary hepatocytes and maintaining liver functions, on which the undifferentiated ES cells also maintained high proliferative capability. Furthermore, ES cell-derived hepatocytes on this hybrid matrix expressed elevated level of liver specific genes and functions together with early expression of definitive hepatocyte marker, asialoglycoprotein receptor (ASGPR). Finally, we isolated a high percentage of cells (about 60%) with ASGPR expression after re-seeding onto PVLA-coated surface, and observed the elimination of the poorly differentiated cells (Gata6(+) and Sox17(+)) and the ones toward another cell lineage (brachyury(+) and Pdx1(+)). The system uses a glycopolymer as an extracellular substratum for isolation and enrichment of ES cell-derived hepatocytes with adequate homogeneity and functionality. Copyright © 2011 Elsevier Ltd. All rights reserved.

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.

PubMed Central

Schena, M; Shalon, D; Heller, R; Chai, A; Brown, P O; Davis, R W

1996-01-01

Microarrays containing 1046 human cDNAs of unknown sequence were printed on glass with high-speed robotics. These 1.0-cm2 DNA "chips" were used to quantitatively monitor differential expression of the cognate human genes using a highly sensitive two-color hybridization assay. Array elements that displayed differential expression patterns under given experimental conditions were characterized by sequencing. The identification of known and novel heat shock and phorbol ester-regulated genes in human T cells demonstrates the sensitivity of the assay. Parallel gene analysis with microarrays provides a rapid and efficient method for large-scale human gene discovery. Images Fig. 1 Fig. 2 Fig. 3 PMID:8855227

Highly efficient red single transverse mode superluminescent diodes

NASA Astrophysics Data System (ADS)

Andreeva, E. V.; Anikeev, A. S.; Il'chenko, S. N.; Chamorovskii, A. Yu.; Yakubovich, S. D.

2017-12-01

Optimisation of the epitaxial growth of AlGaInP/GaInPAs nanoheterostructures and improvement of the technologies of active channel formation and p-contact deposition made it possible to considerably increase the external differential quantum efficiency (up to 0.5 mW mA-1), the catastrophic optical degradation threshold (up to 40 mW), and the spectral width (to FWHM exceeding 15 nm) of single transverse mode superluminescent diodes with the centre wavelength of about 675 nm. Lifetime tests demonstrated high reliability of these diodes at a cw output optical power up to 30 mW.

Efficient Generation of iPS Cells from Skeletal Muscle Stem Cells

PubMed Central

Tan, Kah Yong; Eminli, Sarah; Hettmer, Simone; Hochedlinger, Konrad; Wagers, Amy J.

2011-01-01

Reprogramming of somatic cells into inducible pluripotent stem cells generally occurs at low efficiency, although what limits reprogramming of particular cell types is poorly understood. Recent data suggest that the differentiation status of the cell targeted for reprogramming may influence its susceptibility to reprogramming as well as the differentiation potential of the induced pluripotent stem (iPS) cells that are derived from it. To assess directly the influence of lineage commitment on iPS cell derivation and differentiation, we evaluated reprogramming in adult stem cell and mature cell populations residing in skeletal muscle. Our data using clonal assays and a second-generation inducible reprogramming system indicate that stem cells found in mouse muscle, including resident satellite cells and mesenchymal progenitors, reprogram with significantly greater efficiency than their more differentiated daughters (myoblasts and fibroblasts). However, in contrast to previous reports, we find no evidence of biased differentiation potential among iPS cells derived from myogenically committed cells. These data support the notion that adult stem cells reprogram more efficiently than terminally differentiated cells, and argue against the suggestion that “epigenetic memory” significantly influences the differentiation potential of iPS cells derived from distinct somatic cell lineages in skeletal muscle. PMID:22028872

Differentiation of embryonic stem cells into hepatocytes that coexpress coagulation factors VIII and IX.

PubMed

Cao, Jun; Shang, Chang-zhen; Lü, Li-hong; Qiu, De-chuan; Ren, Meng; Chen, Ya-jin; Min, Jun

2010-11-01

To establish an efficient culture system to support embryonic stem (ES) cell differentiation into hepatocytes that coexpress F-VIII and F-IX. Mouse E14 ES cells were cultured in differentiation medium containing sodium butyrate (SB), basic fibroblast growth factor (bFGF), and/or bone morphogenetic protein 4 (BMP4) to induce the differentiation of endoderm cells and hepatic progenitor cells. Hepatocyte growth factor, oncostatin M, and dexamethasone were then used to induce the maturation of ES cell-derived hepatocytes. The mRNA expression levels of endoderm-specific genes and hepatocyte-specific genes, including the levels of F-VIII and F-IX, were detected by RT-PCR and real-time PCR during various stages of differentiation. Protein expression was examined by immunofluorescence and Western blot. At the final stage of differentiation, flow cytometry was performed to determine the percentage of cells coexpressing F-VIII and F-IX, and ELISA was used to detect the levels of F-VIII and F-IX protein secreted into the culture medium. The expression of endoderm-specific and hepatocyte-specific markers was upregulated to highest level in response to the combination of SB, bFGF, and BMP4. Treatment with the three inducers during hepatic progenitor differentiation significantly enhanced the mRNA and protein levels of F-VIII and F-IX in ES cell-derived hepatocytes. More importantly, F-VIII and F-IX were coexpressed with high efficiency at the final stage of differentiation, and they were also secreted into the culture medium. We have established a novel in vitro differentiation protocol for ES-derived hepatocytes that coexpress F-VIII and F-IX that may provide a foundation for stem cell replacement therapy for hemophilia.

Efficiency of differentiation in the Skaergaard magma chamber

NASA Astrophysics Data System (ADS)

Tegner, C.; Lesher, C. E.; Holness, M. B.; Jakobsen, J. K.; Salmonsen, L.; Humphreys, M.; Thy, P.

2011-12-01

Although it is largely agreed that crystallization occurs inwardly in crystal mushes along the margins of magma chambers, the efficiency and mechanisms of differentiation are not well constrained. The fractionation paradigm hinges on mass exchange between the crystal mush and the main magma reservoir resulting in coarse-grained, refractory (cumulate) rocks of primary crystals, and complementary enrichment of incompatible elements in the main reservoir of magma. Diffusion, convection, liquid immiscibility and compaction have been proposed as mechanisms driving this mass exchange. Here we examine the efficiency of differentiation in basaltic crystal mushes in different regions of the Skaergaard magma chamber. The contents of incompatible elements such as phosphorus and calculated residual porosities are high in the lowermost cumulate rocks of the floor (47-30%) and decrease upsection, persisting at low values in the uppermost two-thirds of the floor rock stratigraphy (~5% residual porosity). The residual porosity is intermediate at the walls (~15%) and highest and more variable at the roof (10-100%). This is best explained by compaction and expulsion of interstitial liquid from the accumulating crystal mush at the floor and the inefficiency of these processes elsewhere in the intrusion. In addition, the roof data imply upwards infiltration of interstitial liquid. Remarkably uniform residual porosity of ~15% for cumulates formed along the walls suggest that their preservation is related to the rheological properties of the mush, i.e. at ≤ 15% porosity the mush is rigid enough to adhere to the wall, while at higher porosity it is easily swept away. We conclude that the efficiency of compaction and differentiation can be extremely variable along the margins of magma chambers. This should be taken into account in models of magma chamber evolution.

808nm high-power high-efficiency GaAsP/GaInP laser bars

NASA Astrophysics Data System (ADS)

Wang, Ye; Yang, Ye; Qin, Li; Wang, Chao; Yao, Di; Liu, Yun; Wang, Lijun

2008-11-01

808nm high power diode lasers, which is rapidly maturing technology technically and commercially since the introduction in 1999 of complete kilowatt-scale diode laser systems, have important applications in the fields of industry and pumping solid-state lasers (DPSSL). High power and high power conversion efficiency are extremely important in diode lasers, and they could lead to new applications where space, weight and electrical power are critical. High efficiency devices generate less waste heat, which means less strain on the cooling system and more tolerance to thermal conductivity variation, a lower junction temperature and longer lifetimes. Diode lasers with Al-free materials have superior power conversion efficiency compared with conventional AlGaAs/GaAs devices because of their lower differential series resistance and higher thermal conductivity. 808nm GaAsP/GaInP broad-waveguide emitting diode laser bars with 1mm cavity length have been fabricated. The peak power can reach to 100.9W at 106.5A at quasicontinuous wave operation (200μs, 1000Hz). The maximum power conversion efficiency is 57.38%. Based on these high power laser bars, we fabricate a 1x3 arrays, the maximum power is 64.3W in continuous wave mode when the current is 25.0A. And the threshold current is 5.9A, the slope efficiency is 3.37 W/A.

A Power-Efficient Bio-Potential Acquisition Device with DS-MDE Sensors for Long-Term Healthcare Monitoring Applications

PubMed Central

Chang, Chia-Lin; Chang, Chih-Wei; Huang, Hong-Yi; Hsu, Chen-Ming; Huang, Chia-Hsuan; Chiou, Jin-Chern; Luo, Ching-Hsing

2010-01-01

This work describes a power-efficient bio-potential acquisition device for long-term healthcare applications that is implemented using novel microelectromechanical dry electrodes (MDE) and a low power bio-potential processing chip. Using micromachining technology, an attempt is also made to enhance the sensing reliability and stability by fabricating a diamond-shaped MDE (DS-MDE) that has a satisfactory self-stability capability and superior electric conductivity when attached onto skin without any extra skin tissue injury technology. To acquire differential bio-potentials such as ECG signals, the proposed processing chip fabricated in a standard CMOS process has a high common mode rejection ratio (C.M.R.R.) differential amplifier and a 12-bit analog-to-digital converter (ADC). Use of the proposed system and integrate simple peripheral commercial devices can obtain the ECG signal efficiently without additional skin tissue injury and ensure continuous monitoring more than 70 hours with a 400 mAh battery. PMID:22399907

A power-efficient bio-potential acquisition device with DS-MDE sensors for long-term healthcare monitoring applications.

PubMed

Chang, Chia-Lin; Chang, Chih-Wei; Huang, Hong-Yi; Hsu, Chen-Ming; Huang, Chia-Hsuan; Chiou, Jin-Chern; Luo, Ching-Hsing

2010-01-01

This work describes a power-efficient bio-potential acquisition device for long-term healthcare applications that is implemented using novel microelectromechanical dry electrodes (MDE) and a low power bio-potential processing chip. Using micromachining technology, an attempt is also made to enhance the sensing reliability and stability by fabricating a diamond-shaped MDE (DS-MDE) that has a satisfactory self-stability capability and superior electric conductivity when attached onto skin without any extra skin tissue injury technology. To acquire differential bio-potentials such as ECG signals, the proposed processing chip fabricated in a standard CMOS process has a high common mode rejection ratio (C.M.R.R.) differential amplifier and a 12-bit analog-to-digital converter (ADC). Use of the proposed system and integrate simple peripheral commercial devices can obtain the ECG signal efficiently without additional skin tissue injury and ensure continuous monitoring more than 70 hours with a 400 mAh battery.

Efficient differentiation of mouse embryonic stem cells into motor neurons.

PubMed

Wu, Chia-Yen; Whye, Dosh; Mason, Robert W; Wang, Wenlan

2012-06-09

Direct differentiation of embryonic stem (ES) cells into functional motor neurons represents a promising resource to study disease mechanisms, to screen new drug compounds, and to develop new therapies for motor neuron diseases such as spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Many current protocols use a combination of retinoic acid (RA) and sonic hedgehog (Shh) to differentiate mouse embryonic stem (mES) cells into motor neurons. However, the differentiation efficiency of mES cells into motor neurons has only met with moderate success. We have developed a two-step differentiation protocol that significantly improves the differentiation efficiency compared with currently established protocols. The first step is to enhance the neuralization process by adding Noggin and fibroblast growth factors (FGFs). Noggin is a bone morphogenetic protein (BMP) antagonist and is implicated in neural induction according to the default model of neurogenesis and results in the formation of anterior neural patterning. FGF signaling acts synergistically with Noggin in inducing neural tissue formation by promoting a posterior neural identity. In this step, mES cells were primed with Noggin, bFGF, and FGF-8 for two days to promote differentiation towards neural lineages. The second step is to induce motor neuron specification. Noggin/FGFs exposed mES cells were incubated with RA and a Shh agonist, Smoothened agonist (SAG), for another 5 days to facilitate motor neuron generation. To monitor the differentiation of mESs into motor neurons, we used an ES cell line derived from a transgenic mouse expressing eGFP under the control of the motor neuron specific promoter Hb9. Using this robust protocol, we achieved 51 ± 0.8% of differentiation efficiency (n = 3; p < 0.01, Student's t-test). Results from immunofluorescent staining showed that GFP+ cells express the motor neuron specific markers, Islet-1 and choline acetyltransferase (ChAT). Our two-step differentiation protocol provides an efficient way to differentiate mES cells into spinal motor neurons.

Association of class II histone deacetylases with heterochromatin protein 1: potential role for histone methylation in control of muscle differentiation.

PubMed

Zhang, Chun Li; McKinsey, Timothy A; Olson, Eric N

2002-10-01

Class II histone deacetylases (HDACs) 4, 5, 7, and 9 repress muscle differentiation through associations with the myocyte enhancer factor 2 (MEF2) transcription factor. MEF2-interacting transcription repressor (MITR) is an amino-terminal splice variant of HDAC9 that also potently inhibits MEF2 transcriptional activity despite lacking a catalytic domain. Here we report that MITR, HDAC4, and HDAC5 associate with heterochromatin protein 1 (HP1), an adaptor protein that recognizes methylated lysines within histone tails and mediates transcriptional repression by recruiting histone methyltransferase. Promyogenic signals provided by calcium/calmodulin-dependent kinase (CaMK) disrupt the interaction of MITR and HDACs with HP1. Since the histone methyl-lysine residues recognized by HP1 also serve as substrates for deacetylation by HDACs, the interaction of MITR and HDACs with HP1 provides an efficient mechanism for silencing MEF2 target genes by coupling histone deacetylation and methylation. Indeed, nucleosomal histones surrounding a MEF2-binding site in the myogenin gene promoter are highly methylated in undifferentiated myoblasts, when the gene is silent, and become acetylated during muscle differentiation, when the myogenin gene is expressed at high levels. The ability of MEF2 to recruit a histone methyltransferase to target gene promoters via HP1-MITR and HP1-HDAC interactions and of CaMK signaling to disrupt these interactions provides an efficient mechanism for signal-dependent regulation of the epigenetic events controlling muscle differentiation.

Association of Class II Histone Deacetylases with Heterochromatin Protein 1: Potential Role for Histone Methylation in Control of Muscle Differentiation

PubMed Central

Zhang, Chun Li; McKinsey, Timothy A.; Olson, Eric N.

2002-01-01

Class II histone deacetylases (HDACs) 4, 5, 7, and 9 repress muscle differentiation through associations with the myocyte enhancer factor 2 (MEF2) transcription factor. MEF2-interacting transcription repressor (MITR) is an amino-terminal splice variant of HDAC9 that also potently inhibits MEF2 transcriptional activity despite lacking a catalytic domain. Here we report that MITR, HDAC4, and HDAC5 associate with heterochromatin protein 1 (HP1), an adaptor protein that recognizes methylated lysines within histone tails and mediates transcriptional repression by recruiting histone methyltransferase. Promyogenic signals provided by calcium/calmodulin-dependent kinase (CaMK) disrupt the interaction of MITR and HDACs with HP1. Since the histone methyl-lysine residues recognized by HP1 also serve as substrates for deacetylation by HDACs, the interaction of MITR and HDACs with HP1 provides an efficient mechanism for silencing MEF2 target genes by coupling histone deacetylation and methylation. Indeed, nucleosomal histones surrounding a MEF2-binding site in the myogenin gene promoter are highly methylated in undifferentiated myoblasts, when the gene is silent, and become acetylated during muscle differentiation, when the myogenin gene is expressed at high levels. The ability of MEF2 to recruit a histone methyltransferase to target gene promoters via HP1-MITR and HP1-HDAC interactions and of CaMK signaling to disrupt these interactions provides an efficient mechanism for signal-dependent regulation of the epigenetic events controlling muscle differentiation. PMID:12242305

Efficient generation of hepatic cells from mesenchymal stromal cells by an innovative bio-microfluidic cell culture device.

PubMed

Yen, Meng-Hua; Wu, Yuan-Yi; Liu, Yi-Shiuan; Rimando, Marilyn; Ho, Jennifer Hui-Chun; Lee, Oscar Kuang-Sheng

2016-08-19

Mesenchymal stromal cells (MSCs) are multipotent and have great potential in cell therapy. Previously we reported the differentiation potential of human MSCs into hepatocytes in vitro and that these cells can rescue fulminant hepatic failure. However, the conventional static culture method neither maintains growth factors at an optimal level constantly nor removes cellular waste efficiently. In addition, not only is the duration of differentiating hepatocyte lineage cells from MSCs required to improve, but also the need for a large number of hepatocytes for cell therapy has not to date been addressed fully. The purpose of this study is to design and develop an innovative microfluidic device to overcome these shortcomings. We designed and fabricated a microfluidic device and a culture system for hepatic differentiation of MSCs using our protocol reported previously. The microfluidic device contains a large culture chamber with a stable uniform flow to allow homogeneous distribution and expansion as well as efficient induction of hepatic differentiation for MSCs. The device enables real-time observation under light microscopy and exhibits a better differentiation efficiency for MSCs compared with conventional static culture. MSCs grown in the microfluidic device showed a higher level of hepatocyte marker gene expression under hepatic induction. Functional analysis of hepatic differentiation demonstrated significantly higher urea production in the microfluidic device after 21 days of hepatic differentiation. The microfluidic device allows the generation of a large number of MSCs and induces hepatic differentiation of MSCs efficiently. The device can be adapted for scale-up production of hepatic cells from MSCs for cellular therapy.

Efficient and Reproducible Myogenic Differentiation from Human iPS Cells: Prospects for Modeling Miyoshi Myopathy In Vitro

PubMed Central

Tanaka, Akihito; Woltjen, Knut; Miyake, Katsuya; Hotta, Akitsu; Ikeya, Makoto; Yamamoto, Takuya; Nishino, Tokiko; Shoji, Emi; Sehara-Fujisawa, Atsuko; Manabe, Yasuko; Fujii, Nobuharu; Hanaoka, Kazunori; Era, Takumi; Yamashita, Satoshi; Isobe, Ken-ichi; Kimura, En; Sakurai, Hidetoshi

2013-01-01

The establishment of human induced pluripotent stem cells (hiPSCs) has enabled the production of in vitro, patient-specific cell models of human disease. In vitro recreation of disease pathology from patient-derived hiPSCs depends on efficient differentiation protocols producing relevant adult cell types. However, myogenic differentiation of hiPSCs has faced obstacles, namely, low efficiency and/or poor reproducibility. Here, we report the rapid, efficient, and reproducible differentiation of hiPSCs into mature myocytes. We demonstrated that inducible expression of myogenic differentiation1 (MYOD1) in immature hiPSCs for at least 5 days drives cells along the myogenic lineage, with efficiencies reaching 70–90%. Myogenic differentiation driven by MYOD1 occurred even in immature, almost completely undifferentiated hiPSCs, without mesodermal transition. Myocytes induced in this manner reach maturity within 2 weeks of differentiation as assessed by marker gene expression and functional properties, including in vitro and in vivo cell fusion and twitching in response to electrical stimulation. Miyoshi Myopathy (MM) is a congenital distal myopathy caused by defective muscle membrane repair due to mutations in DYSFERLIN. Using our induced differentiation technique, we successfully recreated the pathological condition of MM in vitro, demonstrating defective membrane repair in hiPSC-derived myotubes from an MM patient and phenotypic rescue by expression of full-length DYSFERLIN (DYSF). These findings not only facilitate the pathological investigation of MM, but could potentially be applied in modeling of other human muscular diseases by using patient-derived hiPSCs. PMID:23626698

Highly Efficient Differentiation and Enrichment of Spinal Motor Neurons Derived from Human and Monkey Embryonic Stem Cells

PubMed Central

Wada, Tamaki; Honda, Makoto; Minami, Itsunari; Tooi, Norie; Amagai, Yuji; Nakatsuji, Norio; Aiba, Kazuhiro

2009-01-01

Background There are no cures or efficacious treatments for severe motor neuron diseases. It is extremely difficult to obtain naïve spinal motor neurons (sMNs) from human tissues for research due to both technical and ethical reasons. Human embryonic stem cells (hESCs) are alternative sources. Several methods for MN differentiation have been reported. However, efficient production of naïve sMNs and culture cost were not taken into consideration in most of the methods. Methods/Principal Findings We aimed to establish protocols for efficient production and enrichment of sMNs derived from pluripotent stem cells. Nestin+ neural stem cell (NSC) clusters were induced by Noggin or a small molecule inhibitor of BMP signaling. After dissociation of NSC clusters, neurospheres were formed in a floating culture containing FGF2. The number of NSCs in neurospheres could be expanded more than 30-fold via several passages. More than 33% of HB9+ sMN progenitor cells were observed after differentiation of dissociated neurospheres by all-trans retinoic acid (ATRA) and a Shh agonist for another week on monolayer culture. HB9+ sMN progenitor cells were enriched by gradient centrifugation up to 80% purity. These HB9+ cells differentiated into electrophysiologically functional cells and formed synapses with myotubes during a few weeks after ATRA/SAG treatment. Conclusions and Significance The series of procedures we established here, namely neural induction, NSC expansion, sMN differentiation and sMN purification, can provide large quantities of naïve sMNs derived from human and monkey pluripotent stem cells. Using small molecule reagents, reduction of culture cost could be achieved. PMID:19701462

Resource partitioning by evergreen and deciduous species in a tropical dry forest.

PubMed

Álvarez-Yépiz, Juan C; Búrquez, Alberto; Martínez-Yrízar, Angelina; Teece, Mark; Yépez, Enrico A; Dovciak, Martin

2017-02-01

Niche differentiation can lead to coexistence of plant species by partitioning limiting resources. Light partitioning promotes niche differentiation in tropical humid forests, but it is unclear how niche partitioning occurs in tropical dry forests where both light and soil resources can be limiting. We studied the adult niche of four dominant evergreen (cycad, palm) and drought-deciduous (legume, oak) species co-occurring along environmental gradients. We analyzed light intensity and soil fertility effects on key functional traits related to plant carbon and water economy, how these traits determine species' functional strategies, and how these strategies relate to relative species abundance and spatial patterns. Light intensity was negatively associated with a key trait linked to plant water economy (leaf δ 13 C, a proxy for long-term water-use efficiency-WUE), while soil fertility was negatively associated with a key trait for plant carbon economy (LNC, leaf nitrogen content). Evergreens were highly sclerophyllous and displayed an efficient water economy but poor carbon economy, in agreement with a conservative resource-use strategy (i.e., high WUE but low LNC, photosynthetic rates and stature). Conversely, deciduous species, with an efficient carbon economy but poor water economy, exhibited an exploitative resource-use strategy (i.e., high LNC, photosynthetic rates and stature, but low WUE). Evergreen and deciduous species segregated spatially, particularly at fine-scales, as expected for species with different resource-use strategies. The efficient water economy of evergreens was related to their higher relative abundance, suggesting a functional advantage against drought-deciduous species in water-limited environments within seasonally dry tropical forests.

Efficient, Long Term Production of Monocyte-Derived Macrophages from Human Pluripotent Stem Cells under Partly-Defined and Fully-Defined Conditions

PubMed Central

van Wilgenburg, Bonnie; Browne, Cathy; Vowles, Jane; Cowley, Sally A.

2013-01-01

Human macrophages are specialised hosts for HIV-1, dengue virus, Leishmania and Mycobacterium tuberculosis. Yet macrophage research is hampered by lack of appropriate cell models for modelling infection by these human pathogens, because available myeloid cell lines are, by definition, not terminally differentiated like tissue macrophages. We describe here a method for deriving monocytes and macrophages from human Pluripotent Stem Cells which improves on previously published protocols in that it uses entirely defined, feeder- and serum-free culture conditions and produces very consistent, pure, high yields across both human Embryonic Stem Cell (hESC) and multiple human induced Pluripotent Stem Cell (hiPSC) lines over time periods of up to one year. Cumulatively, up to ∼3×107 monocytes can be harvested per 6-well plate. The monocytes produced are most closely similar to the major blood monocyte (CD14+, CD16low, CD163+). Differentiation with M-CSF produces macrophages that are highly phagocytic, HIV-1-infectable, and upon activation produce a pro-inflammatory cytokine profile similar to blood monocyte-derived macrophages. Macrophages are notoriously hard to genetically manipulate, as they recognise foreign nucleic acids; the lentivector system described here overcomes this, as pluripotent stem cells can be relatively simply genetically manipulated for efficient transgene expression in the differentiated cells, surmounting issues of transgene silencing. Overall, the method we describe here is an efficient, effective, scalable system for the reproducible production and genetic modification of human macrophages, facilitating the interrogation of human macrophage biology. PMID:23951090

Functional vascular smooth muscle cells derived from human induced pluripotent stem cells via mesenchymal stem cell intermediates

PubMed Central

Bajpai, Vivek K.; Mistriotis, Panagiotis; Loh, Yuin-Han; Daley, George Q.; Andreadis, Stelios T.

2012-01-01

Aims Smooth muscle cells (SMC) play an important role in vascular homeostasis and disease. Although adult mesenchymal stem cells (MSC) have been used as a source of contractile SMC, they suffer from limited proliferation potential and culture senescence, particularly when originating from older donors. By comparison, human induced pluripotent stem cells (hiPSC) can provide an unlimited source of functional SMC for autologous cell-based therapies and for creating models of vascular disease. Our goal was to develop an efficient strategy to derive functional, contractile SMC from hiPSC. Methods and results We developed a robust, stage-wise, feeder-free strategy for hiPSC differentiation into functional SMC through an intermediate stage of multipotent MSC, which could be coaxed to differentiate into fat, bone, cartilage, and muscle. At this stage, the cells were highly proliferative and displayed higher clonogenic potential and reduced senescence when compared with parental hair follicle mesenchymal stem cells. In addition, when exposed to differentiation medium, the myogenic proteins such as α-smooth muscle actin, calponin, and myosin heavy chain were significantly upregulated and displayed robust fibrillar organization, suggesting the development of a contractile phenotype. Indeed, tissue constructs prepared from these cells exhibited high levels of contractility in response to receptor- and non-receptor-mediated agonists. Conclusion We developed an efficient stage-wise strategy that enabled hiPSC differentiation into contractile SMC through an intermediate population of clonogenic and multipotent MSC. The high yield of MSC and SMC derivation suggests that our strategy may facilitate an acquisition of the large numbers of cells required for regenerative medicine or for studying vascular disease pathophysiology. PMID:22941255

Functional Comparison of Neuronal Cells Differentiated from Human Induced Pluripotent Stem Cell-Derived Neural Stem Cells under Different Oxygen and Medium Conditions.

PubMed

Yamazaki, Kazuto; Fukushima, Kazuyuki; Sugawara, Michiko; Tabata, Yoshikuni; Imaizumi, Yoichi; Ishihara, Yasuharu; Ito, Masashi; Tsukahara, Kappei; Kohyama, Jun; Okano, Hideyuki

2016-12-01

Because neurons are difficult to obtain from humans, generating functional neurons from human induced pluripotent stem cells (hiPSCs) is important for establishing physiological or disease-relevant screening systems for drug discovery. To examine the culture conditions leading to efficient differentiation of functional neural cells, we investigated the effects of oxygen stress (2% or 20% O 2 ) and differentiation medium (DMEM/F12:Neurobasal-based [DN] or commercial [PhoenixSongs Biologicals; PS]) on the expression of genes related to neural differentiation, glutamate receptor function, and the formation of networks of neurons differentiated from hiPSCs (201B7) via long-term self-renewing neuroepithelial-like stem (lt-NES) cells. Expression of genes related to neural differentiation occurred more quickly in PS and/or 2% O 2 than in DN and/or 20% O 2 , resulting in high responsiveness of neural cells to glutamate, N-methyl-d-aspartate (NMDA), α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA), and ( S)-3,5-dihydroxyphenylglycine (an agonist for mGluR 1/5 ), as revealed by calcium imaging assays. NMDA receptors, AMPA receptors, mGluR 1 , and mGluR 5 were functionally validated by using the specific antagonists MK-801, NBQX, JNJ16259685, and 2-methyl-6-(phenylethynyl)-pyridine, respectively. Multielectrode array analysis showed that spontaneous firing occurred earlier in cells cultured in 2% O 2 than in 20% O 2 . Optimization of O 2 tension and culture medium for neural differentiation of hiPSCs can efficiently generate physiologically relevant cells for screening systems.

Clonal population of adult stem cells: life span and differentiation potential.

PubMed

Seruya, Mitchel; Shah, Anup; Pedrotty, Dawn; du Laney, Tracey; Melgiri, Ryan; McKee, J Andrew; Young, Henry E; Niklason, Laura E

2004-01-01

Adult stem cells derived from bone marrow, connective tissue, and solid organs can exhibit a range of differentiation potentials. Some controversy exists regarding the classification of mesenchymal stem cells as bona fide stem cells, which is in part derived from the limited ability to propagate true clonal populations of precursor cells. We isolated putative mesenchymal stem cells from the connective tissue of an adult rat (rMSC), and generated clonal populations via three rounds of dilutional cloning. The replicative potential of the clonal rMSC line far exceeded Hayflick's limit of 50-70 population doublings. The high capacity for self-renewal in vitro correlated with telomerase activity, as demonstrated by telomerase repeat amplification protocol (TRAP) assay. Exposure to nonspecific differentiation culture medium revealed multilineage differentiation potential of rMSC clones. Immunostaining confirmed the appearance of mesodermal phenotypes, including adipocytes possessing lipid-rich vacuoles, chondrocytes depositing pericellular type II collagen, and skeletal myoblasts expressing MyoD1. Importantly, the spectrum of differentiation capability was sustained through repeated passaging. Furthermore, serum-free conditions that led to high-efficiency smooth muscle differentiation were identified. rMSCs plated on collagen IV-coated surfaces and exposed to transforming growth factor-beta1 (TGF-beta1) differentiated into a homogeneous population expressing alpha-actin and calponin. Hence, clonogenic analysis confirmed the presence of a putative MSC population derived from the connective tissue of rat skeletal muscle. The ability to differentiate into a smooth muscle cell (SMC) phenotype, combined with a high proliferative capacity, make such a connective tissue-derived MSC population ideal for applications in vascular tissue construction.

Divergent selection for residual feed intake affects the transcriptomic and proteomic profiles of pig skeletal muscle.

PubMed

Vincent, A; Louveau, I; Gondret, F; Tréfeu, C; Gilbert, H; Lefaucheur, L

2015-06-01

Improving feed efficiency is a relevant strategy to reduce feed cost and environmental waste in livestock production. Selection experiments on residual feed intake (RFI), a measure of feed efficiency, previously indicated that low RFI was associated with lower feed intake, similar growth rate, and greater lean meat content compared with high RFI. To gain insights into the molecular mechanisms underlying these differences, 24 Large White females from 2 lines divergently selected for RFI were examined. Pigs from a low-RFI ("efficient") and high-RFI ("inefficient") line were individually fed ad libitum from 67 d of age (27 kg BW) to slaughter at 115 kg BW (n = 8 per group). Additional pigs of the high-RFI line were feed restricted to the daily feed intake of the ad libitum low-RFI pigs (n = 8) to investigate the impact of selection independently of feed intake. Global gene and protein expression profiles were assessed in the LM collected at slaughter. The analyses involved a porcine commercial microarray and 2-dimensional gel electrophoresis. About 1,000 probes were differentially expressed (P < 0.01) between RFI lines. Only 10% of those probes were also affected by feed restriction. Gene functional classification indicated a greater expression of genes involved in protein synthesis and a lower expression of genes associated with mitochondrial energy metabolism in the low-RFI pigs compared with the high-RFI pigs. At the protein level, 11 unique identified proteins exhibited a differential abundance (P < 0.05) between RFI lines. Differentially expressed proteins were generally not significantly affected by feed restriction. Mitochondrial oxidative proteins such as aconitase hydratase, ATP synthase subunit α, and creatine kinase S-type had a lower abundance in the low-RFI pigs, whereas fructose-biphosphate aldolase A and glyceraldehyde-3-phosphate dehydrogenase, 2 proteins involved in glycolysis, had a greater abundance in those pigs compared with high-RFI pigs. Antioxidant proteins such as superoxide dismutase and glutathione peroxidase 3 at the mRNA level and peroxiredoxin-6 at the protein level were also less expressed in LM of the most efficient pigs, likely related to lower oxidative molecule production. Collectively, both the transcriptomic and proteomic approaches revealed a lower oxidative metabolism in muscle of the low-RFI pigs and all these modifications were largely independent of differences in feed intake.

An efficient transport solver for tokamak plasmas

DOE PAGES

Park, Jin Myung; Murakami, Masanori; St. John, H. E.; ...

2017-01-03

A simple approach to efficiently solve a coupled set of 1-D diffusion-type transport equations with a stiff transport model for tokamak plasmas is presented based on the 4th order accurate Interpolated Differential Operator scheme along with a nonlinear iteration method derived from a root-finding algorithm. Here, numerical tests using the Trapped Gyro-Landau-Fluid model show that the presented high order method provides an accurate transport solution using a small number of grid points with robust nonlinear convergence.

Investigation of potential of differential absorption Lidar techniques for remote sensing of atmospheric pollutants

NASA Technical Reports Server (NTRS)

Butler, C. F.; Shipley, S. T.; Allen, R. J.

1981-01-01

The NASA multipurpose differential absorption lidar (DIAL) system uses two high conversion efficiency dye lasers which are optically pumped by two frequency-doubled Nd:YAG lasers mounted rigidly on a supporting structure that also contains the transmitter, receiver, and data system. The DIAL system hardware design and data acquisition system are described. Timing diagrams, logic diagrams, and schematics, and the theory of operation of the control electronics are presented. Success in obtaining remote measurements of ozone profiles with an airborne systems is reported and results are analyzed.

Method of differential-phase/absolute-amplitude QAM

DOEpatents

Dimsdle, Jeffrey William [Overland Park, KS

2007-07-03

A method of quadrature amplitude modulation involving encoding phase differentially and amplitude absolutely, allowing for a high data rate and spectral efficiency in data transmission and other communication applications, and allowing for amplitude scaling to facilitate data recovery; amplitude scale tracking to track-out rapid and severe scale variations and facilitate successful demodulation and data retrieval; 2.sup.N power carrier recovery; incoherent demodulation where coherent carrier recovery is not possible or practical due to signal degradation; coherent demodulation; multipath equalization to equalize frequency dependent multipath; and demodulation filtering.

Method of differential-phase/absolute-amplitude QAM

DOEpatents

Dimsdle, Jeffrey William [Overland Park, KS

2008-10-21

A method of quadrature amplitude modulation involving encoding phase differentially and amplitude absolutely, allowing for a high data rate and spectral efficiency in data transmission and other communication applications, and allowing for amplitude scaling to facilitate data recovery; amplitude scale tracking to track-out rapid and severe scale variations and facilitate successful demodulation and data retrieval; 2.sup.N power carrier recovery; incoherent demodulation where coherent carrier recovery is not possible or practical due to signal degradation; coherent demodulation; multipath equalization to equalize frequency dependent multipath; and demodulation filtering.

Method of differential-phase/absolute-amplitude QAM

DOEpatents

Dimsdle, Jeffrey William [Overland Park, KS

2009-09-01

A method of quadrature amplitude modulation involving encoding phase differentially and amplitude absolutely, allowing for a high data rate and spectral efficiency in data transmission and other communication applications, and allowing for amplitude scaling to facilitate data recovery; amplitude scale tracking to track-out rapid and severe scale variations and facilitate successful demodulation and data retrieval; 2.sup.N power carrier recovery; incoherent demodulation where coherent carrier recovery is not possible or practical due to signal degradation; coherent demodulation; multipath equalization to equalize frequency dependent multipath; and demodulation filtering.

Method of differential-phase/absolute-amplitude QAM

DOEpatents

Dimsdle, Jeffrey William [Overland Park, KS

2007-07-17

A method of quadrature amplitude modulation involving encoding phase differentially and amplitude absolutely, allowing for a high data rate and spectral efficiency in data transmission and other communication applications, and allowing for amplitude scaling to facilitate data recovery; amplitude scale tracking to track-out rapid and severe scale variations and facilitate successful demodulation and data retrieval; 2.sup.N power carrier recovery; incoherent demodulation where coherent carrier recovery is not possible or practical due to signal degradation; coherent demodulation; multipath equalization to equalize frequency dependent multipath; and demodulation filtering.

Method of differential-phase/absolute-amplitude QAM

DOEpatents

Dimsdle, Jeffrey William

2007-10-02

A method of quadrature amplitude modulation involving encoding phase differentially and amplitude absolutely, allowing for a high data rate and spectral efficiency in data transmission and other communication applications, and allowing for amplitude scaling to facilitate data recovery; amplitude scale tracking to track-out rapid and severe scale variations and facilitate successful demodulation and data retrieval; 2.sup.N power carrier recovery; incoherent demodulation where coherent carrier recovery is not possible or practical due to signal degradation; coherent demodulation; multipath equalization to equalize frequency dependent multipath; and demodulation filtering.

Raman spectroscopy of blood serum for Alzheimer's disease diagnostics: specificity relative to other types of dementia

PubMed Central

Ryzhikova, Elena; Kazakov, Oleksandr; Halamkova, Lenka; Celmins, Dzintra; Malone, Paula; Molho, Eric; Zimmerman, Earl A.; Lednev, Igor K.

2015-01-01

The key moment for efficiently and accurately diagnosing dementia occurs during the early stages. This is particularly true for Alzheimer's disease (AD). In this proof-of-concept study, we applied near infrared (NIR) Raman microspectroscopy of blood serum together with advanced multivariate statistics for the selective identification of AD. We analyzed data from 20 AD patients, 18 patients with other neurodegenerative dementias (OD) and 10 healthy control (HC) subjects. NIR Raman microspectroscopy differentiated patients with more than 95% sensitivity and specificity. We demonstrated the high discriminative power of artificial neural network (ANN) classification models, thus revealing the high potential of this developed methodology for the differential diagnosis of AD. Raman spectroscopic, blood-based tests may aid clinical assessments for the effective and accurate differential diagnosis of AD, decrease the labor, time and cost of diagnosis, and be useful for screening patient populations for AD development and progression. PMID:25256347

Bioengineering a non-genotoxic vector for genetic modification of mesenchymal stem cells.

PubMed

Chen, Xuguang; Nomani, Alireza; Patel, Niket; Nouri, Faranak S; Hatefi, Arash

2018-01-01

Vectors used for stem cell transfection must be non-genotoxic, in addition to possessing high efficiency, because they could potentially transform normal stem cells into cancer-initiating cells. The objective of this research was to bioengineer an efficient vector that can be used for genetic modification of stem cells without any negative somatic or genetic impact. Two types of multifunctional vectors, namely targeted and non-targeted were genetically engineered and purified from E. coli. The targeted vectors were designed to enter stem cells via overexpressed receptors. The non-targeted vectors were equipped with MPG and Pep1 cell penetrating peptides. A series of commercial synthetic non-viral vectors and an adenoviral vector were used as controls. All vectors were evaluated for their efficiency and impact on metabolic activity, cell membrane integrity, chromosomal aberrations (micronuclei formation), gene dysregulation, and differentiation ability of stem cells. The results of this study showed that the bioengineered vector utilizing VEGFR-1 receptors for cellular entry could transfect mesenchymal stem cells with high efficiency without inducing genotoxicity, negative impact on gene function, or ability to differentiate. Overall, the vectors that utilized receptors as ports for cellular entry (viral and non-viral) showed considerably better somato- and genosafety profiles in comparison to those that entered through electrostatic interaction with cellular membrane. The genetically engineered vector in this study demonstrated that it can be safely and efficiently used to genetically modify stem cells with potential applications in tissue engineering and cancer therapy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microprocessor activity controls differential miRNA biogenesis In Vivo.

PubMed

Conrad, Thomas; Marsico, Annalisa; Gehre, Maja; Orom, Ulf Andersson

2014-10-23

In miRNA biogenesis, pri-miRNA transcripts are converted into pre-miRNA hairpins. The in vivo properties of this process remain enigmatic. Here, we determine in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. On the basis of differential processing efficiencies, we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

A pertinent approach to solve nonlinear fuzzy integro-differential equations.

PubMed

Narayanamoorthy, S; Sathiyapriya, S P

2016-01-01

Fuzzy integro-differential equations is one of the important parts of fuzzy analysis theory that holds theoretical as well as applicable values in analytical dynamics and so an appropriate computational algorithm to solve them is in essence. In this article, we use parametric forms of fuzzy numbers and suggest an applicable approach for solving nonlinear fuzzy integro-differential equations using homotopy perturbation method. A clear and detailed description of the proposed method is provided. Our main objective is to illustrate that the construction of appropriate convex homotopy in a proper way leads to highly accurate solutions with less computational work. The efficiency of the approximation technique is expressed via stability and convergence analysis so as to guarantee the efficiency and performance of the methodology. Numerical examples are demonstrated to verify the convergence and it reveals the validity of the presented numerical technique. Numerical results are tabulated and examined by comparing the obtained approximate solutions with the known exact solutions. Graphical representations of the exact and acquired approximate fuzzy solutions clarify the accuracy of the approach.

Comparative shoot proteome analysis of two potato (Solanum tuberosum L.) genotypes contrasting in nitrogen deficiency responses in vitro.

PubMed

Meise, Philipp; Jozefowicz, Anna Maria; Uptmoor, Ralf; Mock, Hans-Peter; Ordon, Frank; Schum, Annegret

2017-08-23

Aiming at a better understanding of the physiological and biochemical background of nitrogen use efficiency, alterations in the shoot proteome under N-deficiency were investigated in two contrasting potato genotypes grown in vitro with 60 and 7.5mM N, respectively. A gel based proteomic approach was applied to identify candidate proteins associated with genotype specific responses to N-deficiency. 21% of the detected proteins differed in abundance between the two genotypes. Between control and N-deficiency conditions 19.5% were differentially accumulated in the sensitive and 15% in the tolerant genotype. 93% of the highly N-deficiency responsive proteins were identified by MALDI TOF/TOF mass spectrometry. The major part was associated with photosynthesis, carbohydrate metabolism, stress response and regulation. Differential accumulation of enzymes involved in the Calvin cycle and glycolysis suggest activation of alternative carbohydrate pathways. In the tolerant genotype, increased abundance under N-deficiency was also found for enzymes involved in chlorophyll synthesis and stability of enzymes, which increase photosynthetic carbon fixation efficiency. Out of a total of 106 differentially abundant proteins, only eight were detected in both genotypes. Our findings suggest that mutually responsive proteins reflect universal stress responses while adaptation to N-deficiency in metabolic pathways is more genotype specific. Nitrogen losses from arable farm land considerably contribute to environmental pollution. In potato, this is a special problem due cultivation on light soils, irrigation and the shallow root system. Therefore, breeding of cultivars with improved nitrogen use efficiency and stable yields under reduced N fertilization is an important issue. Knowledge of genotype dependent adaptation to N-deficiency at the proteome level can help to understand regulation of N efficiency and development of N-efficient cultivars. Copyright © 2017 Elsevier B.V. All rights reserved.

Object-processing neural efficiency differentiates object from spatial visualizers.

PubMed

Motes, Michael A; Malach, Rafael; Kozhevnikov, Maria

2008-11-19

The visual system processes object properties and spatial properties in distinct subsystems, and we hypothesized that this distinction might extend to individual differences in visual processing. We conducted a functional MRI study investigating the neural underpinnings of individual differences in object versus spatial visual processing. Nine participants of high object-processing ability ('object' visualizers) and eight participants of high spatial-processing ability ('spatial' visualizers) were scanned, while they performed an object-processing task. Object visualizers showed lower bilateral neural activity in lateral occipital complex and lower right-lateralized neural activity in dorsolateral prefrontal cortex. The data indicate that high object-processing ability is associated with more efficient use of visual-object resources, resulting in less neural activity in the object-processing pathway.

Dopaminergic Variants in Siblings at High Risk for Autism: Associations With Initiating Joint Attention

PubMed Central

Gangi, Devon N.; Messinger, Daniel S.; Martin, Eden R.; Cuccaro, Michael L.

2016-01-01

Younger siblings of children with autism spectrum disorder (ASD; high-risk siblings) exhibit lower levels of initiating joint attention (IJA; sharing an object or experience with a social partner through gaze and/or gesture) than low-risk siblings of children without ASD. However, high-risk siblings also exhibit substantial variability in this domain. The neurotransmitter dopamine is linked to brain areas associated with reward, motivation, and attention, and common dopaminergic variants have been associated with attention difficulties. We examined whether these common dopaminergic variants, DRD4 and DRD2, explain variability in IJA in high-risk (n = 55) and low-risk (n = 38) siblings. IJA was assessed in the first year during a semi-structured interaction with an examiner. DRD4 and DRD2 genotypes were coded according to associated dopaminergic functioning to create a gene score, with higher scores indicating more genotypes associated with less efficient dopaminergic functioning. Higher dopamine gene scores (indicative of less efficient dopaminergic functioning) were associated with lower levels of IJA in the first year for high-risk siblings, while the opposite pattern emerged in low-risk siblings. Findings suggest differential susceptibility—IJA was differentially associated with dopaminergic functioning depending on familial ASD risk. Understanding genes linked to ASD-relevant behaviors in high-risk siblings will aid in early identification of children at greatest risk for difficulties in these behavioral domains, facilitating targeted prevention and intervention. PMID:26990357

Three-dimensional neural differentiation of embryonic stem cells with ACM induction in microfibrous matrices in bioreactors.

PubMed

Liu, Ning; Ouyang, Anli; Li, Yan; Yang, Shang-Tian

2013-01-01

The clinical use of pluripotent stem cell (PSC)-derived neural cells requires an efficient differentiation process for mass production in a bioreactor. Toward this goal, neural differentiation of murine embryonic stem cells (ESCs) in three-dimensional (3D) polyethylene terephthalate microfibrous matrices was investigated in this study. To streamline the process and provide a platform for process integration, the neural differentiation of ESCs was induced with astrocyte-conditioned medium without the formation of embryoid bodies, starting from undifferentiated ESC aggregates expanded in a suspension bioreactor. The 3D neural differentiation was able to generate a complex neural network in the matrices. When compared to 2D differentiation, 3D differentiation in microfibrous matrices resulted in a higher percentage of nestin-positive cells (68% vs. 54%) and upregulated gene expressions of nestin, Nurr1, and tyrosine hydroxylase. High purity of neural differentiation in 3D microfibrous matrix was also demonstrated in a spinner bioreactor with 74% nestin + cells. This study demonstrated the feasibility of a scalable process based on 3D differentiation in microfibrous matrices for the production of ESC-derived neural cells. © 2013 American Institute of Chemical Engineers.

Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells.

PubMed

Lee, Jieun; Taylor, Sarah E B; Smeriglio, Piera; Lai, Janice; Maloney, William J; Yang, Fan; Bhutani, Nidhi

2015-08-01

Regeneration of human cartilage is inherently inefficient; an abundant autologous source, such as human induced pluripotent stem cells (hiPSCs), is therefore attractive for engineering cartilage. We report a growth factor-based protocol for differentiating hiPSCs into articular-like chondrocytes (hiChondrocytes) within 2 weeks, with an overall efficiency >90%. The hiChondrocytes are stable and comparable to adult articular chondrocytes in global gene expression, extracellular matrix production, and ability to generate cartilage tissue in vitro and in immune-deficient mice. Molecular characterization identified an early SRY (sex-determining region Y) box (Sox)9(low) cluster of differentiation (CD)44(low)CD140(low) prechondrogenic population during hiPSC differentiation. In addition, 2 distinct Sox9-regulated gene networks were identified in the Sox9(low) and Sox9(high) populations providing novel molecular insights into chondrogenic fate commitment and differentiation. Our findings present a favorable method for generating hiPSC-derived articular-like chondrocytes. The hiChondrocytes are an attractive cell source for cartilage engineering because of their abundance, autologous nature, and potential to generate articular-like cartilage rather than fibrocartilage. In addition, hiChondrocytes can be excellent tools for modeling human musculoskeletal diseases in a dish and for rapid drug screening. © FASEB.

Differential effects of the extracellular microenvironment on human embryonic stem cell differentiation into keratinocytes and their subsequent replicative life span.

PubMed

Movahednia, Mohammad Mehdi; Kidwai, Fahad Karim; Zou, Yu; Tong, Huei Jinn; Liu, Xiaochen; Islam, Intekhab; Toh, Wei Seong; Raghunath, Michael; Cao, Tong

2015-04-01

Culture microenvironment plays a critical role in the propagation and differentiation of human embryonic stem cells (hESCs) and their differentiated progenies. Although high efficiency of hESC differentiation to keratinocytes (hESC-Kert) has been achieved, little is known regarding the effects of early culture microenvironment and pertinent extracellular matrix (ECM) interactions during epidermal commitment on subsequent proliferative capacity of hESC-Kert. The aim of this study is to evaluate the effects of the different ECM microenvironments during hESC differentiation on subsequent replicative life span of hESC-Kert. In doing so, H1-hESCs were differentiated to keratinocytes (H1-Kert) in two differentiation systems. The first system employed autologous fibroblast feeder support, in which keratinocytes (H1-Kert(ACC)) were derived by coculture of hESCs with hESC-derived fibroblasts (H1-ebFs). The second system employed a novel decellularized matrix from H1-ebFs to create a dermoepidermal junction-like (DEJ) matrix. H1-Kert(AFF) were derived by differentiation of hESCs on the feeder-free system employing the DEJ matrix. Our study indicated that the feeder-free system with the use of DEJ matrix was more efficient in differentiation of hESCs toward epidermal progenitors. However, the feeder-free system was not sufficient to support the subsequent replicative capacity of differentiated keratinocytes. Of note, H1-Kert(AFF) showed limited replicative capacity with reduced telomere length and early cellular senescence. We further showed that the lack of cell-cell interactions during epidermal commitment led to heightened production of TGF-β1 by hESC-Kert during extended culture, which in turn was responsible for resulting in the limited replicative life span with cellular senescence of hESC-Kert derived under the feeder-free culture system. This study highlights for the first time the importance of the culture microenvironment and cell-ECM interactions during differentiation of hESCs on subsequent replicative life span and cellular senescence of the differentiated keratinocytes, with implications for use of these cells for applications in tissue engineering and regenerative medicine.

Chapter 10: Peak Demand and Time-Differentiated Energy Savings Cross-Cutting Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

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

Kurnik, Charles W; Stern, Frank; Spencer, Justin

Savings from electric energy efficiency measures and programs are often expressed in terms of annual energy and presented as kilowatt-hours per year (kWh/year). However, for a full assessment of the value of these savings, it is usually necessary to consider the measure or program's impact on peak demand as well as time-differentiated energy savings. This cross-cutting protocol describes methods for estimating the peak demand and time-differentiated energy impacts of measures implemented through energy efficiency programs.

Performance Characterization of a Novel Plasma Thruster to Provide a Revolutionary Operationally Responsive Space Capability with Micro- and Nano-Satellites

DTIC Science & Technology

2011-03-24

and radiation resistance of rare earth permanent magnets for applications such as ion thrusters and high efficiency Stirling Radioisotope Generators...from Electron Transitioning Discharge Current Discharge Power Discharge Voltage Θ Divergence Angle Earths Gravity at Sea Level...Hall effect thruster HIVAC High Voltage Hall Accelerator LEO Low Earth Orbit LDS Laser Displacement System LVDT Linear variable differential

TM-30 Guidance

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

Royer, Michael P.

Minimum color quality standards are necessary, because the light sources most efficient at producing lumens are impractical for use in architectural lighting due to poor color rendition. Thus, accurate measures of color rendition and accompanying performance criteria are essential for helping technology developers and users balance tradeoffs between energy efficiency and lighting quality. Setting higher color-rendition criteria while maintaining use of CRI (e.g., CRI ≥ 90) may filter out some unacceptable light sources, but also filters out many highly desirable light sources and requires a greater tradeoff with energy efficiency. In contrast, specifying color rendition using TM-30 Rf, Rg, andmore » Rcs,h1 has been shown to be effective for differentiating desirable sources while maintaining flexibility for technology development and energy efficiency.« less

ASSESSMENT OF CHEMICAL EFFECTS ON NEURONAL DIFFERENTIATION USING THE ARRAYSCAN HIGH CONTENT SCREENING SYSTEM

EPA Science Inventory

The development of alternative methods for toxicity testing is driven by the need for scientifically valid data that can be obtained in a rapid and cost-efficient manner. In vitro systems provide a model in which chemical effects on cellular events can be examined using technique...

Modeling of the WSTF frictional heating apparatus in high pressure systems

NASA Technical Reports Server (NTRS)

Skowlund, Christopher T.

1992-01-01

In order to develop a computer program able to model the frictional heating of metals in high pressure oxygen or nitrogen a number of additions have been made to the frictional heating model originally developed for tests in low pressure helium. These additions include: (1) a physical property package for the gases to account for departures from the ideal gas state; (2) two methods for spatial discretization (finite differences with quadratic interpolation or orthogonal collocation on finite elements) which substantially reduce the computer time required to solve the transient heat balance; (3) more efficient programs for the integration of the ordinary differential equations resulting from the discretization of the partial differential equations; and (4) two methods for determining the best-fit parameters via minimization of the mean square error (either a direct search multivariable simplex method or a modified Levenburg-Marquardt algorithm). The resulting computer program has been shown to be accurate, efficient and robust for determining the heat flux or friction coefficient vs. time at the interface of the stationary and rotating samples.

Fast engineering optimization: A novel highly effective control parameterization approach for industrial dynamic processes.

PubMed

Liu, Ping; Li, Guodong; Liu, Xinggao

2015-09-01

Control vector parameterization (CVP) is an important approach of the engineering optimization for the industrial dynamic processes. However, its major defect, the low optimization efficiency caused by calculating the relevant differential equations in the generated nonlinear programming (NLP) problem repeatedly, limits its wide application in the engineering optimization for the industrial dynamic processes. A novel highly effective control parameterization approach, fast-CVP, is first proposed to improve the optimization efficiency for industrial dynamic processes, where the costate gradient formulae is employed and a fast approximate scheme is presented to solve the differential equations in dynamic process simulation. Three well-known engineering optimization benchmark problems of the industrial dynamic processes are demonstrated as illustration. The research results show that the proposed fast approach achieves a fine performance that at least 90% of the computation time can be saved in contrast to the traditional CVP method, which reveals the effectiveness of the proposed fast engineering optimization approach for the industrial dynamic processes. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Ascorbic acid enhances the cardiac differentiation of induced pluripotent stem cells through promoting the proliferation of cardiac progenitor cells

PubMed Central

Cao, Nan; Liu, Zumei; Chen, Zhongyan; Wang, Jia; Chen, Taotao; Zhao, Xiaoyang; Ma, Yu; Qin, Lianju; Kang, Jiuhong; Wei, Bin; Wang, Liu; Jin, Ying; Yang, Huang-Tian

2012-01-01

Generation of induced pluripotent stem cells (iPSCs) has opened new avenues for the investigation of heart diseases, drug screening and potential autologous cardiac regeneration. However, their application is hampered by inefficient cardiac differentiation, high interline variability, and poor maturation of iPSC-derived cardiomyocytes (iPS-CMs). To identify efficient inducers for cardiac differentiation and maturation of iPSCs and elucidate the mechanisms, we systematically screened sixteen cardiomyocyte inducers on various murine (m) iPSCs and found that only ascorbic acid (AA) consistently and robustly enhanced the cardiac differentiation of eleven lines including eight without spontaneous cardiogenic potential. We then optimized the treatment conditions and demonstrated that differentiation day 2-6, a period for the specification of cardiac progenitor cells (CPCs), was a critical time for AA to take effect. This was further confirmed by the fact that AA increased the expression of cardiovascular but not mesodermal markers. Noteworthily, AA treatment led to approximately 7.3-fold (miPSCs) and 30.2-fold (human iPSCs) augment in the yield of iPS-CMs. Such effect was attributed to a specific increase in the proliferation of CPCs via the MEK-ERK1/2 pathway by through promoting collagen synthesis. In addition, AA-induced cardiomyocytes showed better sarcomeric organization and enhanced responses of action potentials and calcium transients to β-adrenergic and muscarinic stimulations. These findings demonstrate that AA is a suitable cardiomyocyte inducer for iPSCs to improve cardiac differentiation and maturation simply, universally, and efficiently. These findings also highlight the importance of stimulating CPC proliferation by manipulating extracellular microenvironment in guiding cardiac differentiation of the pluripotent stem cells. PMID:22143566

Physical non-viral gene delivery methods for tissue engineering.

PubMed

Mellott, Adam J; Forrest, M Laird; Detamore, Michael S

2013-03-01

The integration of gene therapy into tissue engineering to control differentiation and direct tissue formation is not a new concept; however, successful delivery of nucleic acids into primary cells, progenitor cells, and stem cells has proven exceptionally challenging. Viral vectors are generally highly effective at delivering nucleic acids to a variety of cell populations, both dividing and non-dividing, yet these viral vectors are marred by significant safety concerns. Non-viral vectors are preferred for gene therapy, despite lower transfection efficiencies, and possess many customizable attributes that are desirable for tissue engineering applications. However, there is no single non-viral gene delivery strategy that "fits-all" cell types and tissues. Thus, there is a compelling opportunity to examine different non-viral vectors, especially physical vectors, and compare their relative degrees of success. This review examines the advantages and disadvantages of physical non-viral methods (i.e., microinjection, ballistic gene delivery, electroporation, sonoporation, laser irradiation, magnetofection, and electric field-induced molecular vibration), with particular attention given to electroporation because of its versatility, with further special emphasis on Nucleofection™. In addition, attributes of cellular character that can be used to improve differentiation strategies are examined for tissue engineering applications. Ultimately, electroporation exhibits a high transfection efficiency in many cell types, which is highly desirable for tissue engineering applications, but electroporation and other physical non-viral gene delivery methods are still limited by poor cell viability. Overcoming the challenge of poor cell viability in highly efficient physical non-viral techniques is the key to using gene delivery to enhance tissue engineering applications.

Physical non-viral gene delivery methods for tissue engineering

PubMed Central

Mellott, Adam J.; Forrest, M. Laird; Detamore, Michael S.

2016-01-01

The integration of gene therapy into tissue engineering to control differentiation and direct tissue formation is not a new concept; however, successful delivery of nucleic acids into primary cells, progenitor cells, and stem cells has proven exceptionally challenging. Viral vectors are generally highly effective at delivering nucleic acids to a variety of cell populations, both dividing and non-dividing, yet these viral vectors are marred by significant safety concerns. Non-viral vectors are preferred for gene therapy, despite lower transfection efficiencies, and possess many customizable attributes that are desirable for tissue engineering applications. However, there is no single non-viral gene delivery strategy that “fits-all” cell types and tissues. Thus, there is a compelling opportunity to examine different non-viral vectors, especially physical vectors, and compare their relative degrees of success. This review examines the advantages and disadvantages of physical non-viral methods (i.e., microinjection, ballistic gene delivery, electroporation, sonoporation, laser irradiation, magnetofection, and electric field-induced molecular vibration), with particular attention given to electroporation because of its versatility, with further special emphasis on Nucleofection™. In addition, attributes of cellular character that can be used to improve differentiation strategies are examined for tissue engineering applications. Ultimately, electroporation exhibits a high transfection efficiency in many cell types, which is highly desirable for tissue engineering applications, but electroporation and other physical non-viral gene delivery methods are still limited by poor cell viability. Overcoming the challenge of poor cell viability in highly efficient physical non-viral techniques is the key to using gene delivery to enhance tissue engineering applications. PMID:23099792

First- and Second-Order Sensitivity Analysis of a P-Version Finite Element Equation Via Automatic Differentiation

NASA Technical Reports Server (NTRS)

Hou, Gene

1998-01-01

Sensitivity analysis is a technique for determining derivatives of system responses with respect to design parameters. Among many methods available for sensitivity analysis, automatic differentiation has been proven through many applications in fluid dynamics and structural mechanics to be an accurate and easy method for obtaining derivatives. Nevertheless, the method can be computational expensive and can require a high memory space. This project will apply an automatic differentiation tool, ADIFOR, to a p-version finite element code to obtain first- and second- order then-nal derivatives, respectively. The focus of the study is on the implementation process and the performance of the ADIFOR-enhanced codes for sensitivity analysis in terms of memory requirement, computational efficiency, and accuracy.

[Diagnostic efficiency of decline rate of signal intensity and apparent diffusion coefficient with different b values for differentiating benign and malignant breast lesions on diffusion-weighted 3.0T magnetic resonance imaging].

PubMed

Jiang, Jing; Liu, Wanhua; Ye, Yuanyuan; Wang, Rui; Li, Fengfang; Peng, Chengyu

2014-06-17

To investigate the diagnostic efficiency of decline rate of signal intensity and apparent diffusion coefficient with different b values for differentiating benign and malignant breast lesions on diffusion-weighted 3.0 T magnetic resonance imaging. A total of 152 patients with 162 confirmed histopathologically breast lesions (85 malignant and 77 benign) underwent 3.0 T diffusion-weighted magnetic resonance imaging. Four b values (0, 400, 800 and 1 000 s/mm²) were used. The signal intensity and ADC values of breast lesions were measured respectively. The signal intensity decline rate (SIDR) and apparent diffusion coefficient decline rate (ADCDR) were calculated respectively. SIDR = (signal intensity of lesions with low b value-signal intensity of lesions with high b value)/signal intensity of lesions with low b value, ADCDR = (ADC value of lesions with low b value-ADC value of lesions with high b value) /ADC value of lesions with low b value. The independent sample t-test was employed for statistical analyses and the receiver operating characteristic (ROC) curve for evaluating the diagnosis efficiency of SIDR and ADCDR values. Significant differences were observed in SIDR between benign and malignant breast lesions with b values of 0-400, 400-800 and 800-1 000 s/mm². The sensitivities of SIDR for differentiating benign and malignant breast lesions were 61.2%, 68.2% and 67.1%, the specificities 74.0%, 85.7% and 67.5%, the diagnosis accordance rates 67.3%, 76.5% and 67.3%, the positive predictive values 72.2%, 84.1% and 69.5% and the negative predictive values 63.3%, 71.0% and 65.0% respectively. Significant differences were observed in ADCDR between benign and malignant breast lesions with b values of 400-800 s/mm² and 800-1 000 s/mm². The sensitivities of SDR for differentiating benign and malignant breast lesions were 80.0% and 65.9%, the specificities 72.7% and 65.0%, the diagnostic accordance rates 76.5% and 65.4%, the positive predictive values 76.4% and 67.5% and the negative predictive values 76.7% and 63.3% respectively. The decline rate of signal intensity and apparent diffusion coefficient with different b values may be used for differentiating benign and malignant breast lesions. And the diagnostic efficiency with b values of 400-800 s/mm² is optimal.

Tropism and Infectivity of Influenza Virus, Including Highly Pathogenic Avian H5N1 Virus, in Ferret Tracheal Differentiated Primary Epithelial Cell Cultures

PubMed Central

Zeng, Hui; Goldsmith, Cynthia S.; Maines, Taronna R.; Belser, Jessica A.; Gustin, Kortney M.; Pekosz, Andrew; Zaki, Sherif R.; Katz, Jacqueline M.

2013-01-01

Tropism and adaptation of influenza viruses to new hosts is partly dependent on the distribution of the sialic acid (SA) receptors to which the viral hemagglutinin (HA) binds. Ferrets have been established as a valuable in vivo model of influenza virus pathogenesis and transmission because of similarities to humans in the distribution of HA receptors and in clinical signs of infection. In this study, we developed a ferret tracheal differentiated primary epithelial cell culture model that consisted of a layered epithelium structure with ciliated and nonciliated cells on its apical surface. We found that human-like (α2,6-linked) receptors predominated on ciliated cells, whereas avian-like (α2,3-linked) receptors, which were less abundant, were presented on nonciliated cells. When we compared the tropism and infectivity of three human (H1 and H3) and two avian (H1 and H5) influenza viruses, we observed that the human influenza viruses primarily infected ciliated cells and replicated efficiently, whereas a highly pathogenic avian H5N1 virus (A/Vietnam/1203/2004) replicated efficiently within nonciliated cells despite a low initial infection rate. Furthermore, compared to other influenza viruses tested, VN/1203 virus replicated more efficiently in cells isolated from the lower trachea and at a higher temperature (37°C) compared to a lower temperature (33°C). VN/1203 virus infection also induced higher levels of immune mediator genes and cell death, and virus was recovered from the basolateral side of the cell monolayer. This ferret tracheal differentiated primary epithelial cell culture system provides a valuable in vitro model for studying cellular tropism, infectivity, and the pathogenesis of influenza viruses. PMID:23255802

Tropism and infectivity of influenza virus, including highly pathogenic avian H5N1 virus, in ferret tracheal differentiated primary epithelial cell cultures.

PubMed

Zeng, Hui; Goldsmith, Cynthia S; Maines, Taronna R; Belser, Jessica A; Gustin, Kortney M; Pekosz, Andrew; Zaki, Sherif R; Katz, Jacqueline M; Tumpey, Terrence M

2013-03-01

Tropism and adaptation of influenza viruses to new hosts is partly dependent on the distribution of the sialic acid (SA) receptors to which the viral hemagglutinin (HA) binds. Ferrets have been established as a valuable in vivo model of influenza virus pathogenesis and transmission because of similarities to humans in the distribution of HA receptors and in clinical signs of infection. In this study, we developed a ferret tracheal differentiated primary epithelial cell culture model that consisted of a layered epithelium structure with ciliated and nonciliated cells on its apical surface. We found that human-like (α2,6-linked) receptors predominated on ciliated cells, whereas avian-like (α2,3-linked) receptors, which were less abundant, were presented on nonciliated cells. When we compared the tropism and infectivity of three human (H1 and H3) and two avian (H1 and H5) influenza viruses, we observed that the human influenza viruses primarily infected ciliated cells and replicated efficiently, whereas a highly pathogenic avian H5N1 virus (A/Vietnam/1203/2004) replicated efficiently within nonciliated cells despite a low initial infection rate. Furthermore, compared to other influenza viruses tested, VN/1203 virus replicated more efficiently in cells isolated from the lower trachea and at a higher temperature (37°C) compared to a lower temperature (33°C). VN/1203 virus infection also induced higher levels of immune mediator genes and cell death, and virus was recovered from the basolateral side of the cell monolayer. This ferret tracheal differentiated primary epithelial cell culture system provides a valuable in vitro model for studying cellular tropism, infectivity, and the pathogenesis of influenza viruses.

The Space-Time Conservation Element and Solution Element Method: A New High-Resolution and Genuinely Multidimensional Paradigm for Solving Conservation Laws. 1; The Two Dimensional Time Marching Schemes

NASA Technical Reports Server (NTRS)

Chang, Sin-Chung; Wang, Xiao-Yen; Chow, Chuen-Yen

1998-01-01

A new high resolution and genuinely multidimensional numerical method for solving conservation laws is being, developed. It was designed to avoid the limitations of the traditional methods. and was built from round zero with extensive physics considerations. Nevertheless, its foundation is mathmatically simple enough that one can build from it a coherent, robust. efficient and accurate numerical framework. Two basic beliefs that set the new method apart from the established methods are at the core of its development. The first belief is that, in order to capture physics more efficiently and realistically, the modeling, focus should be placed on the original integral form of the physical conservation laws, rather than the differential form. The latter form follows from the integral form under the additional assumption that the physical solution is smooth, an assumption that is difficult to realize numerically in a region of rapid chance. such as a boundary layer or a shock. The second belief is that, with proper modeling of the integral and differential forms themselves, the resulting, numerical solution should automatically be consistent with the properties derived front the integral and differential forms, e.g., the jump conditions across a shock and the properties of characteristics. Therefore a much simpler and more robust method can be developed by not using the above derived properties explicitly.

SAChES: Scalable Adaptive Chain-Ensemble Sampling.

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

Swiler, Laura Painton; Ray, Jaideep; Ebeida, Mohamed Salah

We present the development of a parallel Markov Chain Monte Carlo (MCMC) method called SAChES, Scalable Adaptive Chain-Ensemble Sampling. This capability is targed to Bayesian calibration of com- putationally expensive simulation models. SAChES involves a hybrid of two methods: Differential Evo- lution Monte Carlo followed by Adaptive Metropolis. Both methods involve parallel chains. Differential evolution allows one to explore high-dimensional parameter spaces using loosely coupled (i.e., largely asynchronous) chains. Loose coupling allows the use of large chain ensembles, with far more chains than the number of parameters to explore. This reduces per-chain sampling burden, enables high-dimensional inversions and the usemore » of computationally expensive forward models. The large number of chains can also ameliorate the impact of silent-errors, which may affect only a few chains. The chain ensemble can also be sampled to provide an initial condition when an aberrant chain is re-spawned. Adaptive Metropolis takes the best points from the differential evolution and efficiently hones in on the poste- rior density. The multitude of chains in SAChES is leveraged to (1) enable efficient exploration of the parameter space; and (2) ensure robustness to silent errors which may be unavoidable in extreme-scale computational platforms of the future. This report outlines SAChES, describes four papers that are the result of the project, and discusses some additional results.« less

A comparison of the Method of Lines to finite difference techniques in solving time-dependent partial differential equations. [with applications to Burger equation and stream function-vorticity problem

NASA Technical Reports Server (NTRS)

Kurtz, L. A.; Smith, R. E.; Parks, C. L.; Boney, L. R.

1978-01-01

Steady state solutions to two time dependent partial differential systems have been obtained by the Method of Lines (MOL) and compared to those obtained by efficient standard finite difference methods: (1) Burger's equation over a finite space domain by a forward time central space explicit method, and (2) the stream function - vorticity form of viscous incompressible fluid flow in a square cavity by an alternating direction implicit (ADI) method. The standard techniques were far more computationally efficient when applicable. In the second example, converged solutions at very high Reynolds numbers were obtained by MOL, whereas solution by ADI was either unattainable or impractical. With regard to 'set up' time, solution by MOL is an attractive alternative to techniques with complicated algorithms, as much of the programming difficulty is eliminated.

Inhibition of master transcription factors in pluripotent cells induces early stage differentiation

PubMed Central

De, Debojyoti; Jeong, Myong-Ho; Leem, Young-Eun; Svergun, Dmitri I.; Wemmer, David E.; Kang, Jong-Sun; Kim, Kyeong Kyu; Kim, Sung-Hou

2014-01-01

The potential for pluripotent cells to differentiate into diverse specialized cell types has given much hope to the field of regenerative medicine. Nevertheless, the low efficiency of cell commitment has been a major bottleneck in this field. Here we provide a strategy to enhance the efficiency of early differentiation of pluripotent cells. We hypothesized that the initial phase of differentiation can be enhanced if the transcriptional activity of master regulators of stemness is suppressed, blocking the formation of functional transcriptomes. However, an obstacle is the lack of an efficient strategy to block protein–protein interactions. In this work, we take advantage of the biochemical property of seventeen kilodalton protein (Skp), a bacterial molecular chaperone that binds directly to sex determining region Y-box 2 (Sox2). The small angle X-ray scattering analyses provided a low resolution model of the complex and suggested that the transactivation domain of Sox2 is probably wrapped in a cleft on Skp trimer. Upon the transduction of Skp into pluripotent cells, the transcriptional activity of Sox2 was inhibited and the expression of Sox2 and octamer-binding transcription factor 4 was reduced, which resulted in the expression of early differentiation markers and appearance of early neuronal and cardiac progenitors. These results suggest that the initial stage of differentiation can be accelerated by inhibiting master transcription factors of stemness. This strategy can possibly be applied to increase the efficiency of stem cell differentiation into various cell types and also provides a clue to understanding the mechanism of early differentiation. PMID:24434556

An efficient and robust algorithm for two dimensional time dependent incompressible Navier-Stokes equations: High Reynolds number flows

NASA Technical Reports Server (NTRS)

Goodrich, John W.

1991-01-01

An algorithm is presented for unsteady two-dimensional incompressible Navier-Stokes calculations. This algorithm is based on the fourth order partial differential equation for incompressible fluid flow which uses the streamfunction as the only dependent variable. The algorithm is second order accurate in both time and space. It uses a multigrid solver at each time step. It is extremely efficient with respect to the use of both CPU time and physical memory. It is extremely robust with respect to Reynolds number.

Hepatic mitochondrial energetics during catch-up fat with high-fat diets rich in lard or safflower oil.

PubMed

Crescenzo, Raffaella; Bianco, Francesca; Falcone, Italia; Tsalouhidou, Sofia; Yepuri, Gayathri; Mougios, Vassilis; Dulloo, Abdul G; Liverini, Giovanna; Iossa, Susanna

2012-09-01

We have investigated whether altered hepatic mitochondrial energetics could explain the differential effects of high-fat diets with low or high ω6 polyunsaturated fatty acid content (lard vs. safflower oil) on the efficiency of body fat recovery (catch-up fat) during refeeding after caloric restriction. After 2 weeks of caloric restriction, rats were isocalorically refed with a low-fat diet (LF) or high-fat diets made from either lard or safflower oil for 1 week, and energy balance and body composition changes were assessed. Hepatic mitochondrial energetics were determined from measurements of liver mitochondrial mass, respiratory capacities, and proton leak. Compared to rats refed the LF, the groups refed high-fat diets showed lower energy expenditure and increased efficiency of fat gain; these differences were less marked with high-safflower oil than with high-lard diet. The increase in efficiency of catch-up fat by the high-fat diets could not be attributed to differences in liver mitochondrial activity. By contrast, the lower fat gain with high-safflower oil than with high-lard diet is accompanied by higher mitochondrial proton leak and increased proportion of arachidonic acid in mitochondrial membranes. In conclusion, the higher efficiency for catch-up fat on high-lard diet than on LF cannot be explained by altered hepatic mitochondrial energetics. By contrast, the ability of the high-safflower oil diet to produce a less pronounced increase in the efficiency of catch-up fat may partly reside in increased incorporation of arachidonic acid in hepatic mitochondrial membranes, leading to enhanced proton leak and mitochondrial uncoupling.

Nitric oxide releasing hydrogel promotes endothelial differentiation of mouse embryonic stem cells.

PubMed

Nie, Yan; Zhang, Kaiyue; Zhang, Shuaiqiang; Wang, Dan; Han, Zhibo; Che, Yongzhe; Kong, Deling; Zhao, Qiang; Han, Zhongchao; He, Zuo-Xiang; Liu, Na; Ma, Fengxia; Li, Zongjin

2017-11-01

Transplantation of endothelial cells (ECs) holds great promise for treating various kinds of ischemic diseases. However, the major challenge in ECs-based therapy in clinical applications is to provide high quality and enough amounts of cells. In this study, we developed a simple and efficient system to direct endothelial differentiation of mouse embryonic stem cells (ESCs) using a controllable chitosan nitric oxide (NO)-releasing hydrogel (CS-NO). ESCs were plated onto the hydrogel culture system, and the expressions of differentiation markers were measured. We found that the expression of Flk-1 (early ECs marker) and VE-cadherin (mature ECs marker) increased obviously under the controlled NO releasing environment. Moreover, the Flk-1 upregulation was accompanied by the activation of the phospho-inositide-3 kinase (PI3K)/Akt signaling. We also found that in the presence of the PI3K inhibitor (LY294002), the endothelial commitment of ESCs was abolished, indicating the importance of Akt phosphorylation in the endothelial differentiation of ESCs. Interestingly, in the absence of NO, the activation of Akt phosphorylation alone by using AKT activator (SC-79) did not profoundly promote the endothelial differentiation of ESCs, suggesting an interdependent relationship between NO and the Akt phosphorylation in driving endothelial fate specification of ESCs. Taken together, we demonstrated that NO releasing in a continuous and controlled manner is a simple and efficient method for directing the endothelial differentiation of ESCs without adding growth factors. Fascinating data continues to show that artificial stem cell niche not only serve as a physical supporting scaffold for stem cells proliferation, but also as a novel platform for directing stem cell differentiation. Because of the lack of proper microenvironment for generating therapeutic endothelial cells (ECs) in vitro, the source of ECs for transplantation is the major limitation in ECs-based therapy to clinical applications. The current study established a feeder cell-free, 2-dimensional culture system for promoting the differentiation processes of embryonic stem cells (ESCs) committed to the endothelial lineage via using a nitric oxide (NO) controlled releasing hydrogel (CS-NO). Notably, the NO releasing from the hydrogel could selectively up-regulate Flk-1 (early ECs marker) and VE-cadherin (mature ECs marker) in the absence of growth factors, which was of crucial importance in the endothelial differentiation of ESCs. In summary, the current study proposes a simple and efficient method for directing the endothelial differentiation of ESCs without extra growth factors. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Differential phase-shift keying and channel equalization in free space optical communication system

NASA Astrophysics Data System (ADS)

Zhang, Dai; Hao, Shiqi; Zhao, Qingsong; Wan, Xiongfeng; Xu, Chenlu

2018-01-01

We present the performance benefits of differential phase-shift keying (DPSK) modulation in eliminating influence from atmospheric turbulence, especially for coherent free space optical (FSO) communication with a high communication rate. Analytic expression of detected signal is derived, based on which, homodyne detection efficiency is calculated to indicate the performance of wavefront compensation. Considered laser pulses always suffer from atmospheric scattering effect by clouds, intersymbol interference (ISI) in high-speed FSO communication link is analyzed. Correspondingly, the channel equalization method of a binormalized modified constant modulus algorithm based on set-membership filtering (SM-BNMCMA) is proposed to solve the ISI problem. Finally, through the comparison with existing channel equalization methods, its performance benefits of both ISI elimination and convergence speed are verified. The research findings have theoretical significance in a high-speed FSO communication system.

Autophagy is essential for the differentiation of porcine PSCs into insulin-producing cells.

PubMed

Ren, Lipeng; Yang, Hong; Cui, Yanhua; Xu, Shuanshuan; Sun, Fen; Tian, Na; Hua, Jinlian; Peng, Sha

2017-07-01

Porcine pancreatic stem cells (PSCs) are seed cells with potential use for diabetes treatment. Stem cell differentiation requires strict control of protein turnover and lysosomal digestion of organelles. Autophagy is a highly conserved process that controls the turnover of organelles and proteins within cells and contributes to the balance of cellular components. However, whether autophagy plays roles in PSC differentiation remains unknown. In this study, we successfully induced porcine PSCs into insulin-producing cells and found that autophagy was activated during the second induction stage. Inhibition of autophagy in the second stage resulted in reduced differentiational efficiency and impaired glucose-stimulated insulin secretion. Moreover, the expression of active β-catenin increased while autophagy was activated but was suppressed when autophagy was inhibited. Therefore, autophagy is essential to the formation of insulin-producing cells, and the effects of autophagy on differentiation may be regulated by canonical Wnt signalling pathway. Copyright © 2017 Elsevier Inc. All rights reserved.

Cross-correlation photothermal optical coherence tomography with high effective resolution.

PubMed

Tang, Peijun; Liu, Shaojie; Chen, Junbo; Yuan, Zhiling; Xie, Bingkai; Zhou, Jianhua; Tang, Zhilie

2017-12-01

We developed a cross-correlation photothermal optical coherence tomography (CC-PTOCT) system for photothermal imaging with high lateral and axial resolution. The CC-PTOCT system consists of a phase-sensitive OCT system, a modulated pumping laser, and a digital cross-correlator. The pumping laser was used to induce the photothermal effect in the sample, causing a slight phase modulation of the OCT signals. A spatial phase differentiation method was employed to reduce phase accumulation. The noise brought by the phase differentiation method and the strong background noise were suppressed efficiently by the cross-correlator, which was utilized to extract the photothermal signals from the modulated signals. Combining the cross-correlation technique with spatial phase differentiation can improve both lateral and axial resolution of the PTOCT imaging system. Clear photothermal images of blood capillaries of a mouse ear in vivo were successfully obtained with high lateral and axial resolution. The experimental results demonstrated that this system can enhance the effective transverse resolution, effective depth resolution, and contrast of the PTOCT image effectively, aiding the ongoing development of the accurate 3D functional imaging.

High-Performance Lithium-Oxygen Battery Electrolyte Derived from Optimum Combination of Solvent and Lithium Salt.

PubMed

Ahn, Su Mi; Suk, Jungdon; Kim, Do Youb; Kang, Yongku; Kim, Hwan Kyu; Kim, Dong Wook

2017-10-01

To fabricate a sustainable lithium-oxygen (Li-O 2 ) battery, it is crucial to identify an optimum electrolyte. Herein, it is found that tetramethylene sulfone (TMS) and lithium nitrate (LiNO 3 ) form the optimum electrolyte, which greatly reduces the overpotential at charge, exhibits superior oxygen efficiency, and allows stable cycling for 100 cycles. Linear sweep voltammetry (LSV) and differential electrochemical mass spectrometry (DEMS) analyses reveal that neat TMS is stable to oxidative decomposition and exhibit good compatibility with a lithium metal. But, when TMS is combined with typical lithium salts, its performance is far from satisfactory. However, the TMS electrolyte containing LiNO 3 exhibits a very low overpotential, which minimizes the side reactions and shows high oxygen efficiency. LSV-DEMS study confirms that the TMS-LiNO 3 electrolyte efficiently produces NO 2 - , which initiates a redox shuttle reaction. Interestingly, this NO 2 - /NO 2 redox reaction derived from the LiNO 3 salt is not very effective in solvents other than TMS. Compared with other common Li-O 2 solvents, TMS seems optimum solvent for the efficient use of LiNO 3 salt. Good compatibility with lithium metal, high dielectric constant, and low donicity of TMS are considered to be highly favorable to an efficient NO 2 - /NO 2 redox reaction, which results in a high-performance Li-O 2 battery.

The differential effects of 2% oxygen preconditioning on the subsequent differentiation of mouse and human pluripotent stem cells.

PubMed

Fynes, Kate; Tostoes, Rui; Ruban, Ludmila; Weil, Ben; Mason, Christopher; Veraitch, Farlan S

2014-08-15

A major challenge facing the development of effective cell therapies is the efficient differentiation of pluripotent stem cells (PSCs) into pure populations. Lowering oxygen tension to physiological levels can affect both the expansion and differentiation stages. However, to date, there are no studies investigating the knock-on effect of culturing PSCs under low oxygen conditions on subsequent lineage commitment at ambient oxygen levels. PSCs were passaged three times at 2% O2 before allowing cells to spontaneously differentiate as embryoid bodies (EBs) in high oxygen (20% O2) conditions. Maintenance of mouse PSCs in low oxygen was associated with a significant increase in the expression of early differentiation markers FGF5 and Eomes, while conversely we observed decreased expression of these genes in human PSCs. Low oxygen preconditioning primed mouse PSCs for their subsequent differentiation into mesodermal and endodermal lineages, as confirmed by increased gene expression of Eomes, Goosecoid, Brachyury, AFP, Sox17, FoxA2, and protein expression of Brachyury, Eomes, Sox17, FoxA2, relative to high oxygen cultures. The effects extended to the subsequent formation of more mature mesodermal lineages. We observed significant upregulation of cardiomyocyte marker Nkx2.5, and critically a decrease in the number of contaminant pluripotent cells after 12 days using a directed cardiomyocyte protocol. However, the impact of low oxygen preconditioning was to prime human cells for ectodermal lineage commitment during subsequent EB differentiation, with significant upregulation of Nestin and β3-tubulin. Our research demonstrates the importance of oxygen tension control during cell maintenance on the subsequent differentiation of both mouse and human PSCs, and highlights the differential effects.

Preparation and Evaluation of Multiple Nanoemulsions Containing Gadolinium (III) Chelate as a Potential Magnetic Resonance Imaging (MRI) Contrast Agent.

PubMed

Sigward, Estelle; Corvis, Yohann; Doan, Bich-Thuy; Kindsiko, Kadri; Seguin, Johanne; Scherman, Daniel; Brossard, Denis; Mignet, Nathalie; Espeau, Philippe; Crauste-Manciet, Sylvie

2015-09-01

The objective was to develop, characterize and assess the potentiality of W1/O/W2 self-emulsifying multiple nanoemulsions to enhance signal/noise ratio for Magnetic Resonance Imaging (MRI). For this purpose, a new formulation, was designed for encapsulation efficiency and stability. Various methods were used to characterize encapsulation efficiency ,in particular calorimetric methods (Differential Scanning Calorimetry (DSC), thermogravimetry analysis) and ultrafiltration. MRI in vitro relaxivities were assessed on loaded DTPA-Gd multiple nanoemulsions. Characterization of the formulation, in particular of encapsulation efficiency was a challenge due to interactions found with ultrafiltration method. Thanks to the specifically developed DSC protocol, we were able to confirm the formation of multiple nanoemulsions, differentiate loaded from unloaded nanoemulsions and measure the encapsulation efficiency which was found to be quite high with a 68% of drug loaded. Relaxivity studies showed that the self-emulsifying W/O/W nanoemulsions were positive contrast agents, exhibiting higher relaxivities than those of the DTPA-Gd solution taken as a reference. New self-emulsifying multiple nanoemulsions that were able to load satisfactory amounts of contrasting agent were successfully developed as potential MRI contrasting agents. A specific DSC protocol was needed to be developed to characterize these complex systems as it would be useful to develop these self-formation formulations.

Building Measures of Instructional Differentiation from Teacher Checklists

ERIC Educational Resources Information Center

Williams, Ryan; Swanlund, Andrew; Miller, Shazia; Konstantopoulos, Spyros; van der Ploeg, Arie

2012-01-01

Differentiated instruction is commonly believed to be critical to improving the quality and efficiency of teachers' instructional repertoires (Fischer & Rose, 2001; Tomlinson, 2004). Tomlinson (2000) describes differentiation in four domains: content, process, product, and learning environment. Content differentiation involves varying…

A Novel In Vitro Method for Detecting Undifferentiated Human Pluripotent Stem Cells as Impurities in Cell Therapy Products Using a Highly Efficient Culture System

PubMed Central

Tano, Keiko; Yasuda, Satoshi; Kuroda, Takuya; Saito, Hirohisa; Umezawa, Akihiro; Sato, Yoji

2014-01-01

Innovative applications of cell therapy products (CTPs) derived from human pluripotent stem cells (hPSCs) in regenerative medicine are currently being developed. The presence of residual undifferentiated hPSCs in CTPs is a quality concern associated with tumorigencity. However, no simple in vitro method for direct detection of undifferentiated hPSCs that contaminate CTPs has been developed. Here, we show a novel approach for direct and sensitive detection of a trace amount of undifferentiated human induced pluripotent stem cells (hiPSCs) using a highly efficient amplification method in combination with laminin-521 and Essential 8 medium. Essential 8 medium better facilitated the growth of hiPSCs dissociated into single cells on laminin-521 than in mTeSR1 medium. hiPSCs cultured on laminin-521 in Essential 8 medium were maintained in an undifferentiated state and they maintained the ability to differentiate into various cell types. Essential 8 medium allowed robust hiPSC proliferation plated on laminin-521 at low cell density, whereas mTeSR1 did not enhance the cell growth. The highly efficient culture system using laminin-521 and Essential 8 medium detected hiPSCs spiked into primary human mesenchymal stem cells (hMSCs) or human neurons at the ratio of 0.001%–0.01% as formed colonies. Moreover, this assay method was demonstrated to detect residual undifferentiated hiPSCs in cell preparations during the process of hMSC differentiation from hiPSCs. These results indicate that our highly efficient amplification system using a combination of laminin-521 and Essential 8 medium is able to detect a trace amount of undifferentiated hPSCs contained as impurities in CTPs and would contribute to quality assessment of hPSC-derived CTPs during the manufacturing process. PMID:25347300

Multi Sensor Fusion Using Fitness Adaptive Differential Evolution

NASA Astrophysics Data System (ADS)

Giri, Ritwik; Ghosh, Arnob; Chowdhury, Aritra; Das, Swagatam

The rising popularity of multi-source, multi-sensor networks supports real-life applications calls for an efficient and intelligent approach to information fusion. Traditional optimization techniques often fail to meet the demands. The evolutionary approach provides a valuable alternative due to its inherent parallel nature and its ability to deal with difficult problems. We present a new evolutionary approach based on a modified version of Differential Evolution (DE), called Fitness Adaptive Differential Evolution (FiADE). FiADE treats sensors in the network as distributed intelligent agents with various degrees of autonomy. Existing approaches based on intelligent agents cannot completely answer the question of how their agents could coordinate their decisions in a complex environment. The proposed approach is formulated to produce good result for the problems that are high-dimensional, highly nonlinear, and random. The proposed approach gives better result in case of optimal allocation of sensors. The performance of the proposed approach is compared with an evolutionary algorithm coordination generalized particle model (C-GPM).

Efficient stage-specific differentiation of human pluripotent stem cells toward retinal photoreceptor cells.

PubMed

Mellough, Carla B; Sernagor, Evelyne; Moreno-Gimeno, Inmaculada; Steel, David H W; Lako, Majlinda

2012-04-01

Recent successes in the stem cell field have identified some of the key chemical and biological cues which drive photoreceptor derivation from human embryonic stem cells (hESC) and human induced pluripotent stem cells (hiPSC); however, the efficiency of this process is variable. We have designed a three-step photoreceptor differentiation protocol combining previously published methods that direct the differentiation of hESC and hiPSC toward a retinal lineage, which we further modified with additional supplements selected on the basis of reports from the eye field and retinal development. We report that hESC and hiPSC differentiating under our regimen over a 60 day period sequentially acquire markers associated with neural, retinal field, retinal pigmented epithelium and photoreceptor cells, including mature photoreceptor markers OPN1SW and RHODOPSIN with a higher efficiency than previously reported. In addition, we report the ability of hESC and hiPSC cultures to generate neural and retinal phenotypes under minimal culture conditions, which may be linked to their ability to endogenously upregulate the expression of a range of factors important for retinal cell type specification. However, cultures that were differentiated with full supplementation under our photoreceptor-induction regimen achieve this within a significantly shorter time frame and show a substantial increase in the expression of photoreceptor-specific markers in comparison to cultures differentiated under minimal conditions. Interestingly, cultures supplemented only with B27 and/or N2 displayed comparable differentiation efficiency to those under full supplementation, indicating a key role for B27 and N2 during the differentiation process. Furthermore, our data highlight an important role for Dkk1 and Noggin in enhancing the differentiation of hESC and hiPSC toward retinal progenitor cells and photoreceptor precursors during the early stages of differentiation, while suggesting that further maturation of these cells into photoreceptors may not require additional factors and can ensue under minimal culture conditions. Copyright © 2012 AlphaMed Press.

Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications.

PubMed

Yu, Fang; Chen, Ming-Hui; Kuo, Lynn; Talbott, Heather; Davis, John S

2015-08-07

Recently, the Bayesian method becomes more popular for analyzing high dimensional gene expression data as it allows us to borrow information across different genes and provides powerful estimators for evaluating gene expression levels. It is crucial to develop a simple but efficient gene selection algorithm for detecting differentially expressed (DE) genes based on the Bayesian estimators. In this paper, by extending the two-criterion idea of Chen et al. (Chen M-H, Ibrahim JG, Chi Y-Y. A new class of mixture models for differential gene expression in DNA microarray data. J Stat Plan Inference. 2008;138:387-404), we propose two new gene selection algorithms for general Bayesian models and name these new methods as the confident difference criterion methods. One is based on the standardized differences between two mean expression values among genes; the other adds the differences between two variances to it. The proposed confident difference criterion methods first evaluate the posterior probability of a gene having different gene expressions between competitive samples and then declare a gene to be DE if the posterior probability is large. The theoretical connection between the proposed first method based on the means and the Bayes factor approach proposed by Yu et al. (Yu F, Chen M-H, Kuo L. Detecting differentially expressed genes using alibrated Bayes factors. Statistica Sinica. 2008;18:783-802) is established under the normal-normal-model with equal variances between two samples. The empirical performance of the proposed methods is examined and compared to those of several existing methods via several simulations. The results from these simulation studies show that the proposed confident difference criterion methods outperform the existing methods when comparing gene expressions across different conditions for both microarray studies and sequence-based high-throughput studies. A real dataset is used to further demonstrate the proposed methodology. In the real data application, the confident difference criterion methods successfully identified more clinically important DE genes than the other methods. The confident difference criterion method proposed in this paper provides a new efficient approach for both microarray studies and sequence-based high-throughput studies to identify differentially expressed genes.

Endodermal differentiation of human pluripotent stem cells to insulin-producing cells in 3D culture

PubMed Central

Takeuchi, Hiroki; Nakatsuji, Norio; Suemori, Hirofumi

2014-01-01

Insulin-producing cells (IPCs) derived from human pluripotent stem cells (hPSCs) may be useful in cell therapy and drug discovery for diabetes. Here, we examined various growth factors and small molecules including those previously reported to develop a robust differentiation method for induction of mature IPCs from hPSCs. We established a protocol that induced PDX1-positive pancreatic progenitor cells at high efficiency, and further induced mature IPCs by treatment with forskolin, dexamethasone, Alk5 inhibitor II and nicotinamide in 3D culture. The cells that differentiated into INSULIN-positive and C-PEPTIDE-positive cells secreted insulin in response to glucose stimulation, indicating a functional IPC phenotype. We also found that this method was applicable to different types of hPSCs. PMID:24671046

Repair kinetics of DNA double-strand breaks and incidence of apoptosis in mouse neural stem/progenitor cells and their differentiated neurons exposed to ionizing radiation.

PubMed

Kashiwagi, Hiroki; Shiraishi, Kazunori; Sakaguchi, Kenta; Nakahama, Tomoya; Kodama, Seiji

2018-05-01

Neuronal loss leads to neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease and Huntington's disease. Because of their long lifespans, neurons are assumed to possess highly efficient DNA repair ability and to be able to protect themselves from deleterious DNA damage such as DNA double-strand breaks (DSBs) produced by intrinsic and extrinsic sources. However, it remains largely unknown whether the DSB repair ability of neurons is more efficient compared with that of other cells. Here, we investigated the repair kinetics of X-ray-induced DSBs in mouse neural cells by scoring the number of phosphorylated 53BP1 foci post irradiation. We found that p53-independent apoptosis was induced time dependently during differentiation from neural stem/progenitor cells (NSPCs) into neurons in culture for 48 h. DSB repair in neurons differentiated from NSPCs in culture was faster than that in mouse embryonic fibroblasts (MEFs), possibly due to the higher DNA-dependent protein kinase activity, but it was similar to that in NSPCs. Further, the incidence of p53-dependent apoptosis induced by X-irradiation in neurons was significantly higher than that in NSPCs. This difference in response of X-ray-induced apoptosis between neurons and NSPCs may reflect a difference in the fidelity of non-homologous end joining or a differential sensitivity to DNA damage other than DSBs.

In vitro differentiation of rat bone marrow mesenchymal stem cells into hepatocytes.

PubMed

Feng, Zhihui; Li, Changying; Jiao, Shuxian; Hu, Bin; Zhao, Lin

2011-01-01

To investigate the mechanism and regulation of differentiation from bone marrow mesenchymal stem cells (BMSCs) into hepatocytes and to find a new source for therapies of hepatic diseases. We isolated BMSCs for subsequent differentiation in the presence of hepatocyte growth factor (HGF) or beta-nerve growth factor (beta-NGF). Cell morphology was observed and cell surface phenotypings were detected by flow cytometry. a1-antitrypsin (AAT) expression of the hepatocytes was confirmed by immunocytochemistry and albumin expression was validated by real time PCR and western blotting. The expression of high-affinity nerve growth factor receptor (TrkA) and the activation of Erk pathway were detected by western blotting. Hepatocyte functional activity was confirmed by uptake of indocyanine green (ICG) assay. Small round cells appeared in the presence of HGF on day 10 or beta-NGF on day 12. Differentiated cells expressed albumin and had functional characteristics of hepatocytes, such as uptake of ICG. BMSCs were positive for TrkA. HGF and beta-NGF significantly upregulated the protein levels of phospho-Erk. BMSCs could differentiate into hepatocytes in the differentiation media including HGF or beta-NGF. Combination of HGF and beta-NGF significantly increased the efficiency of hepatic differentiation.

Low-threshold high-T/0/ constricted double heterojunction AlGaAs diode lasers

NASA Technical Reports Server (NTRS)

Botez, D.; Connolly, J. C.

1980-01-01

Constricted double heterojunction diode lasers of relatively low CW thresholds (28-40 mA) are obtained by growing structures that maximize the amount of current flow into the lasing spot. These values are obtained while still using standard 10 microns wide oxide-defined stripe contacts. Over the 20-70 C temperature interval, threshold current temperature coefficients as high as 320 C and a virtually constant external differential quantum efficiency, are found.

Integrating human stem cell expansion and neuronal differentiation in bioreactors

PubMed Central

Serra, Margarida; Brito, Catarina; Costa, Eunice M; Sousa, Marcos FQ; Alves, Paula M

2009-01-01

Background Human stem cells are cellular resources with outstanding potential for cell therapy. However, for the fulfillment of this application, major challenges remain to be met. Of paramount importance is the development of robust systems for in vitro stem cell expansion and differentiation. In this work, we successfully developed an efficient scalable bioprocess for the fast production of human neurons. Results The expansion of undifferentiated human embryonal carcinoma stem cells (NTera2/cl.D1 cell line) as 3D-aggregates was firstly optimized in spinner vessel. The media exchange operation mode with an inoculum concentration of 4 × 105 cell/mL was the most efficient strategy tested, with a 4.6-fold increase in cell concentration achieved in 5 days. These results were validated in a bioreactor where similar profile and metabolic performance were obtained. Furthermore, characterization of the expanded population by immunofluorescence microscopy and flow cytometry showed that NT2 cells maintained their stem cell characteristics along the bioreactor culture time. Finally, the neuronal differentiation step was integrated in the bioreactor process, by addition of retinoic acid when cells were in the middle of the exponential phase. Neurosphere composition was monitored and neuronal differentiation efficiency evaluated along the culture time. The results show that, for bioreactor cultures, we were able to increase significantly the neuronal differentiation efficiency by 10-fold while reducing drastically, by 30%, the time required for the differentiation process. Conclusion The culture systems developed herein are robust and represent one-step-forward towards the development of integrated bioprocesses, bridging stem cell expansion and differentiation in fully controlled bioreactors. PMID:19772662

Donor cell differentiation, reprogramming, and cloning efficiency: elusive or illusive correlation?

PubMed

Oback, B; Wells, D N

2007-05-01

Compared to other assisted reproductive technologies, mammalian nuclear transfer (NT) cloning is inefficient in generating viable offspring. It has been postulated that nuclear reprogramming and cloning efficiency can be increased by choosing less differentiated cell types as nuclear donors. This hypothesis is mainly supported by comparative mouse cloning experiments using early blastomeres, embryonic stem (ES) cells, and terminally differentiated somatic donor cells. We have re-evaluated these comparisons, taking into account different NT procedures, the use of donor cells from different genetic backgrounds, sex, cell cycle stages, and the lack of robust statistical significance when post-blastocyst development is compared. We argue that while the reprogrammability of early blastomeres appears to be much higher than that of somatic cells, it has so far not been conclusively determined whether differentiation status affects cloning efficiency within somatic donor cell lineages. Copyright (c) 2006 Wiley-Liss, Inc.

Age-dependent epigenetic control of differentiation inhibitors is critical for remyelination efficiency

PubMed Central

Shen, Siming; Sandoval, Juan; Swiss, Victoria A; Li, Jiadong; Dupree, Jeff; Franklin, Robin J M; Casaccia-Bonnefil, Patrizia

2009-01-01

The efficiency of remyelination decreases with age, but the molecular mechanisms responsible for this decline remain only partially understood. In this study, we show that remyelination is regulated by age-dependent epigenetic control of gene expression. In demyelinated young brains, new myelin synthesis is preceded by downregulation of oligodendrocyte differentiation inhibitors and neural stem cell markers, and this is associated with recruitment of histone deacetylases (HDACs) to promoter regions. In demyelinated old brains, HDAC recruitment is inefficient, and this allows the accumulation of transcriptional inhibitors and prevents the subsequent surge in myelin gene expression. Defective remyelination can be recapitulated in vivo in mice receiving systemic administration of pharmacological HDAC inhibitors during cuprizone treatment and is consistent with in vitro results showing defective differentiation of oligodendrocyte progenitors after silencing specific HDAC isoforms. Thus, we suggest that inefficient epigenetic modulation of the oligodendrocyte differentiation program contributes to the age-dependent decline in remyelination efficiency. PMID:19160500

Compact high-pulse-energy ultraviolet laser source for ozone lidar measurements.

PubMed

Elsayed, Khaled A; DeYoung, Russell J; Petway, Larry B; Edwards, William C; Barnes, James C; Elsayed-Ali, Hani E

2003-11-20

An all solid-state Ti:sapphire laser differential absorption lidar transmitter was developed. This all-solid-state laser provides a compact, robust, and highly reliable laser transmitter for potential application in differential absorption lidar measurements of atmospheric ozone. Two compact, high-energy-pulsed, and injection-seeded Ti:sapphire lasers operating at a pulse repetition frequency of 30 Hz and wavelengths of 867 and 900 nm, with M2 of 1.3, have been experimentally demonstrated and their properties compared with model results. The output pulse energy was 115 mJ at 867 nm and 105 mJ at 900 nm, with a slope efficiency of 40% and 32%, respectively. At these energies, the beam quality was good enough so that we were able to achieve 30 mJ of ultraviolet laser output at 289 and 300 nm after frequency tripling with two lithium triborate nonlinear crystals.

In vitro generation of three-dimensional substrate-adherent embryonic stem cell-derived neural aggregates for application in animal models of neurological disorders.

PubMed

Hargus, Gunnar; Cui, Yi-Fang; Dihné, Marcel; Bernreuther, Christian; Schachner, Melitta

2012-05-01

In vitro-differentiated embryonic stem (ES) cells comprise a useful source for cell replacement therapy, but the efficiency and safety of a translational approach are highly dependent on optimized protocols for directed differentiation of ES cells into the desired cell types in vitro. Furthermore, the transplantation of three-dimensional ES cell-derived structures instead of a single-cell suspension may improve graft survival and function by providing a beneficial microenvironment for implanted cells. To this end, we have developed a new method to efficiently differentiate mouse ES cells into neural aggregates that consist predominantly (>90%) of postmitotic neurons, neural progenitor cells, and radial glia-like cells. When transplanted into the excitotoxically lesioned striatum of adult mice, these substrate-adherent embryonic stem cell-derived neural aggregates (SENAs) showed significant advantages over transplanted single-cell suspensions of ES cell-derived neural cells, including improved survival of GABAergic neurons, increased cell migration, and significantly decreased risk of teratoma formation. Furthermore, SENAs mediated functional improvement after transplantation into animal models of Parkinson's disease and spinal cord injury. This unit describes in detail how SENAs are efficiently derived from mouse ES cells in vitro and how SENAs are isolated for transplantation. Furthermore, methods are presented for successful implantation of SENAs into animal models of Huntington's disease, Parkinson's disease, and spinal cord injury to study the effects of stem cell-derived neural aggregates in a disease context in vivo.

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

PubMed Central

2012-01-01

Background RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. Results Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. Conclusions This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates. PMID:22985019

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing.

PubMed

Robles, José A; Qureshi, Sumaira E; Stephen, Stuart J; Wilson, Susan R; Burden, Conrad J; Taylor, Jennifer M

2012-09-17

RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates.

Mechanical characterization and durability of sintered porous transport layers for polymer electrolyte membrane electrolysis

NASA Astrophysics Data System (ADS)

Borgardt, Elena; Panchenko, Olha; Hackemüller, Franz Josef; Giffin, Jürgen; Bram, Martin; Müller, Martin; Lehnert, Werner; Stolten, Detlef

2018-01-01

Differential pressure electrolysis offers the potential for more efficient hydrogen compression. Due to the differential pressures acting within the electrolytic cell, the porous transport layer (PTL) is subjected to high stress. For safety reasons, the PTL's mechanical stability must be ensured. However, the requirements for high porosity and low thickness stand in contrast to that for mechanical stability. Porous transport layers for polymer electrolyte membrane (PEM) electrolysis are typically prepared by means of the thermal sintering of titanium powder. Thus far, the factors that influence the mechanical strength of the sintered bodies and how all requirements can be simultaneously fulfilled have not been investigated. Here, the static and dynamic mechanical properties of thin sintered titanium sheets are investigated ex-situ via tensile tests and periodic loading in a test cell, respectively. In order for a sintered PTL with a thickness of 500 μm and porosities above 25% to be able to withstand 50 bar differential pressure in the cell, the maximum flow field width should be limited to 3 mm. Thus, a method was developed to test the suitability of PTL materials for use in electrolysis for various differential pressures and flow field widths.

Differentiation of human foreskin fibroblast-derived induced pluripotent stem cells into hepatocyte-like cells.

PubMed

Wang, Jianjun; Zhao, Ping; Wan, Zhihong; Jin, Xueyuan; Cheng, Yongqian; Yan, Tao; Qing, Song; Ding, Ning; Xin, Shaojie

2016-10-01

The aim of this study was to investigate the differentiation potential of induced pluripotent stem cells (iPSCs) derived from human foreskin fibroblasts (HFFs) into hepatocyte-like cells (HLCs). The iPSCs were firstly induced by transduction of OCT4, SOX2, KLF4, and c-MYC into HFFs using retrovirus. Afterwards, expressions of pluripotency factors were identified by semiquantitative reverse transcription-polymerase chain reaction and immunofluorescence staining, and karyotype, embryoid, and teratoma were observed by microscope. Then, iPSCs were gradually differentiated into endoderm cells, hepatic progenitor cells, and mature HLCs by special culture medium. During this process, differentiation efficiency into each kind of cells was evaluated by detecting SOX17, HNF4a, and ALB using flow cytometry, respectively. Besides, enzyme-linked immunosorbent assay was conducted to detect the secretion of ALB in iPSC-induced HLCs and quantitative reverse transcription-polymerase chain reaction was performed to detect the expression levels of hepatocyte-specific genes. The iPSCs were successfully induced by HFFs, which exhibited typical embryonic stem cells morphology, positive alkaline phosphatase staining, normal diploid karyotype, and positive expression of various pluripotency factors. Meanwhile, spherical embryoid and teratoma with 3 germ layers were formed by iPSCs. The iPSCs were consecutively induced into endoderm cells, hepatic progenitor cells and mature HLCs, and the differentiation efficiency was 55.7 ± 2.9%, 45.7 ± 4.8%, and 35.0 ± 3.9%, respectively. Besides, the secretion of ALB and expression of various hepatocyte-specific genes was highly detected in iPSC-induced HLCs. The iPSCs were successfully derived from HFFs and then differentiated into HLCs, which proved a new source for hepatocyte transplantation. HFFs were successfully induced into iPSCs by transduction of OCT4, SOX2, KLF4, and c-MYC. Positive expressions of various pluripotency factors were exhibited in HFFs-induced iPSCs. The iPSCs were consecutively induced into endoderm cells, hepatic progenitor cells, and mature HLCs. Various hepatocyte-specific genes were highly expressed in iPSC-induced HLCs. Copyright © 2016 John Wiley & Sons, Ltd.

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

PubMed Central

Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; Pai, E. F.; Pearson, A. R.; Olson, J. S.; Anfinrud, P. A.; Ernst, O. P.; Dwayne Miller, R. J.

2015-01-01

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs. PMID:26798825

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography.

PubMed

Mueller, C; Marx, A; Epp, S W; Zhong, Y; Kuo, A; Balo, A R; Soman, J; Schotte, F; Lemke, H T; Owen, R L; Pai, E F; Pearson, A R; Olson, J S; Anfinrud, P A; Ernst, O P; Dwayne Miller, R J

2015-09-01

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.

Induced Pluripotent Stem Cells: Generation, Characterization, and Differentiation--Methods and Protocols.

PubMed

Graversen, Veronica Kon; Chavala, Sai H

2016-01-01

Reprogramming fibroblasts into induced pluripotent stem cells (iPSC) remains a promising technique for cell replacement therapy. Diverse populations of somatic cells have been examined for their reprogramming potential. Recently, ocular ciliary body epithelial cells (CECs) have been reprogrammed with high reprogramming efficiency and single transcription factor reprogramming, making them an exciting candidate for cellular reprogramming strategies.

Meta-analysis of RNA-Seq data across cohorts in a multi-season feed efficiency study of crossbred beef steers accounts for biological and technical variability within season

USDA-ARS?s Scientific Manuscript database

High-throughput sequencing is often used for studies of the transcriptome, particularly for comparisons between experimental conditions. Due to sequencing costs, a limited number of biological replicates are typically considered in such experiments, leading to low detection power for differential ex...

Activin A Modulates CRIPTO-1/HNF4α+ Cells to Guide Cardiac Differentiation from Human Embryonic Stem Cells

PubMed Central

Duelen, Robin; Gilbert, Guillaume; Patel, Abdulsamie; de Schaetzen, Nathalie; De Waele, Liesbeth; Roderick, Llewelyn; Sipido, Karin R.; Verfaillie, Catherine M.; Buyse, Gunnar M.

2017-01-01

The use of human pluripotent stem cells in basic and translational cardiac research requires efficient differentiation protocols towards cardiomyocytes. In vitro differentiation yields heterogeneous populations of ventricular-, atrial-, and nodal-like cells hindering their potential applications in regenerative therapies. We described the effect of the growth factor Activin A during early human embryonic stem cell fate determination in cardiac differentiation. Addition of high levels of Activin A during embryoid body cardiac differentiation augmented the generation of endoderm derivatives, which in turn promoted cardiomyocyte differentiation. Moreover, a dose-dependent increase in the coreceptor expression of the TGF-β superfamily member CRIPTO-1 was observed in response to Activin A. We hypothesized that interactions between cells derived from meso- and endodermal lineages in embryoid bodies contributed to improved cell maturation in early stages of cardiac differentiation, improving the beating frequency and the percentage of contracting embryoid bodies. Activin A did not seem to affect the properties of cardiomyocytes at later stages of differentiation, measuring action potentials, and intracellular Ca2+ dynamics. These findings are relevant for improving our understanding on human heart development, and the proposed protocol could be further explored to obtain cardiomyocytes with functional phenotypes, similar to those observed in adult cardiac myocytes. PMID:28163723

A semi-direct procedure using a local relaxation factor and its application to an internal flow problem

NASA Technical Reports Server (NTRS)

Chang, S. C.

1984-01-01

Generally, fast direct solvers are not directly applicable to a nonseparable elliptic partial differential equation. This limitation, however, is circumvented by a semi-direct procedure, i.e., an iterative procedure using fast direct solvers. An efficient semi-direct procedure which is easy to implement and applicable to a variety of boundary conditions is presented. The current procedure also possesses other highly desirable properties, i.e.: (1) the convergence rate does not decrease with an increase of grid cell aspect ratio, and (2) the convergence rate is estimated using the coefficients of the partial differential equation being solved.

Efficient spin-filter and negative differential resistance behaviors in FeN4 embedded graphene nanoribbon device

NASA Astrophysics Data System (ADS)

Liu, N.; Liu, J. B.; Yao, K. L.; Ni, Y.; Wang, S. L.

2016-03-01

In this paper, we propose a new device of spintronics by embedding two FeN4 molecules into armchair graphene nanoribbon and sandwiching them between N-doped graphene nanoribbon electrodes. Our first-principle quantum transport calculations show that the device is a perfect spin filter with high spin-polarizations both in parallel configuration (PC) and antiparallel configuration (APC). Moreover, negative differential resistance phenomena are obtained for the spin-down current in PC, and the spin-up and spin-down currents in APC. These transport properties are explained by the bias-dependent evolution of molecular orbitals and the transmission spectra.

Adaptive mesh strategies for the spectral element method

NASA Technical Reports Server (NTRS)

Mavriplis, Catherine

1992-01-01

An adaptive spectral method was developed for the efficient solution of time dependent partial differential equations. Adaptive mesh strategies that include resolution refinement and coarsening by three different methods are illustrated on solutions to the 1-D viscous Burger equation and the 2-D Navier-Stokes equations for driven flow in a cavity. Sharp gradients, singularities, and regions of poor resolution are resolved optimally as they develop in time using error estimators which indicate the choice of refinement to be used. The adaptive formulation presents significant increases in efficiency, flexibility, and general capabilities for high order spectral methods.

High-order fractional partial differential equation transform for molecular surface construction.

PubMed

Hu, Langhua; Chen, Duan; Wei, Guo-Wei

2013-01-01

Fractional derivative or fractional calculus plays a significant role in theoretical modeling of scientific and engineering problems. However, only relatively low order fractional derivatives are used at present. In general, it is not obvious what role a high fractional derivative can play and how to make use of arbitrarily high-order fractional derivatives. This work introduces arbitrarily high-order fractional partial differential equations (PDEs) to describe fractional hyperdiffusions. The fractional PDEs are constructed via fractional variational principle. A fast fractional Fourier transform (FFFT) is proposed to numerically integrate the high-order fractional PDEs so as to avoid stringent stability constraints in solving high-order evolution PDEs. The proposed high-order fractional PDEs are applied to the surface generation of proteins. We first validate the proposed method with a variety of test examples in two and three-dimensional settings. The impact of high-order fractional derivatives to surface analysis is examined. We also construct fractional PDE transform based on arbitrarily high-order fractional PDEs. We demonstrate that the use of arbitrarily high-order derivatives gives rise to time-frequency localization, the control of the spectral distribution, and the regulation of the spatial resolution in the fractional PDE transform. Consequently, the fractional PDE transform enables the mode decomposition of images, signals, and surfaces. The effect of the propagation time on the quality of resulting molecular surfaces is also studied. Computational efficiency of the present surface generation method is compared with the MSMS approach in Cartesian representation. We further validate the present method by examining some benchmark indicators of macromolecular surfaces, i.e., surface area, surface enclosed volume, surface electrostatic potential and solvation free energy. Extensive numerical experiments and comparison with an established surface model indicate that the proposed high-order fractional PDEs are robust, stable and efficient for biomolecular surface generation.

Traction Drives for Zero Stick-Slip Robots, and Reaction Free, Momentum Balanced Systems

NASA Technical Reports Server (NTRS)

Anderson, William J.; Shipitalo, William; Newman, Wyatt

1995-01-01

Two differential (dual input, single output) drives (a roller-gear and a pure roller), and a momentum balanced (single input, dual output) drive (pure roller ) were designed, fabricated, and tested. The differential drives are each rated at 295 rad/sec (2800 rpm) input speed, 450 N-m (4,000 in-lbf) output torque. The momentum balanced drive is rated at 302 rad/sec (2880 rpm) input speed, and dual output torques of 434N-m (3840 in-lbf). The Dual Input Differential Roller-Gear Drive (DC-700) has a planetary roller-gear system with a reduction ratio (one input driving the output with the second input fixed) of 29.23: 1. The Dual Input Differential Roller Drive (DC-500) has a planetary roller system with a reduction ratio of approximately 24:1. Each of the differential drives features dual roller-gear or roller arrangements consisting of a sun, four first row planets, four second row planets, and a ring. The Momentum Balanced (Grounded Ring) Drive (DC-400) has a planetary roller system with a reduction ratio of 24:1 with both outputs counterrotating at equal speed. Its single roller cluster consists of a sun, five first and five second row planets, a roller cage or spider and a ring. Outputs are taken from both the roller cage and the ring which counterrotate. Test results reported for all three drives include angular and torque ripple (linearity and cogging), viscous and Coulomb friction, and forward and reverse power efficiency. Of the two differential drives, the Differential Roller Drive had better linearity and less cogging than did the Differential Roller-Gear Drive, but it had higher friction and lower efficiency (particularly at low power throughput levels). Use of full preloading rather than a variable preload system in the Differential Roller Drive assessed a heavy penalty in part load efficiency. Maximum measured efficiency (ratio of power out to power in) was 95% for the Differential Roller-Gear Drive and 86% for the Differential Roller Drive. The Momentum Balanced (Grounded Ring) Drive performed as expected kinematically. Reduction r-atios to the two counterrotating outputs (design nominal=24:1) were measured to be 23.98:1 and 24.12:1 at zero load.. At 25ONm (2200 in-lbf) output torque the ratio changed 2% due to roller creep. This drive was the smoothest of all three as determined from linearity and cogging tests, and maximum measured efficiency (ratio of power out to power in) was 95%. The disadvantages of full preloading as comvared to variable preload were apparent in this drive as in the Differential Roller Drive. Efficiencies at part load were low, but improved dramatically with increases in torque. These were consistent with friction measurements which indicated losses primarily from Coulomb friction. The initial preload level setting was low so roller slip was encountered at higher torques during testing.

Simultaneous suppression of TGF-β and ERK signaling contributes to the highly efficient and reproducible generation of mouse embryonic stem cells from previously considered refractory and non-permissive strains.

PubMed

Hassani, Seyedeh-Nafiseh; Totonchi, Mehdi; Farrokhi, Ali; Taei, Adeleh; Larijani, Mehran Rezaei; Gourabi, Hamid; Baharvand, Hossein

2012-06-01

Mouse embryonic stem cells (ESCs) are pluripotent stem cell lines derived from pre-implantation embryos. The efficiency of mESC generation is affected by genetic variation in mice; that is, some mouse strains are refractory or non-permissive to ESC establishment. Developing an efficient method to derive mESCs from strains of various genetic backgrounds should be valuable for establishment of ESCs in various mammalian species. In the present study, we identified dual inhibition of TGF-β and ERK1/2, by SB431542 and PD0325901, respectively led to the highly efficient and reproducible generation of mESC lines from NMRI, C57BL/6, BALB/c, DBA/2, and FVB/N strains, which previously considered refractory or non-permissive for ESC establishment. These mESCs expressed pluripotency markers and retained the capacity to differentiate into derivatives of all three germ layers. The evaluated lines exhibited high rates of chimerism when reintroduced into blastocysts. To our knowledge, this is the first report of efficient (100%) mESC lines generation from different genetic backgrounds. The application of these two inhibitors will not only solve the problems of mESC derivation but also clarifies new signaling pathways in pluripotent mESCs.

Enhancement of the performance of GaN IMPATT diodes by negative differential mobility

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

Dai, Yang; Yang, Lin’an, E-mail: layang@xidian.edu.cn; Chen, Qing

2016-05-15

A theoretical analysis of high-efficiency punch-through operation GaN-based terahertz IMPATT diodes has been carried out in this paper. It is shown that the negative differential mobility (NDM) characteristics of GaN coupled with the space charge effect acting as a self-feedback system can markedly increase the drift velocity of injection carriers, and thereby enhance diode performance under appropriate external RF voltage. The behavior of traveling electrons in the transit zone is investigated in detail. It is found that the IMPATT diode with a punch-through structure operating in the NDM mode exhibits superior characteristics compared with the equivalent diode operating in themore » Si-like constant mobility mode. In particular, the NDM-mode diode can tolerate a larger RF voltage swing than that operating in constant mobility mode. Numerical simulation results reveal that the highest efficiency of 26.6% and maximum RF power of 2.29 W can be achieved for the NDM-mode diode at a frequency of 225 GHz. A highest efficiency of 19.0% and maximum RF power of 1.58 W are obtained for the diode with constant mobility.« less

Optimal layout design of obstacles for panic evacuation using differential evolution

NASA Astrophysics Data System (ADS)

Zhao, Yongxiang; Li, Meifang; Lu, Xin; Tian, Lijun; Yu, Zhiyong; Huang, Kai; Wang, Yana; Li, Ting

2017-01-01

To improve the pedestrian outflow in panic situations by suitably placing an obstacle in front of the exit, it is vital to understand the physical mechanism behind the evacuation efficiency enhancement. In this paper, a robust differential evolution is firstly employed to optimize the geometrical parameters of different shaped obstacles in order to achieve an optimal evacuation efficiency. Moreover, it is found that all the geometrical parameters of obstacles could markedly influence the evacuation efficiency of pedestrians, and the best way for achieving an optimal pedestrian outflow is to slightly shift the obstacle from the center of the exit which is consistent with findings of extant literature. Most importantly, by analyzing the profiles of density, velocity and specific flow, as well as the spatial distribution of crowd pressure, we have proven that placing an obstacle in panic situations does not reduce or absorb the pressure in the region of exit, on the contrary, promotes the pressure to a much higher level, hence the physical mechanism behind the evacuation efficiency enhancement is not a pressure decrease in the region of exit, but a significant reduction of high density region by effective separation in space which finally causes the increasing of escape speed and evacuation outflow. Finally, it is clearly demonstrated that the panel-like obstacle is considerably more robust and stable than the pillar-like obstacle to guarantee the enhancement of evacuation efficiency under different initial pedestrian distributions, different initial crowd densities as well as different desired velocities.

Computational simulation and aerodynamic sensitivity analysis of film-cooled turbines

NASA Astrophysics Data System (ADS)

Massa, Luca

A computational tool is developed for the time accurate sensitivity analysis of the stage performance of hot gas, unsteady turbine components. An existing turbomachinery internal flow solver is adapted to the high temperature environment typical of the hot section of jet engines. A real gas model and film cooling capabilities are successfully incorporated in the software. The modifications to the existing algorithm are described; both the theoretical model and the numerical implementation are validated. The accuracy of the code in evaluating turbine stage performance is tested using a turbine geometry typical of the last stage of aeronautical jet engines. The results of the performance analysis show that the predictions differ from the experimental data by less than 3%. A reliable grid generator, applicable to the domain discretization of the internal flow field of axial flow turbine is developed. A sensitivity analysis capability is added to the flow solver, by rendering it able to accurately evaluate the derivatives of the time varying output functions. The complex Taylor's series expansion (CTSE) technique is reviewed. Two of them are used to demonstrate the accuracy and time dependency of the differentiation process. The results are compared with finite differences (FD) approximations. The CTSE is more accurate than the FD, but less efficient. A "black box" differentiation of the source code, resulting from the automated application of the CTSE, generates high fidelity sensitivity algorithms, but with low computational efficiency and high memory requirements. New formulations of the CTSE are proposed and applied. Selective differentiation of the method for solving the non-linear implicit residual equation leads to sensitivity algorithms with the same accuracy but improved run time. The time dependent sensitivity derivatives are computed in run times comparable to the ones required by the FD approach.

Efficiently and easily integrating differential equations with JiTCODE, JiTCDDE, and JiTCSDE

NASA Astrophysics Data System (ADS)

Ansmann, Gerrit

2018-04-01

We present a family of Python modules for the numerical integration of ordinary, delay, or stochastic differential equations. The key features are that the user enters the derivative symbolically and it is just-in-time-compiled, allowing the user to efficiently integrate differential equations from a higher-level interpreted language. The presented modules are particularly suited for large systems of differential equations such as those used to describe dynamics on complex networks. Through the selected method of input, the presented modules also allow almost complete automatization of the process of estimating regular as well as transversal Lyapunov exponents for ordinary and delay differential equations. We conceptually discuss the modules' design, analyze their performance, and demonstrate their capabilities by application to timely problems.

DEVELOPMENT OF AG-1 SECTION FI ON METAL MEDIA FILTERS - 9061

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

Adamson, D; Charles A. Waggoner, C

Development of a metal media standard (FI) for ASME AG-1 (Code on Nuclear Air and Gas Treatment) has been under way for almost ten years. This paper will provide a brief history of the development process of this section and a detailed overview of its current content/status. There have been at least two points when dramatic changes have been made in the scope of the document due to feedback from the full Committee on Nuclear Air and Gas Treatment (CONAGT). Development of the proposed section has required resolving several difficult issues associated with scope; namely, filtering efficiency, operating conditions (mediamore » velocity, pressure drop, etc.), qualification testing, and quality control/acceptance testing. A proposed version of Section FI is currently undergoing final revisions prior to being submitted for balloting. The section covers metal media filters of filtering efficiencies ranging from medium (less than 99.97%) to high (99.97% and greater). Two different types of high efficiency filters are addressed; those units intended to be a direct replacement of Section FC fibrous glass HEPA filters and those that will be placed into newly designed systems capable of supporting greater static pressures and differential pressures across the filter elements. Direct replacements of FC HEPA filters in existing systems will be required to meet equivalent qualification and testing requirements to those contained in Section FC. A series of qualification and quality assurance test methods have been identified for the range of filtering efficiencies covered by this proposed standard. Performance characteristics of sintered metal powder vs. sintered metal fiber media are dramatically different with respect to parameters like differential pressures and rigidity of the media. Wide latitude will be allowed for owner specification of performance criteria for filtration units that will be placed into newly designed systems. Such allowances will permit use of the most appropriate metal media for a system as specified by the owner with respect to material of manufacture, media velocity, system maximum static pressure, maximum differential pressure across the filter, and similar parameters.« less

Explanation of low efficiency droop in semipolar (202¯1¯) InGaN/GaN LEDs through evaluation of carrier recombination coefficients.

PubMed

Monavarian, Morteza; Rashidi, Arman; Aragon, Andrew; Oh, Sang H; Nami, Mohsen; DenBaars, Steve P; Feezell, Daniel

2017-08-07

We report the carrier dynamics and recombination coefficients in single-quantum-well semipolar (202¯1¯) InGaN/GaN light-emitting diodes emitting at 440 nm with 93% peak internal quantum efficiency. The differential carrier lifetime is analyzed for various injection current densities from 5 A/cm 2 to 10 kA/cm 2 , and the corresponding carrier densities are obtained. The coupling of internal quantum efficiency and differential carrier lifetime vs injected carrier density (n) enables the separation of the radiative and nonradiative recombination lifetimes and the extraction of the Shockley-Read-Hall (SRH) nonradiative (A), radiative (B), and Auger (C) recombination coefficients and their n-dependency considering the saturation of the SRH recombination rate and phase-space filling. The results indicate a three to four-fold higher A and a nearly two-fold higher B0 for this semipolar orientation compared to that of c-plane reported using a similar approach [A. David and M. J. Grundmann, Appl. Phys. Lett. 96, 103504 (2010)]. In addition, the carrier density in semipolar (202¯1¯) is found to be lower than the carrier density in c-plane for a given current density, which is important for suppressing efficiency droop. The semipolar LED also shows a two-fold lower C0 compared to c-plane, which is consistent with the lower relative efficiency droop for the semipolar LED (57% vs. 69%). The lower carrier density, higher B 0 coefficient, and lower C 0 (Auger) coefficient are directly responsible for the high efficiency and low efficiency droop reported in semipolar (202¯1¯) LEDs.

Explanation of low efficiency droop in semipolar (202¯1¯) InGaN/GaN LEDs through evaluation of carrier recombination coefficients

NASA Astrophysics Data System (ADS)

Monavarian, Morteza; Rashidi, Arman; Aragon, Andrew; Oh, Sang H.; Nami, Mohsen; DenBaars, Steve P.; Feezell, Daniel

2017-08-01

We report the carrier dynamics and recombination coefficients in single-quantum-well semipolar $(20\\bar 2\\bar 1)$ InGaN/GaN light-emitting diodes emitting at 440 nm with 93% peak internal quantum efficiency. The differential carrier lifetime is analyzed for various injection current densities from 5 $A/cm^2$ to 10 $kA/cm^2$, and the corresponding carrier densities are obtained. The coupling of internal quantum efficiency and differential carrier lifetime vs injected carrier density ($n$) enables the separation of the radiative and nonradiative recombination lifetimes and the extraction of the Shockley-Read-Hall (SRH) nonradiative ($A$), radiative ($B$), and Auger ($C$) recombination coefficients and their $n$-dependency considering the saturation of the SRH recombination rate and phase-space filling. The results indicate a three to four-fold higher $A$ and a nearly two-fold higher $B_0$ for this semipolar orientation compared to that of $c$-plane reported using a similar approach [A. David and M. J. Grundmann, Appl. Phys. Lett. 96, 103504 (2010)]. In addition, the carrier density in semipolar $(20\\bar 2\\bar 1)$ is found to be lower than the carrier density in $c$-plane for a given current density, which is important for suppressing efficiency droop. The semipolar LED also shows a two-fold lower $C_0$ compared to $c$-plane, which is consistent with the lower relative efficiency droop for the semipolar LED (57% vs. 69%). The lower carrier density, higher $B_0$ coefficient, and lower $C_0$ (Auger) coefficient are directly responsible for the high efficiency and low efficiency droop reported in semipolar $(20\\bar 2\\bar 1)$ LEDs.

Differential changes in photosynthetic capacity, 77 K chlorophyll fluorescence and chloroplast ultrastructure between Zn-efficient and Zn-inefficient rice genotypes (Oryza sativa) under low zinc stress.

PubMed

Chen, Wenrong; Yang, Xiaoe; He, Zhenli; Feng, Ying; Hu, Fenghong

2008-01-01

The relationship of zinc (Zn) efficiency in rice to differential tolerance of photosynthetic capacity and chloroplast function to low Zn stress was studied using Zn-efficient (IR8192) and Zn-inefficient (Erjiufeng) rice genotypes (Oryza sativa L.). Zinc deficiency caused extensive declines in leaf chlorophyll (Chl) content, ratios of chl a:b, Pn, Fv/Fm and Fv/Fo, indicating that the intrinsic quantum efficiency of the photosystem II (PSII) units was damaged. A greater decline was observed in the inefficient genotype (Erjiufeng) than the efficient genotype (IR8192). The 77 K chl fluorescence emission spectrum revealed that Zn deficiency blocked energy spillover from PSII to PSI and more excitation energy was distributed to PSII in IR8192 than Erjiufeng. The spectrum of Zn-deficient Erjiufeng was completely disordered, implying that the photosynthetic centers were seriously damaged. Electron microscopy showed that Zn deficiency caused a severe damage to the fine structure of chloroplasts, but IR8192 had a better preserved chloroplast ultrastructure as compared with Erjiufeng. These differences may result from the higher levels of the antioxidant enzyme activities and lower oxidant stress level in IR8192. These results indicate that Zn deficiency decreases leaf photosynthetic capacity primarily by reducing the number of PSII units per unit leaf area, and also reducing the photochemical capacity of the remaining PSII units. Therefore, the maintenance of more efficient photochemical capacity under low Zn stress is a key factor for the high Zn efficiency in rice, which may result from less antioxidant damage caused by low Zn to the chloroplast ultrastructure.

Turbomachinery Airfoil Design Optimization Using Differential Evolution

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.; Biegel, Bryan A. (Technical Monitor)

2002-01-01

An aerodynamic design optimization procedure that is based on a evolutionary algorithm known at Differential Evolution is described. Differential Evolution is a simple, fast, and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems, including highly nonlinear systems with discontinuities and multiple local optima. The method is combined with a Navier-Stokes solver that evaluates the various intermediate designs and provides inputs to the optimization procedure. An efficient constraint handling mechanism is also incorporated. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated. Substantial reductions in the overall computing time requirements are achieved by using the algorithm in conjunction with neural networks.

Differential tracking data types for accurate and efficient Mars planetary navigation

NASA Technical Reports Server (NTRS)

Edwards, C. D., Jr.; Kahn, R. D.; Folkner, W. M.; Border, J. S.

1991-01-01

Ways in which high-accuracy differential observations of two or more deep space vehicles can dramatically extend the power of earth-based tracking over conventional range and Doppler tracking are discussed. Two techniques - spacecraft-spacecraft differential very long baseline interferometry (S/C-S/C Delta(VLBI)) and same-beam interferometry (SBI) - are discussed. The tracking and navigation capabilities of conventional range, Doppler, and quasar-relative Delta(VLBI) are reviewed, and the S/C-S/C Delta (VLBI) and SBI types are introduced. For each data type, the formation of the observable is discussed, an error budget describing how physical error sources manifest themselves in the observable is presented, and potential applications of the technique for Space Exploration Initiative scenarios are examined. Requirements for spacecraft and ground systems needed to enable and optimize these types of observations are discussed.

Investigation on the energy absorption performance of a fixed-bottom pressure-differential wave energy converter

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

Babarit, A.; Wendt, F.; Yu, Y. -H.

2017-04-01

In this article, we investigate the energy absorption performance of a fixed-bottom pressure-differential wave energy converter. Two versions of the technology are considered: one has the moving surfaces on the bottom of the air chambers whereas the other has the moving surfaces on the top. We developed numerical models in the frequency domain, thereby enabling the power absorption of the two versions of the device to be assessed. It is observed that the moving surfaces on the top allow for easier tuning of the natural period of the system. Taking into account stroke limitations, the design is optimized. Results indicatemore » that the pressure-differential wave energy converter is a highly efficient technology both with respect to energy absorption and selected economic performance indicators.« less

Speedup for quantum optimal control from automatic differentiation based on graphics processing units

NASA Astrophysics Data System (ADS)

Leung, Nelson; Abdelhafez, Mohamed; Koch, Jens; Schuster, David

2017-04-01

We implement a quantum optimal control algorithm based on automatic differentiation and harness the acceleration afforded by graphics processing units (GPUs). Automatic differentiation allows us to specify advanced optimization criteria and incorporate them in the optimization process with ease. We show that the use of GPUs can speedup calculations by more than an order of magnitude. Our strategy facilitates efficient numerical simulations on affordable desktop computers and exploration of a host of optimization constraints and system parameters relevant to real-life experiments. We demonstrate optimization of quantum evolution based on fine-grained evaluation of performance at each intermediate time step, thus enabling more intricate control on the evolution path, suppression of departures from the truncated model subspace, as well as minimization of the physical time needed to perform high-fidelity state preparation and unitary gates.

A Two-Stage Estimation Method for Random Coefficient Differential Equation Models with Application to Longitudinal HIV Dynamic Data.

PubMed

Fang, Yun; Wu, Hulin; Zhu, Li-Xing

2011-07-01

We propose a two-stage estimation method for random coefficient ordinary differential equation (ODE) models. A maximum pseudo-likelihood estimator (MPLE) is derived based on a mixed-effects modeling approach and its asymptotic properties for population parameters are established. The proposed method does not require repeatedly solving ODEs, and is computationally efficient although it does pay a price with the loss of some estimation efficiency. However, the method does offer an alternative approach when the exact likelihood approach fails due to model complexity and high-dimensional parameter space, and it can also serve as a method to obtain the starting estimates for more accurate estimation methods. In addition, the proposed method does not need to specify the initial values of state variables and preserves all the advantages of the mixed-effects modeling approach. The finite sample properties of the proposed estimator are studied via Monte Carlo simulations and the methodology is also illustrated with application to an AIDS clinical data set.

Heme oxygenase-1 affects generation and spontaneous cardiac differentiation of induced pluripotent stem cells.

PubMed

Stepniewski, Jacek; Pacholczak, Tomasz; Skrzypczyk, Aniela; Ciesla, Maciej; Szade, Agata; Szade, Krzysztof; Bidanel, Romain; Langrzyk, Agnieszka; Grochowski, Radoslaw; Vandermeeren, Felix; Kachamakova-Trojanowska, Neli; Jez, Mateusz; Drabik, Grazyna; Nakanishi, Mahito; Jozkowicz, Alicja; Dulak, Jozef

2018-02-01

Cellular stress can influence efficiency of iPSCs generation and their differentiation. However, the role of intracellular cytoprotective factors in these processes is still not well known. Therefore, we investigated the effect of HO-1 (Hmox1) or Nrf2 (Nfe2l2), two major cytoprotective genes. Hmox1 -/- fibroblasts demonstrated decreased reprogramming efficiency in comparison to Hmox1 +/+ cells. Reversely, pharmacological enhancement of HO-1 resulted in higher number of iPSCs colonies. Importantly, elevated level of both p53 and p53-regulated miR-34a and 14-3-3σ was observed in HO-1-deficient fibroblasts whereas downregulation of p53 in these cells markedly increased their reprogramming efficiency. In human fibroblasts HO-1 silencing also induced p53 expression and affected reprogramming outcome. Hmox1 +/+ and Hmox1 -/- iPSCs similarly differentiated in vitro to cells originating from three germ layers, however, lower number of contracting cells was observed during this process in HO-1-deficient cells indicating attenuated cardiac differentiation. Importantly, silencing of Hmox1 in murine ESC using CRISPR/Cas-9 editing also impaired their spontaneous cardiac differentiation. Decreased reprogramming efficiency was also observed in Nrf2-lacking fibroblasts. Reversely, sulforaphane, a Nrf2 activator, increased the number of iPSCs colonies. However, both Nfe2l2 +/+ and Nfe2l2 -/- iPSCs showed similar pluripotency and differentiation capacity. These results indicate that regulation of HO-1 expression can further optimize generation and cardiac differentiation of iPSCs. © 2018 IUBMB Life, 70(2):129-142, 2018. © 2018 International Union of Biochemistry and Molecular Biology.

Solving SAT Problem Based on Hybrid Differential Evolution Algorithm

NASA Astrophysics Data System (ADS)

Liu, Kunqi; Zhang, Jingmin; Liu, Gang; Kang, Lishan

Satisfiability (SAT) problem is an NP-complete problem. Based on the analysis about it, SAT problem is translated equally into an optimization problem on the minimum of objective function. A hybrid differential evolution algorithm is proposed to solve the Satisfiability problem. It makes full use of strong local search capacity of hill-climbing algorithm and strong global search capability of differential evolution algorithm, which makes up their disadvantages, improves the efficiency of algorithm and avoids the stagnation phenomenon. The experiment results show that the hybrid algorithm is efficient in solving SAT problem.

Pancreatic differentiation of Pdx1-GFP reporter mouse induced pluripotent stem cells.

PubMed

Porciuncula, Angelo; Kumar, Anujith; Rodriguez, Saray; Atari, Maher; Araña, Miriam; Martin, Franz; Soria, Bernat; Prosper, Felipe; Verfaillie, Catherine; Barajas, Miguel

2016-12-01

Efficient induction of defined lineages in pluripotent stem cells constitutes the determinant step for the generation of therapeutically relevant replacement cells to potentially treat a wide range of diseases, including diabetes. Pancreatic differentiation has remained an important challenge in large part because of the need to differentiate uncommitted pluripotent stem cells into highly specialized hormone-secreting cells, which has been shown to require a developmentally informed step-by-step induction procedure. Here, in the framework of using induced pluripotent stem cells (iPSCs) to generate pancreatic cells for pancreatic diseases, we have generated and characterized iPSCs from Pdx1-GFP transgenic mice. The use of a GFP reporter knocked into the endogenous Pdx1 promoter allowed us to monitor pancreatic induction based on the expression of Pdx1, a pancreatic master transcription factor, and to isolate a pure Pdx1-GFP + population for downstream applications. Differentiated cultures timely expressed markers specific to each stage and end-stage progenies acquired a rather immature beta-cell phenotype, characterized by polyhormonal expression even among cells highly expressing the Pdx1-GFP reporter. Our findings highlight the utility of employing a fluorescent protein reporter under the control of a master developmental gene in order to devise novel differentiation protocols for relevant cell types for degenerative diseases such as pancreatic beta cells for diabetes. Copyright © 2016 International Society of Differentiation. Published by Elsevier B.V. All rights reserved.

Substantial Differentiation of Human Neural Stem Cells Into Motor Neurons on a Biomimetic Polyureaa

PubMed Central

Yun, Donghwa; Lee, Young M.; Laughter, Melissa R.; Freed, Curt R.

2015-01-01

To find the first restorative treatment for spinal cord injury (SCI), researchers have focused on stem cell therapies. However, one obstacle is the lack of an implantable cell scaffold that can support efficient motor neuron (MN) differentiation and proliferation. We aimed to overcome this through the use of an RGD functionalized novel biomimetic polyurea, optimized to encourage efficient differentiation of MNs. Images taken after 14-days showed increased differentiation (~40%) of hNSCs into MNs as well as increased cell count on the biomimetic polymer compared to PDL-Laminin coating, indicating that the RGD-polyurea provides a favorable microenvironment for hNSC survival, having promising implications for future SCI therapies. PMID:26033933

Enhancement of caffeic acid phenethyl ester on all-trans retinoic acid-induced differentiation in human leukemia HL-60 cells

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

Kuo, H.-C.; Kuo, W.-H.; Lee, Y.-J.

2006-10-01

All-trans retinoic acid (ATRA) induces complete remission in a high proportion of patients with acute promyelocytic leukemia (APL); however, the response is sometimes very slow. Furthermore, relapse and resistance to treatment often occur despite continued treatment with ATRA. Thereafter, combination treatment strategies have been suggested to circumvent these problems. The present study demonstrates that caffeic acid phenethyl ester (CAPE), a major component of honeybee propolis, enhanced ATRA-induced granulocytic differentiation in HL-60, a human promyelocytic cell line. The differentiation was assessed by Wright-Giemsa stain, nitroblue tetrazolium reduction, and membrane differentiation marker CD11b. In addition, CAPE enhanced ATRA-induced cell cycle arrest atmore » the G1 phase by decreasing the association of cdk2-cyclin E complex. Finally, it was demonstrated that CAPE promoted the ATRA-mediated nuclear transcription activation of RAR{alpha} assessed by EMSA assay and enhanced the expression of target genes including RAR{alpha}, C/EBP{epsilon}, and p21 protein resulting in the differentiation development of leukemia. It is suggested that CAPE possesses the potential to enhance the efficiency of ATRA in the differentiation therapy of APL.« less

Porous graphene-based membranes for water purification from metal ions at low differential pressures.

PubMed

Park, Jaewoo; Bazylewski, Paul; Fanchini, Giovanni

2016-05-14

A new generation of membranes for water purification based on weakly oxidized and nanoporous few-layer graphene is here introduced. These membranes dramatically decrease the high energy requirements of water purification by reverse osmosis. They combine the advantages of porous and non-oxidized single-layer graphene, offering energy-efficient water filtration at relatively low differential pressures, and highly oxidized graphene oxide, exhibiting high performance in terms of impurity adsorption. In the reported fabrication process, leaks between juxtaposed few-layer graphene flakes are sealed by thermally annealed colloidal silica, in a treatment that precedes the opening of (sub)nanometre-size pores in graphene. This process, explored for the first time in this work, results in nanoporous graphene flakes that are water-tight at the edges without occluding the (sub)nanopores. With this method, removal of impurities from water occurs through a combination of size-based pore rejection and pore-edge adsorption. Thinness of graphene flakes allows these membranes to achieve water purification from metal ions in concentrations of few parts-per-million at differential pressures as low as 30 kPa, outperforming existing graphene or graphene oxide purification systems with comparable flow rates.

Porous graphene-based membranes for water purification from metal ions at low differential pressures

NASA Astrophysics Data System (ADS)

Park, Jaewoo; Bazylewski, Paul; Fanchini, Giovanni

2016-05-01

A new generation of membranes for water purification based on weakly oxidized and nanoporous few-layer graphene is here introduced. These membranes dramatically decrease the high energy requirements of water purification by reverse osmosis. They combine the advantages of porous and non-oxidized single-layer graphene, offering energy-efficient water filtration at relatively low differential pressures, and highly oxidized graphene oxide, exhibiting high performance in terms of impurity adsorption. In the reported fabrication process, leaks between juxtaposed few-layer graphene flakes are sealed by thermally annealed colloidal silica, in a treatment that precedes the opening of (sub)nanometre-size pores in graphene. This process, explored for the first time in this work, results in nanoporous graphene flakes that are water-tight at the edges without occluding the (sub)nanopores. With this method, removal of impurities from water occurs through a combination of size-based pore rejection and pore-edge adsorption. Thinness of graphene flakes allows these membranes to achieve water purification from metal ions in concentrations of few parts-per-million at differential pressures as low as 30 kPa, outperforming existing graphene or graphene oxide purification systems with comparable flow rates.

P-channel differential multiple-time programmable memory cells by laterally coupled floating metal gate fin field-effect transistors

NASA Astrophysics Data System (ADS)

Wang, Tai-Min; Chien, Wei-Yu; Hsu, Chia-Ling; Lin, Chrong Jung; King, Ya-Chin

2018-04-01

In this paper, we present a new differential p-channel multiple-time programmable (MTP) memory cell that is fully compatible with advanced 16 nm CMOS fin field-effect transistors (FinFET) logic processes. This differential MTP cell stores complementary data in floating gates coupled by a slot contact structure, which make different read currents possible on a single cell. In nanoscale CMOS FinFET logic processes, the gate dielectric layer becomes too thin to retain charges inside floating gates for nonvolatile data storage. By using a differential architecture, the sensing window of the cell can be extended and maintained by an advanced blanket boost scheme. The charge retention problem in floating gate cells can be improved by periodic restoring lost charges when significant read window narrowing occurs. In addition to high programming efficiency, this p-channel MTP cells also exhibit good cycling endurance as well as disturbance immunity. The blanket boost scheme can remedy the charge loss problem under thin gate dielectrics.

Pluripotent hybrid cells contribute to extraembryonic as well as embryonic tissues.

PubMed

Do, Jeong Tae; Choi, Hyun Woo; Choi, Youngsok; Schöler, Hans R

2011-06-01

The restricted gene expression of a differentiated cell can be reversed by forming hybrid with embryonic stem cells (ESCs). The resulting hybrid cells showed not only an ESC-specific marker expression but also a differentiation potential similar to the pluripotent fusion partner. Here, we evaluated whether the tetraploid fusion hybrid cells have a unique differentiation potential compared with diploid pluripotent cells. The first Oct4-GFP-positive cells were observed at day 2 following fusion between ESCs and neurosphere cells (OG2(+/-)/ROSA26(+/-)). Reprogramming efficiency was as high as 94.5% at passage 5 and 96.4% at passage 13. We have found that the tetraploid hybrid cells could form chimera with contribution to placenta after blastocyst injection. This result indicates that the tetraploid pluripotent fusion hybrid cells have wide range of differentiation potential. Therefore, we suggest that once the somatic cells are reprogrammed by fusion with ESCs, the tetraploid hybrid cells contributed to the extraembryonic as well as embryonic tissues.

Suppression subtractive hybridization as a tool to identify anthocyanin metabolism-related genes in apple skin.

PubMed

Ban, Yusuke; Moriguchi, Takaya

2010-01-01

The pigmentation of anthocyanins is one of the important determinants for consumer preference and marketability in horticultural crops such as fruits and flowers. To elucidate the mechanisms underlying the physiological process leading to the pigmentation of anthocyanins, identification of the genes differentially expressed in response to anthocyanin accumulation is a useful strategy. Currently, microarrays have been widely used to isolate differentially expressed genes. However, the use of microarrays is limited by its high cost of special apparatus and materials. Therefore, availability of microarrays is limited and does not come into common use at present. Suppression subtractive hybridization (SSH) is an alternative tool that has been widely used to identify differentially expressed genes due to its easy handling and relatively low cost. This chapter describes the procedures for SSH, including RNA extraction from polysaccharides and polyphenol-rich samples, poly(A)+ RNA purification, evaluation of subtraction efficiency, and differential screening using reverse northern in apple skin.

Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes.

PubMed

Verkest, Aurine; Byzova, Marina; Martens, Cindy; Willems, Patrick; Verwulgen, Tom; Slabbinck, Bram; Rombaut, Debbie; Van de Velde, Jan; Vandepoele, Klaas; Standaert, Evi; Peeters, Marrit; Van Lijsebettens, Mieke; Van Breusegem, Frank; De Block, Marc

2015-08-01

To increase both the yield potential and stability of crops, integrated breeding strategies are used that have mostly a direct genetic basis, but the utility of epigenetics to improve complex traits is unclear. A better understanding of the status of the epigenome and its contribution to agronomic performance would help in developing approaches to incorporate the epigenetic component of complex traits into breeding programs. Starting from isogenic canola (Brassica napus) lines, epilines were generated by selecting, repeatedly for three generations, for increased energy use efficiency and drought tolerance. These epilines had an enhanced energy use efficiency, drought tolerance, and nitrogen use efficiency. Transcriptome analysis of the epilines and a line selected for its energy use efficiency solely revealed common differentially expressed genes related to the onset of stress tolerance-regulating signaling events. Genes related to responses to salt, osmotic, abscisic acid, and drought treatments were specifically differentially expressed in the drought-tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine-4 of histone 3, further supported the phenotype by targeting drought-responsive genes and facilitating the transcription of the differentially expressed genes. From these results, we conclude that the canola epigenome can be shaped by selection to increase energy use efficiency and stress tolerance. Hence, these findings warrant the further development of strategies to incorporate epigenetics into breeding. © 2015 American Society of Plant Biologists. All Rights Reserved.

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

Yelundur, Vijay

Suniva, Inc., in collaboration with the University Center for Excellence in Photovoltaics (UCEP) at the Georgia Institute of Technology (GIT) proposed this comprehensive three year program to enable the development of an advanced high performance product that will help the US regain its competitive edge in PV. This project was designed to overcome cost and efficiency barriers through advances in PV science, technology innovation, low-cost manufacturing and full production of ~22.5% efficient n-type Si cells in Norcross, GA. At the heart of the project is the desire to complement the technology being developed concurrently under the Solarmat and ARPAe initiativesmore » to develop a differentiated product superior in both performance and cost effectiveness to the competing alternatives available on the market, and push towards achieving SunShot objectives while ensuring a sustainable business model based on US manufacturing. A significant reduction of the costs in modules produced today will need to combine reductions in wafer costs, cell processing costs as well as module fabrication costs while delivering a product that is not only more efficient under test conditions but also increases the energy yield in outdoor operations. This project will result in a differentiated high performance product and technology that is consistent with sustaining PV manufacturing in the US for a longer term and further highlights the need for continued support for developing the next generation concepts that can keep US manufacturing thriving to support the growing demand for PV in the US and consistent with the US government’s mandates for energy independence.« less

Tailored HIV-1 vectors for genetic modification of primary human dendritic cells and monocytes.

PubMed

Durand, Stéphanie; Nguyen, Xuan-Nhi; Turpin, Jocelyn; Cordeil, Stephanie; Nazaret, Nicolas; Croze, Séverine; Mahieux, Renaud; Lachuer, Joël; Legras-Lachuer, Catherine; Cimarelli, Andrea

2013-01-01

Monocyte-derived dendritic cells (MDDCs) play a key role in the regulation of the immune system and are the target of numerous gene therapy applications. The genetic modification of MDDCs is possible with human immunodeficiency virus type 1 (HIV-1)-derived lentiviral vectors (LVs) but requires high viral doses to bypass their natural resistance to viral infection, and this in turn affects their physiological properties. To date, a single viral protein is able to counter this restrictive phenotype, Vpx, a protein derived from members of the HIV-2/simian immunodeficiency virus SM lineage that counters at least two restriction factors present in myeloid cells. By tagging Vpx with a short heterologous membrane-targeting domain, we have obtained HIV-1 LVs incorporating high levels of this protein (HIV-1-Src-Vpx). These vectors efficiently transduce differentiated MDDCs and monocytes either as previously purified populations or as populations within unsorted peripheral blood mononuclear cells (PBMCs). In addition, these vectors can be efficiently pseudotyped with receptor-specific envelopes, further restricting their cellular tropism almost uniquely to MDDCs. Compared to conventional HIV-1 LVs, these novel vectors allow for an efficient genetic modification of MDDCs and, more importantly, do not cause their maturation or affect their survival, which are unwanted side effects of the transduction process. This study describes HIV-1-Src-Vpx LVs as a novel potent tool for the genetic modification of differentiated MDDCs and of circulating monocyte precursors with strong potential for a wide range of gene therapy applications.

Improved hematopoietic differentiation efficiency of gene-corrected beta-thalassemia induced pluripotent stem cells by CRISPR/Cas9 system.

PubMed

Song, Bing; Fan, Yong; He, Wenyin; Zhu, Detu; Niu, Xiaohua; Wang, Ding; Ou, Zhanhui; Luo, Min; Sun, Xiaofang

2015-05-01

The generation of beta-thalassemia (β-Thal) patient-specific induced pluripotent stem cells (iPSCs), subsequent homologous recombination-based gene correction of disease-causing mutations/deletions in the β-globin gene (HBB), and their derived hematopoietic stem cell (HSC) transplantation offers an ideal therapeutic solution for treating this disease. However, the hematopoietic differentiation efficiency of gene-corrected β-Thal iPSCs has not been well evaluated in the previous studies. In this study, we used the latest gene-editing tool, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), to correct β-Thal iPSCs; gene-corrected cells exhibit normal karyotypes and full pluripotency as human embryonic stem cells (hESCs) showed no off-targeting effects. Then, we evaluated the differentiation efficiency of the gene-corrected β-Thal iPSCs. We found that during hematopoietic differentiation, gene-corrected β-Thal iPSCs showed an increased embryoid body ratio and various hematopoietic progenitor cell percentages. More importantly, the gene-corrected β-Thal iPSC lines restored HBB expression and reduced reactive oxygen species production compared with the uncorrected group. Our study suggested that hematopoietic differentiation efficiency of β-Thal iPSCs was greatly improved once corrected by the CRISPR/Cas9 system, and the information gained from our study would greatly promote the clinical application of β-Thal iPSC-derived HSCs in transplantation.

On mixed derivatives type high dimensional multi-term fractional partial differential equations approximate solutions

NASA Astrophysics Data System (ADS)

Talib, Imran; Belgacem, Fethi Bin Muhammad; Asif, Naseer Ahmad; Khalil, Hammad

2017-01-01

In this research article, we derive and analyze an efficient spectral method based on the operational matrices of three dimensional orthogonal Jacobi polynomials to solve numerically the mixed partial derivatives type multi-terms high dimensions generalized class of fractional order partial differential equations. We transform the considered fractional order problem to an easily solvable algebraic equations with the aid of the operational matrices. Being easily solvable, the associated algebraic system leads to finding the solution of the problem. Some test problems are considered to confirm the accuracy and validity of the proposed numerical method. The convergence of the method is ensured by comparing our Matlab software simulations based obtained results with the exact solutions in the literature, yielding negligible errors. Moreover, comparative results discussed in the literature are extended and improved in this study.

Dopaminergic variants in siblings at high risk for autism: Associations with initiating joint attention.

PubMed

Gangi, Devon N; Messinger, Daniel S; Martin, Eden R; Cuccaro, Michael L

2016-11-01

Younger siblings of children with autism spectrum disorder (ASD; high-risk siblings) exhibit lower levels of initiating joint attention (IJA; sharing an object or experience with a social partner through gaze and/or gesture) than low-risk siblings of children without ASD. However, high-risk siblings also exhibit substantial variability in this domain. The neurotransmitter dopamine is linked to brain areas associated with reward, motivation, and attention, and common dopaminergic variants have been associated with attention difficulties. We examined whether these common dopaminergic variants, DRD4 and DRD2, explain variability in IJA in high-risk (n = 55) and low-risk (n = 38) siblings. IJA was assessed in the first year during a semi-structured interaction with an examiner. DRD4 and DRD2 genotypes were coded according to associated dopaminergic functioning to create a gene score, with higher scores indicating more genotypes associated with less efficient dopaminergic functioning. Higher dopamine gene scores (indicative of less efficient dopaminergic functioning) were associated with lower levels of IJA in the first year for high-risk siblings, while the opposite pattern emerged in low-risk siblings. Findings suggest differential susceptibility-IJA was differentially associated with dopaminergic functioning depending on familial ASD risk. Understanding genes linked to ASD-relevant behaviors in high-risk siblings will aid in early identification of children at greatest risk for difficulties in these behavioral domains, facilitating targeted prevention and intervention. Autism Res 2016, 9: 1142-1150. © 2016 International Society for Autism Research, Wiley Periodicals, Inc. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.

Individual Differences in Sentence Comprehension: A Functional Magnetic Resonance Imaging Investigation of Syntactic and Lexical Processing Demands

PubMed Central

Prat, Chantel S.; Keller, Timothy A.; Just, Marcel Adam

2008-01-01

Language comprehension is neurally underpinned by a network of collaborating cortical processing centers; individual differences in comprehension must be related to some set of this network’s properties. This study investigated the neural bases of individual differences during sentence comprehension by examining the network’s response to two variations in processing demands: reading sentences containing words of high versus low lexical frequency and having simpler versus more complex syntax. In a functional magnetic resonance imaging study, readers who were independently identified as having high or low working memory capacity for language exhibited three differentiating properties of their language network, namely, neural efficiency, adaptability, and synchronization. First, greater efficiency (defined as a reduction in activation associated with improved performance) was manifested as less activation in the bilateral middle frontal and right lingual gyri in high-capacity readers. Second, increased adaptability was indexed by larger lexical frequency effects in high-capacity readers across bilateral middle frontal, bilateral inferior occipital, and right temporal regions. Third, greater synchronization was observed in high-capacity readers between left temporal and left inferior frontal, left parietal, and right occipital regions. Synchronization interacted with adaptability, such that functional connectivity remained constant or increased with increasing lexical and syntactic demands in high-capacity readers, whereas low-capacity readers either showed no reliable differentiation or a decrease in functional connectivity with increasing demands. These results are among the first to relate multiple cortical network properties to individual differences in reading capacity and suggest a more general framework for understanding the relation between neural function and individual differences in cognitive performance. PMID:17892384

Individual differences in sentence comprehension: a functional magnetic resonance imaging investigation of syntactic and lexical processing demands.

PubMed

Prat, Chantel S; Keller, Timothy A; Just, Marcel Adam

2007-12-01

Language comprehension is neurally underpinned by a network of collaborating cortical processing centers; individual differences in comprehension must be related to some set of this network's properties. This study investigated the neural bases of individual differences during sentence comprehension by examining the network's response to two variations in processing demands: reading sentences containing words of high versus low lexical frequency and having simpler versus more complex syntax. In a functional magnetic resonance imaging study, readers who were independently identified as having high or low working memory capacity for language exhibited three differentiating properties of their language network, namely, neural efficiency, adaptability, and synchronization. First, greater efficiency (defined as a reduction in activation associated with improved performance) was manifested as less activation in the bilateral middle frontal and right lingual gyri in high-capacity readers. Second, increased adaptability was indexed by larger lexical frequency effects in high-capacity readers across bilateral middle frontal, bilateral inferior occipital, and right temporal regions. Third, greater synchronization was observed in high-capacity readers between left temporal and left inferior frontal, left parietal, and right occipital regions. Synchronization interacted with adaptability, such that functional connectivity remained constant or increased with increasing lexical and syntactic demands in high-capacity readers, whereas low-capacity readers either showed no reliable differentiation or a decrease in functional connectivity with increasing demands. These results are among the first to relate multiple cortical network properties to individual differences in reading capacity and suggest a more general framework for understanding the relation between neural function and individual differences in cognitive performance.

Efficient generation of transgene- and feeder-free induced pluripotent stem cells from human dental mesenchymal stem cells and their chemically defined differentiation into cardiomyocytes.

PubMed

Tan, Xiaobing; Dai, Qingli; Guo, Tao; Xu, Jingshu; Dai, Qingyuan

2018-01-22

Advance in stem cell research resulted in several processes to generate induced pluripotent stem cells (iPSCs) from adult somatic cells. In our previous study, the reprogramming of iPSCs from human dental mesenchymal stem cells (MSCs) including SCAP and DPSCs, has been reported. Herein, safe iPSCs were reprogrammed from SCAP and DPSCs using non-integrating RNA virus vector, which is an RNA virus carrying no risk of altering host genome. DPSCs- and SCAP-derived iPSCs exhibited the characteristics of the classical morphology with human embryonic stem cells (hESCs) without integration of foreign genes, indicating the potential of their clinical application. Moreover, induced PSCs showed the capacity of self-renewal and differentiation into cardiac myocytes. We have achieved the differentiation of hiPSCs to cardiomyocytes lineage under serum and feeder-free conditions, using a chemically defined medium CDM3. In CDM3, hiPSCs differentiation is highly generating cardiomyocytes. The results showed this protocol produced contractile sheets of up to 97.2% TNNT2 cardiomyocytes after purification. Furthermore, derived hiPSCs differentiated to mature cells of the three embryonic germ layers in vivo and in vitro of beating cardiomyocytes. The above whole protocol enables the generation of large scale of highly pure cardiomyocytes as needed for cellular therapy. Copyright © 2017. Published by Elsevier Inc.

A Long-Acting BMP-2 Release System Based on Poly(3-hydroxybutyrate) Nanoparticles Modified by Amphiphilic Phospholipid for Osteogenic Differentiation

PubMed Central

Peng, Xiaochun; Chen, Yunsu; Li, Yamin; Wang, Yiming

2016-01-01

We explored a novel poly(3-hydroxybutyrate) (PHB) nanoparticle loaded with hydrophilic recombinant human BMP-2 with amphiphilic phospholipid (BPC-PHB NP) for a rapid-acting and long-acting delivery system of BMP-2 for osteogenic differentiation. The BPC-PHB NPs were prepared by a solvent evaporation method and showed a spherical particle with a mean particle size of 253.4 nm, mean zeta potential of −22.42 mV, and high entrapment efficiency of 77.18%, respectively. For BPC-PHB NPs, a short initial burst release of BMP-2 from NPs in 24 h was found and it has steadily risen to reach about 80% in 20 days for in vitro test. BPC-PHB NPs significantly reduced the burst release of BMP-2, as compared to that of PHB NPs loading BMP-2 without PL (B-PHB NPs). BPC-PHB NPs maintained the content of BMP-2 for a long-term osteogenic differentiation. The OCT-1 cells with BPC-PHB NPs have high ALP activity in comparison with others. The gene markers for osteogenic differentiation were significantly upregulated for sample with BPC-PHB NPs, implying that BPC-PHB NPs can be used as a rapid-acting and long-acting BMP-2 delivery system for osteogenic differentiation. PMID:27379249

Cell therapy from bench to bedside: Hepatocytes from fibroblasts - the truth and myth of transdifferentiation.

PubMed

Sanal, Madhusudana Girija

2015-06-07

Hepatocyte transplantation is an alternative to liver transplantation in certain disorders such as inherited liver diseases and liver failure. It is a relatively less complicated surgical procedure, and has the advantage that it can be repeated several times if unsuccessful. Another advantage is that hepatocytes can be isolated from partly damaged livers which are not suitable for liver transplantation. Despite these advantages hepatocyte transplantation is less popular. Important issues are poor engraftment of the transplanted cells and the scarcity of donor hepatocytes. Generation of "hepatocyte like cells"/iHeps from embryonic stem cells (ES) and induced pluripotent stem cells (iPSCs) by directed differentiation is an emerging solution to the latter issue. Direct conversation or trans-differentiation of fibroblasts to "hepatocyte like cells" is another way which is, being explored. However this method has several inherent and technical disadvantages compared to the directed differentiation from ES or iPSC. There are several methods claiming to be "highly efficient" for generating "highly functional" "hepatocyte like cells". Currently different groups are working independently and coming up with differentiation protocols and each group claiming an advantage for their protocol. Directed differentiation protocols need to be designed, compared, analyzed and tweaked systematically and logically than empirically. There is a need for a well-coordinated global initiative comparable to the Human Genome Project to achieve this goal in the near future.

Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species.

PubMed

Man, Orna; Pilpel, Yitzhak

2007-03-01

A major challenge in comparative genomics is to understand how phenotypic differences between species are encoded in their genomes. Phenotypic divergence may result from differential transcription of orthologous genes, yet less is known about the involvement of differential translation regulation in species phenotypic divergence. In order to assess translation effects on divergence, we analyzed approximately 2,800 orthologous genes in nine yeast genomes. For each gene in each species, we predicted translation efficiency, using a measure of the adaptation of its codons to the organism's tRNA pool. Mining this data set, we found hundreds of genes and gene modules with correlated patterns of translational efficiency across the species. One signal encompassed entire modules that are either needed for oxidative respiration or fermentation and are efficiently translated in aerobic or anaerobic species, respectively. In addition, the efficiency of translation of the mRNA splicing machinery strongly correlates with the number of introns in the various genomes. Altogether, we found extensive selection on synonymous codon usage that modulates translation according to gene function and organism phenotype. We conclude that, like factors such as transcription regulation, translation efficiency affects and is affected by the process of species divergence.

Neutron-Encoded Protein Quantification by Peptide Carbamylation

NASA Astrophysics Data System (ADS)

Ulbrich, Arne; Merrill, Anna E.; Hebert, Alexander S.; Westphall, Michael S.; Keller, Mark P.; Attie, Alan D.; Coon, Joshua J.

2014-01-01

We describe a chemical tag for duplex proteome quantification using neutron encoding (NeuCode). The method utilizes the straightforward, efficient, and inexpensive carbamylation reaction. We demonstrate the utility of NeuCode carbamylation by accurately measuring quantitative ratios from tagged yeast lysates mixed in known ratios and by applying this method to quantify differential protein expression in mice fed a either control or high-fat diet.

Human cardiomyocyte generation from pluripotent stem cells: A state-of-art.

PubMed

Talkhabi, Mahmood; Aghdami, Nasser; Baharvand, Hossein

2016-01-15

The human heart is considered a non-regenerative organ. Worldwide, cardiovascular diseases continue to be the leading cause of death. Despite advances in cardiac treatment, myocardial repair remains severely limited by the lack of an appropriate source of viable cardiomyocytes (CMs) to replace damaged tissue. Human pluripotent stem cells (hPSCs), embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) can efficiently be differentiated into functional CMs necessary for cell replacement therapy and other potential applications. The number of protocols that derive CMs from hPSCs has increased exponentially over the past decade following observation of the first human beating CMs. A number of highly efficient, chemical based protocols have been developed to generate human CMs (hCMs) in small-scale and large-scale suspension systems. To reduce the heterogeneity of hPSC-derived CMs, the differentiation protocols were modulated to exclusively generate atrial-, ventricular-, and nodal-like CM subtypes. Recently, remarkable advances have been achieved in hCM generation including chemical-based cardiac differentiation, cardiac subtype specification, large-scale suspension culture differentiation, and development of chemically defined culture conditions. These hCMs could be useful particularly in the context of in vitro disease modeling, pharmaceutical screening and in cellular replacement therapies once the safety issues are overcome. Herein we review recent progress in the in vitro generation of CMs and cardiac subtypes from hPSCs and discuss their potential applications and current limitations. Copyright © 2015 Elsevier Inc. All rights reserved.

Robust generation and expansion of skeletal muscle progenitors and myocytes from human pluripotent stem cells.

PubMed

Shelton, Michael; Kocharyan, Avetik; Liu, Jun; Skerjanc, Ilona S; Stanford, William L

2016-05-15

Human pluripotent stem cells provide a developmental model to study early embryonic and tissue development, tease apart human disease processes, perform drug screens to identify potential molecular effectors of in situ regeneration, and provide a source for cell and tissue based transplantation. Highly efficient differentiation protocols have been established for many cell types and tissues; however, until very recently robust differentiation into skeletal muscle cells had not been possible unless driven by transgenic expression of master regulators of myogenesis. Nevertheless, several breakthrough protocols have been published in the past two years that efficiently generate cells of the skeletal muscle lineage from pluripotent stem cells. Here, we present an updated version of our recently described 50-day protocol in detail, whereby chemically defined media are used to drive and support muscle lineage development from initial CHIR99021-induced mesoderm through to PAX7-expressing skeletal muscle progenitors and mature skeletal myocytes. Furthermore, we report an optional method to passage and expand differentiating skeletal muscle progenitors approximately 3-fold every 2weeks using Collagenase IV and continued FGF2 supplementation. Both protocols have been optimized using a variety of human pluripotent stem cell lines including patient-derived induced pluripotent stem cells. Taken together, our differentiation and expansion protocols provide sufficient quantities of skeletal muscle progenitors and myocytes that could be used for a variety of studies. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Overexpression of hTERT increases stem-like properties and decreases spontaneous differentiation in human mesenchymal stem cell lines

PubMed Central

2010-01-01

To overcome loss of stem-like properties and spontaneous differentiation those hinder the expansion and application of human mesenchymal stem cells (hMSCs), we have clonally isolated permanent and stable human MSC lines by ectopic overexpression of primary cell cultures of hMSCs with HPV 16 E6E7 and human telomerase reverse transcriptase (hTERT) genes. These cells were found to have a differentiation potential far beyond the ordinary hMSCs. They expressed trophoectoderm and germline specific markers upon differentiation with BMP4 and retinoic acid, respectively. Furthermore, they displayed higher osteogenic and neural differentiation efficiency than primary hMSCs or hMSCs expressed HPV16 E6E7 alone with a decrease in methylation level as proven by a global CpG island methylation profile analysis. Notably, the demethylated CpG islands were highly associated with development and differentiation associated genes. Principal component analysis further pointed out the expression profile of the cells converged toward embryonic stem cells. These data demonstrate these cells not only are a useful tool for the studies of cell differentiation both for the mesenchymal and neurogenic lineages, but also provide a valuable source of cells for cell therapy studies in animal models of skeletal and neurological disorders. PMID:20670406

Two Legendre-Dual-Petrov-Galerkin Algorithms for Solving the Integrated Forms of High Odd-Order Boundary Value Problems

PubMed Central

Abd-Elhameed, Waleed M.; Doha, Eid H.; Bassuony, Mahmoud A.

2014-01-01

Two numerical algorithms based on dual-Petrov-Galerkin method are developed for solving the integrated forms of high odd-order boundary value problems (BVPs) governed by homogeneous and nonhomogeneous boundary conditions. Two different choices of trial functions and test functions which satisfy the underlying boundary conditions of the differential equations and the dual boundary conditions are used for this purpose. These choices lead to linear systems with specially structured matrices that can be efficiently inverted, hence greatly reducing the cost. The various matrix systems resulting from these discretizations are carefully investigated, especially their complexities and their condition numbers. Numerical results are given to illustrate the efficiency of the proposed algorithms, and some comparisons with some other methods are made. PMID:24616620

Metabolic differences of industrial acarbose-producing Actinoplanes sp. A56 under various osmolality levels.

PubMed

Li, Kun-tai; Peng, Wei-fu; Xia, Wei; Huang, Lin; Cheng, Xin

2016-01-01

Many investigations have revealed that a certain concentration of osmolality was indispensable for efficient acarbose production, but little information was available on the response mechanism of acarbose-producing strains to osmotic stress. By using the gas chromatography-mass spectrometry (GC-MS) analysis coupled with the enzyme activity determination of central carbon metabolism, the present work investigated the metabolic characteristics of industrial acarbose-producing Actinoplanes sp. A56 under various osmolality levels. Relatively high osmolality (450-500 mOsm/kg) appeared to favor efficient acarbose production by Actinoplanes sp. A56, although it inhibited cell growth. Further GC-MS analysis showed that fatty acids were the uppermost differential intracellular metabolites under various osmolality levels, and the relatively high osmolality resulted in increases in levels of fatty acids.

Improving cluster-based missing value estimation of DNA microarray data.

PubMed

Brás, Lígia P; Menezes, José C

2007-06-01

We present a modification of the weighted K-nearest neighbours imputation method (KNNimpute) for missing values (MVs) estimation in microarray data based on the reuse of estimated data. The method was called iterative KNN imputation (IKNNimpute) as the estimation is performed iteratively using the recently estimated values. The estimation efficiency of IKNNimpute was assessed under different conditions (data type, fraction and structure of missing data) by the normalized root mean squared error (NRMSE) and the correlation coefficients between estimated and true values, and compared with that of other cluster-based estimation methods (KNNimpute and sequential KNN). We further investigated the influence of imputation on the detection of differentially expressed genes using SAM by examining the differentially expressed genes that are lost after MV estimation. The performance measures give consistent results, indicating that the iterative procedure of IKNNimpute can enhance the prediction ability of cluster-based methods in the presence of high missing rates, in non-time series experiments and in data sets comprising both time series and non-time series data, because the information of the genes having MVs is used more efficiently and the iterative procedure allows refining the MV estimates. More importantly, IKNN has a smaller detrimental effect on the detection of differentially expressed genes.

Efficiency of B-mode Ultrasound and Strain Elastography in Differentiating Between Benign and Malignant Cervical Lymph Nodes.

PubMed

Turgut, Eser; Celenk, Cetin; Tanrivermis Sayit, Asli; Bekci, Tumay; Gunbey, Hediye Pinar; Aslan, Kerim

2017-09-01

The purpose of this study was to evaluate the diagnostic accuracy and efficiency of ultrasonography (US), especially when combined with strain elastography (SE), in differentiating between benign and malignant cervical lymph nodes (LNs). Forty-one LNs were examined by B-mode US, power Doppler US, and SE. The following imaging features were analyzed: shape, echogenicity, echogenic hilum, calcification, intranodal vascular pattern, elasticity scores (5 categories), and strain ratio. The average strain ratio was calculated as the mean strain of the adjacent sternocleidomastoid muscle divided by the mean strain of the target LN. The results of the US and SE features were compared with the histopathologic findings. The imaging features that were significantly associated with malignant LNs were an increased short-to-long axis diameter ratio, abnormal or absence of hilum, microcalcification, type 2-3-4 vascularity, 3-4-5 elasticity scores, and a high level of strain ratio (P < 0.05). The cutoff value of the strain index was detected as 1.18. According to this, there was a significant difference (P = 0.004) in the strain index between benign and malignant LNs. Strain elastography is useful in differentiating between benign and malignant cervical LNs, thereby informing decisions to perform a biopsy and/or surgery, and facilitating follow-up.

microRNAs differentially modulated in response to heat and drought stress in durum wheat cultivars with contrasting water use efficiency.

PubMed

Giusti, Lorenzo; Mica, Erica; Bertolini, Edoardo; De Leonardis, Anna Maria; Faccioli, Primetta; Cattivelli, Luigi; Crosatti, Cristina

2017-05-01

Plant stress response is a complex molecular process based on transcriptional and posttranscriptional regulation of many stress-related genes. microRNAs are the best-studied class of small RNAs known to play key regulatory roles in plant response to stress, besides being involved in plant development and organogenesis. We analyzed the leaf miRNAome of two durum wheat cultivars (Cappelli and Ofanto) characterized by a contrasting water use efficiency, exposed to heat stress, and mild and severe drought stress. On the whole, we identified 98 miRNA highly similar to previously known miRNAs and grouped in 47 MIR families, as well as 85 novel candidate miRNA, putatively wheat specific. A total of 80 known and novel miRNA precursors were found differentially expressed between the two cultivars or modulated by stress and many of them showed a cultivar-specific expression profile. Interestingly, most in silico predicted targets of the miRNAs coming from the differentially expressed precursors have been experimentally linked in other species to mechanisms controlling stomatal movement, a finding in agreement with previous results showing that Cappelli has a lower stomatal conductance than Ofanto. Selected miRNAs were validated through a standardized and reliable stem-loop qRT-PCR procedure.

High precision locating control system based on VCM for Talbot lithography

NASA Astrophysics Data System (ADS)

Yao, Jingwei; Zhao, Lixin; Deng, Qian; Hu, Song

2016-10-01

Aiming at the high precision and efficiency requirements of Z-direction locating in Talbot lithography, a control system based on Voice Coil Motor (VCM) was designed. In this paper, we built a math model of VCM and its moving characteristic was analyzed. A double-closed loop control strategy including position loop and current loop were accomplished. The current loop was implemented by driver, in order to achieve the rapid follow of the system current. The position loop was completed by the digital signal processor (DSP) and the position feedback was achieved by high precision linear scales. Feed forward control and position feedback Proportion Integration Differentiation (PID) control were applied in order to compensate for dynamic lag and improve the response speed of the system. And the high precision and efficiency of the system were verified by simulation and experiments. The results demonstrated that the performance of Z-direction gantry was obviously improved, having high precision, quick responses, strong real-time and easily to expend for higher precision.

Sperm competition dynamics: ejaculate fertilising efficiency changes differentially with time.

PubMed

Pizzari, Tommaso; Worley, Kirsty; Burke, Terry; Froman, David P

2008-12-16

A fundamental challenge in evolutionary biology is to resolve the mechanisms that maintain paternity a hypervariable fitness component. Because females are often sexually promiscuous, this challenge hinges on establishing the mechanisms through which the ejaculates of different males compete for fertilisation (sperm competition). The competitive quality of an ejaculate is mediated by the relative number of live sperm and their motile performance. The differential rate at which rival ejaculates lose their fertilising efficiency over time is therefore expected to influence the outcome of sperm competition. Here, we artificially inseminated into sets of replicate domestic hens, Gallus gallus domesticus, experimentally engineered heterospermic ejaculates containing a large number of low-quality sperm from one male, and a lower number of high-quality sperm from another male. Large, low-quality ejaculates fertilised the first eggs produced after insemination, but small, high-quality ejaculates prevailed in the long run despite their numerical disadvantage. Together, these results provide the first experimental demonstration that the relative competitive value of an ejaculate changes drastically over the time during which competing ejaculates are stored within the reproductive tract of a female, resulting in a marked temporal pattern of variation in paternity. A high level of replication makes these results robust. However, our study was restricted to few males of a well characterised study population, and future work should explore the generality of these results.

Sperm competition dynamics: ejaculate fertilising efficiency changes differentially with time

PubMed Central

2008-01-01

Background A fundamental challenge in evolutionary biology is to resolve the mechanisms that maintain paternity a hypervariable fitness component. Because females are often sexually promiscuous, this challenge hinges on establishing the mechanisms through which the ejaculates of different males compete for fertilisation (sperm competition). The competitive quality of an ejaculate is mediated by the relative number of live sperm and their motile performance. The differential rate at which rival ejaculates lose their fertilising efficiency over time is therefore expected to influence the outcome of sperm competition. Results Here, we artificially inseminated into sets of replicate domestic hens, Gallus gallus domesticus, experimentally engineered heterospermic ejaculates containing a large number of low-quality sperm from one male, and a lower number of high-quality sperm from another male. Large, low-quality ejaculates fertilised the first eggs produced after insemination, but small, high-quality ejaculates prevailed in the long run despite their numerical disadvantage. Conclusion Together, these results provide the first experimental demonstration that the relative competitive value of an ejaculate changes drastically over the time during which competing ejaculates are stored within the reproductive tract of a female, resulting in a marked temporal pattern of variation in paternity. A high level of replication makes these results robust. However, our study was restricted to few males of a well characterised study population, and future work should explore the generality of these results. PMID:19087292

Hybrid WDM/OCDMA for next generation access network

NASA Astrophysics Data System (ADS)

Wang, Xu; Wada, Naoya; Miyazaki, T.; Cincotti, G.; Kitayama, Ken-ichi

2007-11-01

Hybrid wavelength division multiplexing/optical code division multiple access (WDM/OCDMA) passive optical network (PON), where asynchronous OCDMA traffic transmits over WDM network, can be one potential candidate for gigabit-symmetric fiber-to-the-home (FTTH) services. In a cost-effective WDM/OCDMA network, a large scale multi-port encoder/decoder can be employed in the central office, and a low cost encoder/decoder will be used in optical network unit (ONU). The WDM/OCDMA system could be one promising solution to the symmetric high capacity access network with high spectral efficiency, cost effective, good flexibility and enhanced security. Asynchronous WDM/OCDMA systems have been experimentally demonstrated using superstructured fiber Bragg gratings (SSFBG) and muti-port OCDMA en/decoders. The total throughput has reached above Tera-bit/s with spectral efficiency of about 0.41. The key enabling techniques include ultra-long SSFBG, multi-port E/D with high power contrast ratio, optical thresholding, differential phase shift keying modulation with balanced detection, forward error correction, and etc. Using multi-level modulation formats to carry multi-bit information with single pulse, the total capacity and spectral efficiency could be further enhanced.

Erythrocyte Enrichment in Hematopoietic Progenitor Cell Cultures Based on Magnetic Susceptibility of the Hemoglobin

PubMed Central

Jin, Xiaoxia; Abbot, Stewart; Zhang, Xiaokui; Kang, Lin; Voskinarian-Berse, Vanessa; Zhao, Rui; Kameneva, Marina V.; Moore, Lee R.; Chalmers, Jeffrey J.; Zborowski, Maciej

2012-01-01

Using novel media formulations, it has been demonstrated that human placenta and umbilical cord blood-derived CD34+ cells can be expanded and differentiated into erythroid cells with high efficiency. However, obtaining mature and functional erythrocytes from the immature cell cultures with high purity and in an efficient manner remains a significant challenge. A distinguishing feature of a reticulocyte and maturing erythrocyte is the increasing concentration of hemoglobin and decreasing cell volume that results in increased cell magnetophoretic mobility (MM) when exposed to high magnetic fields and gradients, under anoxic conditions. Taking advantage of these initial observations, we studied a noninvasive (label-free) magnetic separation and analysis process to enrich and identify cultured functional erythrocytes. In addition to the magnetic cell separation and cell motion analysis in the magnetic field, the cell cultures were characterized for cell sedimentation rate, cell volume distributions using differential interference microscopy, immunophenotyping (glycophorin A), hemoglobin concentration and shear-induced deformability (elongation index, EI, by ektacytometry) to test for mature erythrocyte attributes. A commercial, packed column high-gradient magnetic separator (HGMS) was used for magnetic separation. The magnetically enriched fraction comprised 80% of the maturing cells (predominantly reticulocytes) that showed near 70% overlap of EI with the reference cord blood-derived RBC and over 50% overlap with the adult donor RBCs. The results demonstrate feasibility of label-free magnetic enrichment of erythrocyte fraction of CD34+ progenitor-derived cultures based on the presence of paramagnetic hemoglobin in the maturing erythrocytes. PMID:22952572

A Convenient and Efficient Method to Enrich and Maintain Highly Proliferative Human Fetal Liver Stem Cells

PubMed Central

Guo, Xuan; Wang, Shu; Dou, Ya-ling; Guo, Xiang-fei; Chen, Zhao-li; Wang, Xin-wei; Shen, Zhi-qiang; Qiu, Zhi-gang

2015-01-01

Abstract Pluripotent human hepatic stem cells have broad research and clinical applications, which are, however, restricted by both limited resources and technical difficulties with respect to isolation of stem cells from the adult or fetal liver. In this study, we developed a convenient and efficient method involving a two-step in situ collagenase perfusion, gravity sedimentation, and Percoll density gradient centrifugation to enrich and maintain highly proliferative human fetal liver stem cells (hFLSCs). Using this method, the isolated hFLSCs entered into the exponential growth phase within 10 days and maintained sufficient proliferative activity to permit subculture for at least 20 passages without differentiation. Immunocytochemistry, immunofluorescence, and flow cytometry results showed that these cells expressed stem cell markers, such as c-kit, CD44, epithelial cell adhesion molecule (EpCAM), oval cell marker-6 (OV-6), epithelial marker cytokeratin 18 (CK18), biliary ductal marker CK19, and alpha-fetoprotein (AFP). Gene expression analysis showed that these cells had stable mRNA expression of c-Kit, EpCAM, neural cell adhesion molecule (NCAM), CK19, CK18, AFP, and claudin 3 (CLDN-3) throughout each passage while maintaining low levels of ALB, but with complete absence of cytochrome P450 3A4 (C3A4), phosphoenolpyruvate carboxykinase (PEPCK), telomeric repeat binding factor (TRF), and connexin 26 (CX26) expression. When grown in appropriate medium, these isolated liver stem cells could differentiate into hepatocytes, cholangiocytes, osteoblasts, adipocytes, or endothelial cells. Thus, we have demonstrated a more economical and efficient method to isolate hFLSCs than magnetic-activated cell sorting (MACS). This novel approach may provide an excellent tool to isolate highly proliferative hFLSCs for tissue engineering and regenerative therapies. PMID:25556695

A Convenient and Efficient Method to Enrich and Maintain Highly Proliferative Human Fetal Liver Stem Cells.

PubMed

Guo, Xuan; Wang, Shu; Dou, Ya-ling; Guo, Xiang-fei; Chen, Zhao-li; Wang, Xin-wei; Shen, Zhi-qiang; Qiu, Zhi-gang; Jin, Min; Li, Jun-wen

2015-06-01

Pluripotent human hepatic stem cells have broad research and clinical applications, which are, however, restricted by both limited resources and technical difficulties with respect to isolation of stem cells from the adult or fetal liver. In this study, we developed a convenient and efficient method involving a two-step in situ collagenase perfusion, gravity sedimentation, and Percoll density gradient centrifugation to enrich and maintain highly proliferative human fetal liver stem cells (hFLSCs). Using this method, the isolated hFLSCs entered into the exponential growth phase within 10 days and maintained sufficient proliferative activity to permit subculture for at least 20 passages without differentiation. Immunocytochemistry, immunofluorescence, and flow cytometry results showed that these cells expressed stem cell markers, such as c-kit, CD44, epithelial cell adhesion molecule (EpCAM), oval cell marker-6 (OV-6), epithelial marker cytokeratin 18 (CK18), biliary ductal marker CK19, and alpha-fetoprotein (AFP). Gene expression analysis showed that these cells had stable mRNA expression of c-Kit, EpCAM, neural cell adhesion molecule (NCAM), CK19, CK18, AFP, and claudin 3 (CLDN-3) throughout each passage while maintaining low levels of ALB, but with complete absence of cytochrome P450 3A4 (C3A4), phosphoenolpyruvate carboxykinase (PEPCK), telomeric repeat binding factor (TRF), and connexin 26 (CX26) expression. When grown in appropriate medium, these isolated liver stem cells could differentiate into hepatocytes, cholangiocytes, osteoblasts, adipocytes, or endothelial cells. Thus, we have demonstrated a more economical and efficient method to isolate hFLSCs than magnetic-activated cell sorting (MACS). This novel approach may provide an excellent tool to isolate highly proliferative hFLSCs for tissue engineering and regenerative therapies.

From Physics Model to Results: An Optimizing Framework for Cross-Architecture Code Generation

DOE PAGES

Blazewicz, Marek; Hinder, Ian; Koppelman, David M.; ...

2013-01-01

Starting from a high-level problem description in terms of partial differential equations using abstract tensor notation, the Chemora framework discretizes, optimizes, and generates complete high performance codes for a wide range of compute architectures. Chemora extends the capabilities of Cactus, facilitating the usage of large-scale CPU/GPU systems in an efficient manner for complex applications, without low-level code tuning. Chemora achieves parallelism through MPI and multi-threading, combining OpenMP and CUDA. Optimizations include high-level code transformations, efficient loop traversal strategies, dynamically selected data and instruction cache usage strategies, and JIT compilation of GPU code tailored to the problem characteristics. The discretization ismore » based on higher-order finite differences on multi-block domains. Chemora's capabilities are demonstrated by simulations of black hole collisions. This problem provides an acid test of the framework, as the Einstein equations contain hundreds of variables and thousands of terms.« less

Growth Factor-Activated Stem Cell Circuits and Stromal Signals Cooperatively Accelerate Non-Integrated iPSC Reprogramming of Human Myeloid Progenitors

PubMed Central

Park, Tea Soon; Huo, Jeffrey S.; Peters, Ann; Talbot, C. Conover; Verma, Karan; Zimmerlin, Ludovic; Kaplan, Ian M.; Zambidis, Elias T.

2012-01-01

Nonviral conversion of skin or blood cells into clinically useful human induced pluripotent stem cells (hiPSC) occurs in only rare fractions (∼0.001%–0.5%) of donor cells transfected with non-integrating reprogramming factors. Pluripotency induction of developmentally immature stem-progenitors is generally more efficient than differentiated somatic cell targets. However, the nature of augmented progenitor reprogramming remains obscure, and its potential has not been fully explored for improving the extremely slow pace of non-integrated reprogramming. Here, we report highly optimized four-factor reprogramming of lineage-committed cord blood (CB) myeloid progenitors with bulk efficiencies of ∼50% in purified episome-expressing cells. Lineage-committed CD33+CD45+CD34− myeloid cells and not primitive hematopoietic stem-progenitors were the main targets of a rapid and nearly complete non-integrated reprogramming. The efficient conversion of mature myeloid populations into NANOG+TRA-1-81+ hiPSC was mediated by synergies between hematopoietic growth factor (GF), stromal activation signals, and episomal Yamanaka factor expression. Using a modular bioinformatics approach, we demonstrated that efficient myeloid reprogramming correlated not to increased proliferation or endogenous Core factor expressions, but to poised expression of GF-activated transcriptional circuits that commonly regulate plasticity in both hematopoietic progenitors and embryonic stem cells (ESC). Factor-driven conversion of myeloid progenitors to a high-fidelity pluripotent state was further accelerated by soluble and contact-dependent stromal signals that included an implied and unexpected role for Toll receptor-NFκB signaling. These data provide a paradigm for understanding the augmented reprogramming capacity of somatic progenitors, and reveal that efficient induced pluripotency in other cell types may also require extrinsic activation of a molecular framework that commonly regulates self-renewal and differentiation in both hematopoietic progenitors and ESC. PMID:22905176

Efficient computation of the Grünwald-Letnikov fractional diffusion derivative using adaptive time step memory

NASA Astrophysics Data System (ADS)

MacDonald, Christopher L.; Bhattacharya, Nirupama; Sprouse, Brian P.; Silva, Gabriel A.

2015-09-01

Computing numerical solutions to fractional differential equations can be computationally intensive due to the effect of non-local derivatives in which all previous time points contribute to the current iteration. In general, numerical approaches that depend on truncating part of the system history while efficient, can suffer from high degrees of error and inaccuracy. Here we present an adaptive time step memory method for smooth functions applied to the Grünwald-Letnikov fractional diffusion derivative. This method is computationally efficient and results in smaller errors during numerical simulations. Sampled points along the system's history at progressively longer intervals are assumed to reflect the values of neighboring time points. By including progressively fewer points backward in time, a temporally 'weighted' history is computed that includes contributions from the entire past of the system, maintaining accuracy, but with fewer points actually calculated, greatly improving computational efficiency.

Interband cascade lasers with >40% continuous-wave wallplug efficiency at cryogenic temperatures

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

Canedy, C. L.; Kim, C. S.; Merritt, C. D.

2015-09-21

Broad-area 10-stage interband cascade lasers (ICLs) emitting at λ = 3.0–3.2 μm are shown to maintain continuous-wave (cw) wallplug efficiencies exceeding 40% at temperatures up to 125 K, despite having a design optimized for operation at ambient and above. The cw threshold current density at 80 K is only 11 A/cm{sup 2} for a 2 mm cavity with anti-reflection/high-reflection coatings on the two facets. The external differential quantum efficiency for a 1-mm-long cavity with the same coatings is 70% per stage at 80 K, and still above 65% at 150 K. The results demonstrate that at cryogenic temperatures, where free carrier absorption losses are minimized, ICLs can convert electricalmore » to optical energy nearly as efficiently as the best specially designed intersubband-based quantum cascade lasers.« less

A Comprehensive Comparison of Multiparty Secure Additions with Differential Privacy

PubMed Central

Goryczka, Slawomir; Xiong, Li

2016-01-01

This paper considers the problem of secure data aggregation (mainly summation) in a distributed setting, while ensuring differential privacy of the result. We study secure multiparty addition protocols using well known security schemes: Shamir’s secret sharing, perturbation-based, and various encryptions. We supplement our study with our new enhanced encryption scheme EFT, which is efficient and fault tolerant. Differential privacy of the final result is achieved by either distributed Laplace or Geometric mechanism (respectively DLPA or DGPA), while approximated differential privacy is achieved by diluted mechanisms. Distributed random noise is generated collectively by all participants, which draw random variables from one of several distributions: Gamma, Gauss, Geometric, or their diluted versions. We introduce a new distributed privacy mechanism with noise drawn from the Laplace distribution, which achieves smaller redundant noise with efficiency. We compare complexity and security characteristics of the protocols with different differential privacy mechanisms and security schemes. More importantly, we implemented all protocols and present an experimental comparison on their performance and scalability in a real distributed environment. Based on the evaluations, we identify our security scheme and Laplace DLPA as the most efficient for secure distributed data aggregation with privacy. PMID:28919841

A Comprehensive Comparison of Multiparty Secure Additions with Differential Privacy.

PubMed

Goryczka, Slawomir; Xiong, Li

2017-01-01

This paper considers the problem of secure data aggregation (mainly summation) in a distributed setting, while ensuring differential privacy of the result. We study secure multiparty addition protocols using well known security schemes: Shamir's secret sharing, perturbation-based, and various encryptions. We supplement our study with our new enhanced encryption scheme EFT, which is efficient and fault tolerant. Differential privacy of the final result is achieved by either distributed Laplace or Geometric mechanism (respectively DLPA or DGPA), while approximated differential privacy is achieved by diluted mechanisms. Distributed random noise is generated collectively by all participants, which draw random variables from one of several distributions: Gamma, Gauss, Geometric, or their diluted versions. We introduce a new distributed privacy mechanism with noise drawn from the Laplace distribution, which achieves smaller redundant noise with efficiency. We compare complexity and security characteristics of the protocols with different differential privacy mechanisms and security schemes. More importantly, we implemented all protocols and present an experimental comparison on their performance and scalability in a real distributed environment. Based on the evaluations, we identify our security scheme and Laplace DLPA as the most efficient for secure distributed data aggregation with privacy.

Cloning from stem cells: different lineages, different species, same story.

PubMed

Oback, Björn

2009-01-01

Following nuclear transfer (NT), the most stringent measure of extensive donor cell reprogramming is development into viable offspring. This is referred to as cloning efficiency and quantified as the proportion of cloned embryos transferred into surrogate mothers that survive into adulthood. Cloning efficiency depends on the ability of the enucleated recipient cell to carry out the reprogramming reactions ('reprogramming ability') and the ability of the nuclear donor cell to be reprogrammed ('reprogrammability'). It has been postulated that reprogrammability of the somatic donor cell epigenome is inversely proportional to its differentiation status. In order to test this hypothesis, reprogrammability was compared between undifferentiated stem cells and their differentiated isogenic progeny. In the mouse, cells of divergent differentiation status from the neuronal, haematopoietic and skin epithelial lineage were tested. In cattle and deer, skeletal muscle and antler cells, respectively, were used as donors. No conclusive correlation between differentiation status and cloning efficiency was found, indicating that somatic donor cell type may not be the limiting factor for cloning success. This may reflect technical limitations of the NT-induced reprogramming assay. Alternatively, differentiation status and reprogrammability may be unrelated, making all cells equally difficult to reprogramme once they have left the ground state of pluripotency.

Scaffolding for Three-Dimensional Embryonic Vasculogenesis

NASA Astrophysics Data System (ADS)

Kraehenbuehl, Thomas P.; Aday, Sezin; Ferreira, Lino S.

Biomaterial scaffolds have great potential to support efficient vascular differentiation of embryonic stem cells. Vascular cell fate-specific biochemical and biophysical cues have been identified and incorporated into three-dimensional (3D) biomaterials to efficiently direct embryonic vasculogenesis. The resulting vascular-like tissue can be used for regenerative medicine applications, further elucidation of biophysical and biochemical cues governing vasculogenesis, and drug discovery. In this chapter, we give an overview on the following: (1) developmental cues for directed differentiation of human embryonic stem cells (hESCs) into vascular cells, (2) 3D vascular differentiation in embryoid bodies (EBs), (3) preparation of 3D scaffolds for the vascular differentiation of hESCs, and (4) the most significant studies combining scaffolding and hESCs for development of vascular-like tissue.

Synthetic niches for differentiation of human embryonic stem cells bypassing embryoid body formation.

PubMed

Liu, Yarong; Fox, Victoria; Lei, Yuning; Hu, Biliang; Joo, Kye-Il; Wang, Pin

2014-07-01

The unique self-renewal and pluripotency features of human embryonic stem cells (hESCs) offer the potential for unlimited development of novel cell therapies. Currently, hESCs are cultured and differentiated using methods, such as monolayer culture and embryoid body (EB) formation. As such, achieving efficient differentiation into higher order structures remains a challenge, as well as maintaining cell viability during differentiation into homogeneous cell populations. Here, we describe the application of highly porous polymer scaffolds as synthetic stem cell niches. Bypassing the EB formation step, these scaffolds are capable of three-dimensional culture of undifferentiated hESCs and subsequent directed differentiation into three primary germ layers. H9 hESCs were successfully maintained and proliferated in biodegradable polymer scaffolds based on poly (lactic-co-glycolic acid) (PLGA). The results showed that cells within PLGA scaffolds retained characteristics of undifferentiated pluripotent stem cells. Moreover, the scaffolds allowed differentiation towards the lineage of interest by the addition of growth factors to the culture system. The in vivo transplantation study revealed that the scaffolds could provide a microenvironment that enabled hESCs to interact with their surroundings, thereby promoting cell differentiation. Therefore, this approach, which provides a unique culture/differentiation system for hESCs, will find its utility in various stem cell-based tissue-engineering applications. © 2013 Wiley Periodicals, Inc.

Therapeutic cloning in the mouse

PubMed Central

Mombaerts, Peter

2003-01-01

Nuclear transfer technology can be applied to produce autologous differentiated cells for therapeutic purposes, a concept termed therapeutic cloning. Countless articles have been published on the ethics and politics of human therapeutic cloning, reflecting the high expectations from this new opportunity for rejuvenation of the aging or diseased body. Yet the research literature on therapeutic cloning, strictly speaking, is comprised of only four articles, all in the mouse. The efficiency of derivation of embryonic stem cell lines via nuclear transfer is remarkably consistent among these reports. However, the efficiency is so low that, in its present form, the concept is unlikely to become widespread in clinical practice. PMID:12949262

A power-efficient switchable CML driver at 10 Gbps

NASA Astrophysics Data System (ADS)

Peipei, Chen; Lei, Li; Huihua, Liu

2016-02-01

High static power limits the application of conventional current-mode logic(CML). This paper presents a power-efficient switchable CML driver, which achieves a significant current saving by 75% compared with conventional ones. Implemented in the 130 nm CMOS technology process, the proposed CML driver just occupies an area about 0.003 mm2 and provides a robust differential signal of 1600 mV for 10 Gbps optical line terminal (OLT) with a total current of 10 mA. The peak-to-peak jitter is about 4 ps (0.04TUI) and the offset voltage is 347.2 mV @ 1600 mVPP.

Spontaneous In Vivo Chondrogenesis of Bone Marrow-Derived Mesenchymal Progenitor Cells by Blocking Vascular Endothelial Growth Factor Signaling.

PubMed

Marsano, Anna; Medeiros da Cunha, Carolina M; Ghanaati, Shahram; Gueven, Sinan; Centola, Matteo; Tsaryk, Roman; Barbeck, Mike; Stuedle, Chiara; Barbero, Andrea; Helmrich, Uta; Schaeren, Stefan; Kirkpatrick, James C; Banfi, Andrea; Martin, Ivan

2016-12-01

: Chondrogenic differentiation of bone marrow-derived mesenchymal stromal/stem cells (MSCs) can be induced by presenting morphogenetic factors or soluble signals but typically suffers from limited efficiency, reproducibility across primary batches, and maintenance of phenotypic stability. Considering the avascular and hypoxic milieu of articular cartilage, we hypothesized that sole inhibition of angiogenesis can provide physiological cues to direct in vivo differentiation of uncommitted MSCs to stable cartilage formation. Human MSCs were retrovirally transduced to express a decoy soluble vascular endothelial growth factor (VEGF) receptor-2 (sFlk1), which efficiently sequesters endogenous VEGF in vivo, seeded on collagen sponges and immediately implanted ectopically in nude mice. Although naïve cells formed vascularized fibrous tissue, sFlk1-MSCs abolished vascular ingrowth into engineered constructs, which efficiently and reproducibly developed into hyaline cartilage. The generated cartilage was phenotypically stable and showed no sign of hypertrophic evolution up to 12 weeks. In vitro analyses indicated that spontaneous chondrogenic differentiation by blockade of angiogenesis was related to the generation of a hypoxic environment, in turn activating the transforming growth factor-β pathway. These findings suggest that VEGF blockade is a robust strategy to enhance cartilage repair by endogenous or grafted mesenchymal progenitors. This article outlines the general paradigm of controlling the fate of implanted stem/progenitor cells by engineering their ability to establish specific microenvironmental conditions rather than directly providing individual morphogenic cues. Chondrogenic differentiation of mesenchymal stromal/stem cells (MSCs) is typically targeted by morphogen delivery, which is often associated with limited efficiency, stability, and robustness. This article proposes a strategy to engineer MSCs with the capacity to establish specific microenvironmental conditions, supporting their own targeted differentiation program. Sole blockade of angiogenesis mediated by transduction for sFlk-1, without delivery of additional morphogens, is sufficient for inducing MSC chondrogenic differentiation. The findings represent a relevant step forward in the field because the method allowed reducing interdonor variability in MSC differentiation efficiency and, importantly, onset of a stable, nonhypertrophic chondrocyte phenotype. ©AlphaMed Press.

High‐Performance Lithium‐Oxygen Battery Electrolyte Derived from Optimum Combination of Solvent and Lithium Salt

PubMed Central

Ahn, Su Mi; Suk, Jungdon; Kim, Do Youb; Kim, Hwan Kyu

2017-01-01

Abstract To fabricate a sustainable lithium‐oxygen (Li‐O2) battery, it is crucial to identify an optimum electrolyte. Herein, it is found that tetramethylene sulfone (TMS) and lithium nitrate (LiNO3) form the optimum electrolyte, which greatly reduces the overpotential at charge, exhibits superior oxygen efficiency, and allows stable cycling for 100 cycles. Linear sweep voltammetry (LSV) and differential electrochemical mass spectrometry (DEMS) analyses reveal that neat TMS is stable to oxidative decomposition and exhibit good compatibility with a lithium metal. But, when TMS is combined with typical lithium salts, its performance is far from satisfactory. However, the TMS electrolyte containing LiNO3 exhibits a very low overpotential, which minimizes the side reactions and shows high oxygen efficiency. LSV‐DEMS study confirms that the TMS‐LiNO3 electrolyte efficiently produces NO2 −, which initiates a redox shuttle reaction. Interestingly, this NO2 −/NO2 redox reaction derived from the LiNO3 salt is not very effective in solvents other than TMS. Compared with other common Li‐O2 solvents, TMS seems optimum solvent for the efficient use of LiNO3 salt. Good compatibility with lithium metal, high dielectric constant, and low donicity of TMS are considered to be highly favorable to an efficient NO2 −/NO2 redox reaction, which results in a high‐performance Li‐O2 battery. PMID:29051863

Biodegradable poly-ε-caprolactone microcarriers for efficient production of human mesenchymal stromal cells and secreted cytokines in batch and fed-batch bioreactors.

PubMed

Lam, Alan Tin-Lun; Li, Jian; Toh, Jessica Pei-Wen; Sim, Eileen Jia-Hui; Chen, Allen Kuan-Liang; Chan, Jerry Kok-Yen; Choolani, Mahesh; Reuveny, Shaul; Birch, William R; Oh, Steve Kah-Weng

2017-03-01

Large numbers of human mesenchymal stromal cells (MSCs) used for a variety of applications in tissue engineering and cell therapy can be generated by scalable expansion in a bioreactor using microcarriers (MCs) systems. However, the enzymatic digestion process needed to detach cells from the growth surface can affect cell viability and potentially the potency and differentiation efficiency. Thus, the main aim of our study was to develop biocompatible and biodegradable MCs that can support high MSC yields while maintaining their differentiation capability and potency. After cell expansion, the cells that covered MCs can be directly implanted in vivo without the need for cell harvesting or use of scaffold. Poly-ε-caprolactone (PCL) is known as a biocompatible and biodegradable material. However, it cannot be used for generation of MCs because its high density (1.14 g/cm 3 ) would exclude its applicability for suspension MCs in stirred reactors. In this article, we describe expansion and potency of MSCs propagated on low-density (1.06 g/cm 3 ) porous PCL MCs coated with extracellular matrices (LPCLs) in suspended stirred reactors. Using these LPCLs, cell yields of about 4 × 10 4 cells/cm 2 and 7- to 10-fold increases were obtained using four different MSC lines (bone marrow, cord blood, fetal and Wharton's jelly). These yields were comparable with those obtained using non-degradable MCs (Cytodex 3) and higher than two-dimensional monolayer (MNL) cultures. A fed-batch process, which demonstrated faster cell expansion (4.5 × 10 4 cells/cm 2 in 5 days as compared with 7 days in batch culture) and about 70% reduction in growth media usage, was developed and scaled up from 100-mL spinner flask to 1-L controlled bioreactor. Surface marker expression, trilineage differentiation and clonogenic potential of the MSCs expanded on LPCL were not affected. Cytokine secretion kinetics, which occurred mostly during late logarithmic phase, was usually comparable with that obtained in Cytodex 3 cultures and higher than MNL cultures. In conclusion, biodegradable LPCL can be used to efficiently expand a variety of MSC lines in stirred scalable reactors in a cost-effective manner while maintaining surface markers expression, differentiation capability and high levels of cytokine secretion. This study is the first step in testing these cell-biodegradable porous MC aggregates for tissue engineering and cell therapy, such as bone and cartilage regeneration, or wound healing. Copyright © 2017 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Integration mechanisms and hospital efficiency in integrated health care delivery systems.

PubMed

Wan, Thomas T H; Lin, Blossom Yen-Ju; Ma, Allen

2002-04-01

This study analyzes integration mechanisms that affect system performances measured by indicators of efficiency in integrated delivery systems (IDSs) in the United States. The research question is, do integration mechanisms improve IDSs' efficiency in hospital care? American Hospital Association's Annual Survey (1998) and Dorenfest's Survey on Information Systems in Integrated Healthcare Delivery Systems (1998) were used to conduct the study, using IDS as the unit of analysis. A covariance structure equation model of the effects of system integration mechanisms on IDS performance was formulated and validated by an empirical examination of IDSs. The study sample includes 973 hospital-based integrated health care delivery systems operating in the United States, carried in the list of Dorenfests Survey on Information Systems in Integrated Health care Delivery Systems. The measurement indicators of system integration mechanisms are categorized into six related domains: informatic integration, case management, hybrid physician-hospital integration, forward integration, backward integration, and high tech medical services. The multivariate analysis reveals that integration mechanisms in system operation are positively correlated and positively affect IDSs' efficiency. The six domains of integration mechanisms account for 58.9% of the total variance in hospital performance. The service differentiation strategy such as having more high tech medical services have much stronger influences on efficiency than other integration mechanisms do. The beneficial effects of integration mechanisms have been realized in IDS performance. High efficiency in hospital care can be achieved by employing proper integration strategies in operations.

An Optimized and Simplified System of Mouse Embryonic Stem Cell Cardiac Differentiation for the Assessment of Differentiation Modifiers

PubMed Central

Hartman, Matthew E.; Librande, Jason R.; Medvedev, Ivan O.; Ahmad, Rabiah N.; Moussavi-Harami, Farid; Gupta, Pritha P.; Chien, Wei-Ming; Chin, Michael T.

2014-01-01

Generating cardiomyocytes from embryonic stem cells is an important technique for understanding cardiovascular development, the origins of cardiovascular diseases and also for providing potential reagents for cardiac repair. Numerous methods have been published but often are technically challenging, complex, and are not easily adapted to assessment of specific gene contributions to cardiac myocyte differentiation. Here we report the development of an optimized protocol to induce the differentiation of mouse embryonic stem cells to cardiac myocytes that is simplified and easily adapted for genetic studies. Specifically, we made four critical findings that distinguish our protocol: 1) mouse embryonic stem cells cultured in media containing CHIR99021 and PD0325901 to maintain pluripotency will efficiently form embryoid bodies containing precardiac mesoderm when cultured in these factors at a reduced dosage, 2) low serum conditions promote cardiomyocyte differentiation and can be used in place of commercially prepared StemPro nutrient supplement, 3) the Wnt inhibitor Dkk-1 is dispensable for efficient cardiac differentiation and 4) tracking differentiation efficiency may be done with surface expression of PDGFRα alone. In addition, cardiac mesodermal precursors generated by this system can undergo lentiviral infection to manipulate the expression of specific target molecules to assess effects on cardiac myocyte differentiation and maturation. Using this approach, we assessed the effects of CHF1/Hey2 on cardiac myocyte differentiation, using both gain and loss of function. Overexpression of CHF1/Hey2 at the cardiac mesoderm stage had no apparent effect on cardiac differentiation, while knockdown of CHF1/Hey2 resulted in increased expression of atrial natriuretic factor and connexin 43, suggesting an alteration in the phenotype of the cardiomyocytes. In summary we have generated a detailed and simplified protocol for generating cardiomyocytes from mES cells that is optimized for investigating factors that affect cardiac differentiation. PMID:24667642

Approaches to quantitating the results of differentially dyed cottons

USDA-ARS?s Scientific Manuscript database

The differential dyeing (DD) method has served as a subjective method for visually determining immature cotton fibers. In an attempt to quantitate the results of the differential dyeing method, and thus offer an efficient means of elucidating cotton maturity without visual discretion, image analysi...

Direct Validation of Differential Prediction.

ERIC Educational Resources Information Center

Lunneborg, Clifford E.

Using academic achievement data for 655 University students, direct validation of differential predictions based on a battery of aptitude/achievement measures selected for their differential prediction efficiency was attempted. In the cross-validation of the prediction of actual differences among five academic area GPA's, this set of differential…

A complex mechanism determines polarity of DNA replication fork arrest by the replication terminator complex of Bacillus subtilis.

PubMed

Duggin, Iain G; Matthews, Jacqueline M; Dixon, Nicholas E; Wake, R Gerry; Mackay, Joel P

2005-04-01

Two dimers of the replication terminator protein (RTP) of Bacillus subtilis bind to a chromosomal DNA terminator site to effect polar replication fork arrest. Cooperative binding of the dimers to overlapping half-sites within the terminator is essential for arrest. It was suggested previously that polarity of fork arrest is the result of the RTP dimer at the blocking (proximal) side within the complex binding very tightly and the permissive-side RTP dimer binding relatively weakly. In order to investigate this "differential binding affinity" model, we have constructed a series of mutant terminators that contain half-sites of widely different RTP binding affinities in various combinations. Although there appeared to be a correlation between binding affinity at the proximal half-site and fork arrest efficiency in vivo for some terminators, several deviated significantly from this correlation. Some terminators exhibited greatly reduced binding cooperativity (and therefore have reduced affinity at each half-site) but were highly efficient in fork arrest, whereas one terminator had normal affinity over the proximal half-site, yet had low fork arrest efficiency. The results show clearly that there is no direct correlation between the RTP binding affinity (either within the full complex or at the proximal half-site within the full complex) and the efficiency of replication fork arrest in vivo. Thus, the differential binding affinity over the proximal and distal half-sites cannot be solely responsible for functional polarity of fork arrest. Furthermore, efficient fork arrest relies on features in addition to the tight binding of RTP to terminator DNA.

A new inverter topology using GTO commutation. [Gate Turn Off thyristor

NASA Technical Reports Server (NTRS)

Rippel, W. E.

1983-01-01

A new N-phase, forced commutated bridge inverter topology has been developed wherein a single Gate Turn Off Thyristor (GTO) is used to commutate each of 2N main Thyristors (SCRs). Since, for most applications, the primary loss mechanism is the SCR forward drop, very high efficiencies are possible. Compared with conventional pure SCR and pure GTO inverters, cost per kW is lower - in the former case due to the large cost differential between GTOs and SCRs. Other advantages of the new inverter include high power density, low switching losses and stresses, modulation flexibility and amenability to high voltage and high frequency operation.

Efficient solution of ordinary differential equations modeling electrical activity in cardiac cells.

PubMed

Sundnes, J; Lines, G T; Tveito, A

2001-08-01

The contraction of the heart is preceded and caused by a cellular electro-chemical reaction, causing an electrical field to be generated. Performing realistic computer simulations of this process involves solving a set of partial differential equations, as well as a large number of ordinary differential equations (ODEs) characterizing the reactive behavior of the cardiac tissue. Experiments have shown that the solution of the ODEs contribute significantly to the total work of a simulation, and there is thus a strong need to utilize efficient solution methods for this part of the problem. This paper presents how an efficient implicit Runge-Kutta method may be adapted to solve a complicated cardiac cell model consisting of 31 ODEs, and how this solver may be coupled to a set of PDE solvers to provide complete simulations of the electrical activity.

Comparative study of human-induced pluripotent stem cells derived from bone marrow cells, hair keratinocytes, and skin fibroblasts.

PubMed

Streckfuss-Bömeke, Katrin; Wolf, Frieder; Azizian, Azadeh; Stauske, Michael; Tiburcy, Malte; Wagner, Stefan; Hübscher, Daniela; Dressel, Ralf; Chen, Simin; Jende, Jörg; Wulf, Gerald; Lorenz, Verena; Schön, Michael P; Maier, Lars S; Zimmermann, Wolfram H; Hasenfuss, Gerd; Guan, Kaomei

2013-09-01

Induced pluripotent stem cells (iPSCs) provide a unique opportunity for the generation of patient-specific cells for use in disease modelling, drug screening, and regenerative medicine. The aim of this study was to compare human-induced pluripotent stem cells (hiPSCs) derived from different somatic cell sources regarding their generation efficiency and cardiac differentiation potential, and functionalities of cardiomyocytes. We generated hiPSCs from hair keratinocytes, bone marrow mesenchymal stem cells (MSCs), and skin fibroblasts by using two different virus systems. We show that MSCs and fibroblasts are more easily reprogrammed than keratinocytes. This corresponds to higher methylation levels of minimal promoter regions of the OCT4 and NANOG genes in keratinocytes than in MSCs and fibroblasts. The success rate and reprogramming efficiency was significantly higher by using the STEMCCA system than the OSNL system. All analysed hiPSCs are pluripotent and show phenotypical characteristics similar to human embryonic stem cells. We studied the cardiac differentiation efficiency of generated hiPSC lines (n = 24) and found that MSC-derived hiPSCs exhibited a significantly higher efficiency to spontaneously differentiate into beating cardiomyocytes when compared with keratinocyte-, and fibroblast-derived hiPSCs. There was no significant difference in the functionalities of the cardiomyocytes derived from hiPSCs with different origins, showing the presence of pacemaker-, atrial-, ventricular- and Purkinje-like cardiomyocytes, and exhibiting rhythmic Ca2+ transients and Ca2+ sparks in hiPSC-derived cardiomyocytes. Furthermore, spontaneously and synchronously beating and force-developing engineered heart tissues were generated. Human-induced pluripotent stem cells can be reprogrammed from all three somatic cell types, but with different efficiency. All analysed iPSCs can differentiate into cardiomyocytes, and the functionalities of cardiomyocytes derived from different cell origins are similar. However, MSC-derived hiPSCs revealed a higher cardiac differentiation efficiency than keratinocyte- and fibroblast-derived hiPSCs.

Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing.

PubMed

Mora-Castilla, Sergio; To, Cuong; Vaezeslami, Soheila; Morey, Robert; Srinivasan, Srimeenakshi; Dumdie, Jennifer N; Cook-Andersen, Heidi; Jenkins, Joby; Laurent, Louise C

2016-08-01

As the cost of next-generation sequencing has decreased, library preparation costs have become a more significant proportion of the total cost, especially for high-throughput applications such as single-cell RNA profiling. Here, we have applied novel technologies to scale down reaction volumes for library preparation. Our system consisted of in vitro differentiated human embryonic stem cells representing two stages of pancreatic differentiation, for which we prepared multiple biological and technical replicates. We used the Fluidigm (San Francisco, CA) C1 single-cell Autoprep System for single-cell complementary DNA (cDNA) generation and an enzyme-based tagmentation system (Nextera XT; Illumina, San Diego, CA) with a nanoliter liquid handler (mosquito HTS; TTP Labtech, Royston, UK) for library preparation, reducing the reaction volume down to 2 µL and using as little as 20 pg of input cDNA. The resulting sequencing data were bioinformatically analyzed and correlated among the different library reaction volumes. Our results showed that decreasing the reaction volume did not interfere with the quality or the reproducibility of the sequencing data, and the transcriptional data from the scaled-down libraries allowed us to distinguish between single cells. Thus, we have developed a process to enable efficient and cost-effective high-throughput single-cell transcriptome sequencing. © 2016 Society for Laboratory Automation and Screening.

An intermittent rocking platform for integrated expansion and differentiation of human pluripotent stem cells to cardiomyocytes in suspended microcarrier cultures.

PubMed

Ting, Sherwin; Chen, Allen; Reuveny, Shaul; Oh, Steve

2014-09-01

The development of novel platforms for large scale production of human embryonic stem cells (hESC) derived cardiomyocytes (CM) becomes more crucial as the demand for CMs in preclinical trials, high throughput cardio toxicity assays and future regenerative therapeutics rises. To this end, we have designed a microcarrier (MC) suspension agitated platform that integrates pluripotent hESC expansion followed by CM differentiation in a continuous, homogenous process. Hydrodynamic shear stresses applied during the hESC expansion and CM differentiation steps drastically reduced the capability of the cells to differentiate into CMs. Applying vigorous stirring during pluripotent hESC expansion on Cytodex 1 MC in spinner cultures resulted in low CM yields in the following differentiation step (cardiac troponin-T (cTnT): 22.83±2.56%; myosin heavy chain (MHC): 19.30±5.31%). Whereas the lower shear experienced in side to side rocker (wave type) platform resulted in higher CM yields (cTNT: 47.50±7.35%; MHC: 42.85±2.64%). The efficiency of CM differentiation is also affected by the hydrodynamic shear stress applied during the first 3days of the differentiation stage. Even low shear applied continuously by side to side rocker agitation resulted in very low CM differentiation efficiency (cTnT<5%; MHC<2%). Simply by applying intermittent agitation during these 3days followed by continuous agitation for the subsequent 9days, CM differentiation efficiency can be substantially increased (cTNT: 65.73±10.73%; MHC: 59.73±9.17%). These yields are 38.3% and 39.3% higher (for cTnT and MHC respectively) than static culture control. During the hESC expansion phase, cells grew on continuously agitated rocker platform as pluripotent cell/MC aggregates (166±88×10(5)μm(2)) achieving a cell concentration of 3.74±0.55×10(6)cells/mL (18.89±2.82 fold expansion) in 7days. These aggregates were further differentiated into CMs using a WNT modulation differentiation protocol for the subsequent 12days on a rocking platform with an intermittent agitation regime during the first 3days. Collectively, the integrated MC rocker platform produced 190.5±58.8×10(6) CMs per run (31.75±9.74 CM/hESC seeded). The robustness of the system was demonstrated by using 2 cells lines, hESC (HES-3) and human induced pluripotent stem cell (hiPSC) IMR-90. The CM/MC aggregates formed extensive sarcomeres that exhibited cross-striations confirming cardiac ontogeny. Functionality of the CMs was demonstrated by monitoring the effect of inotropic drug, Isoproterenol on beating frequency. In conclusion, we have developed a simple robust and scalable platform that integrates both hESC expansion and CM differentiation in one unit process which is capable of meeting the need for large amounts of CMs. Copyright © 2014. Published by Elsevier B.V.

Differential effects of high-fat diets varying in fatty acid composition on the efficiency of lean and fat tissue deposition during weight recovery after low food intake.

PubMed

Dulloo, A G; Mensi, N; Seydoux, J; Girardier, L

1995-02-01

The energetics of body weight recovery after low food intake was examined in the rat during refeeding for 2 weeks with isocaloric amounts of high-fat (HF) diets providing 50% of energy as either lard, coconut oil, olive oil, safflower oil, menhaden fish oil, or a mixture of all these fat types. The results indicate that for both body fat and protein, the efficiency of deposition was dependent on the dietary fat type. The most striking differences were found (1) between diets rich in n-3 and n-6 polyunsaturated fatty acids (PUFA), with the diet high in fish oil resulting in a greater body fat deposition and lower protein gain than the diet high in safflower oil; and (2) between diets rich in long-chain (LCT) and medium-chain triglycerides (MCT), with the diet high in lard resulting in a greater gain in both body fat and protein than the diet high in coconut oil. Furthermore, the diet high in olive oil (a monounsaturated fat) and the mixed-fat diet (containing all fat types) were found to be similar to the fish oil diet in that the efficiency of fat deposition was greater (and that of protein gain lower) than with the diet high in safflower oil. Neither the efficiency of fat gain nor that of protein gain were found to correlate with fasting plasma insulin, the insulin to glucose ratio, or plasma lipids.(ABSTRACT TRUNCATED AT 250 WORDS)

RAMAN spectroscopy imaging improves the diagnosis of papillary thyroid carcinoma

NASA Astrophysics Data System (ADS)

Rau, Julietta V.; Graziani, Valerio; Fosca, Marco; Taffon, Chiara; Rocchia, Massimiliano; Crucitti, Pierfilippo; Pozzilli, Paolo; Onetti Muda, Andrea; Caricato, Marco; Crescenzi, Anna

2016-10-01

Recent investigations strongly suggest that Raman spectroscopy (RS) can be used as a clinical tool in cancer diagnosis to improve diagnostic accuracy. In this study, we evaluated the efficiency of Raman imaging microscopy to discriminate between healthy and neoplastic thyroid tissue, by analyzing main variants of Papillary Thyroid Carcinoma (PTC), the most common type of thyroid cancer. We performed Raman imaging of large tissue areas (from 100 × 100 μm2 up to 1 × 1 mm2), collecting 38 maps containing about 9000 Raman spectra. Multivariate statistical methods, including Linear Discriminant Analysis (LDA), were applied to translate Raman spectra differences between healthy and PTC tissues into diagnostically useful information for a reliable tissue classification. Our study is the first demonstration of specific biochemical features of the PTC profile, characterized by significant presence of carotenoids with respect to the healthy tissue. Moreover, this is the first evidence of Raman spectra differentiation between classical and follicular variant of PTC, discriminated by LDA with high efficiency. The combined histological and Raman microscopy analyses allow clear-cut integration of morphological and biochemical observations, with dramatic improvement of efficiency and reliability in the differential diagnosis of neoplastic thyroid nodules, paving the way to integrative findings for tumorigenesis and novel therapeutic strategies.

NGF-conjugated iron oxide nanoparticles promote differentiation and outgrowth of PC12 cells

NASA Astrophysics Data System (ADS)

Marcus, M.; Skaat, H.; Alon, N.; Margel, S.; Shefi, O.

2014-12-01

The search for regenerative agents that promote neuronal differentiation and repair is of great importance. Nerve growth factor (NGF) which is an essential contributor to neuronal differentiation has shown high pharmacological potential for the treatment of central neurodegenerative diseases such as Alzheimer's and Parkinson's. However, growth factors undergo rapid degradation, leading to a short biological half-life. In our study, we describe a new nano-based approach to enhance the NGF activity resulting in promoted neuronal differentiation. We covalently conjugated NGF to iron oxide nanoparticles (NGF-NPs) and studied the effect of the novel complex on the differentiation of PC12 cells. We found that the NGF-NP treatment, at the same concentration as free NGF, significantly promoted neurite outgrowth and increased the complexity of the neuronal branching trees. Examination of neuronal differentiation gene markers demonstrated higher levels of expression in PC12 cells treated with the conjugated factor. By manipulating the NGF specific receptor, TrkA, we have demonstrated that NGF-NPs induce cell differentiation via the regular pathway. Importantly, we have shown that NGF-NPs undergo slower degradation than free NGF, extending their half-life and increasing NGF availability. Even a low concentration of conjugated NGF treatment has led to an effective response. We propose the use of the NGF-NP complex which has magnetic characteristics, also as a useful method to enhance NGF efficiency and activity, thus, paving the way for substantial neuronal repair therapeutics.The search for regenerative agents that promote neuronal differentiation and repair is of great importance. Nerve growth factor (NGF) which is an essential contributor to neuronal differentiation has shown high pharmacological potential for the treatment of central neurodegenerative diseases such as Alzheimer's and Parkinson's. However, growth factors undergo rapid degradation, leading to a short biological half-life. In our study, we describe a new nano-based approach to enhance the NGF activity resulting in promoted neuronal differentiation. We covalently conjugated NGF to iron oxide nanoparticles (NGF-NPs) and studied the effect of the novel complex on the differentiation of PC12 cells. We found that the NGF-NP treatment, at the same concentration as free NGF, significantly promoted neurite outgrowth and increased the complexity of the neuronal branching trees. Examination of neuronal differentiation gene markers demonstrated higher levels of expression in PC12 cells treated with the conjugated factor. By manipulating the NGF specific receptor, TrkA, we have demonstrated that NGF-NPs induce cell differentiation via the regular pathway. Importantly, we have shown that NGF-NPs undergo slower degradation than free NGF, extending their half-life and increasing NGF availability. Even a low concentration of conjugated NGF treatment has led to an effective response. We propose the use of the NGF-NP complex which has magnetic characteristics, also as a useful method to enhance NGF efficiency and activity, thus, paving the way for substantial neuronal repair therapeutics. Electronic supplementary information (ESI) available: Conjugation ratio determination and supplementary figures. See DOI: 10.1039/c4nr05193a

Cloud-based solution to identify statistically significant MS peaks differentiating sample categories.

PubMed

Ji, Jun; Ling, Jeffrey; Jiang, Helen; Wen, Qiaojun; Whitin, John C; Tian, Lu; Cohen, Harvey J; Ling, Xuefeng B

2013-03-23

Mass spectrometry (MS) has evolved to become the primary high throughput tool for proteomics based biomarker discovery. Until now, multiple challenges in protein MS data analysis remain: large-scale and complex data set management; MS peak identification, indexing; and high dimensional peak differential analysis with the concurrent statistical tests based false discovery rate (FDR). "Turnkey" solutions are needed for biomarker investigations to rapidly process MS data sets to identify statistically significant peaks for subsequent validation. Here we present an efficient and effective solution, which provides experimental biologists easy access to "cloud" computing capabilities to analyze MS data. The web portal can be accessed at http://transmed.stanford.edu/ssa/. Presented web application supplies large scale MS data online uploading and analysis with a simple user interface. This bioinformatic tool will facilitate the discovery of the potential protein biomarkers using MS.

Research on channel characteristics of differential multi pulse position modulation without background noise

NASA Astrophysics Data System (ADS)

Gao, Zhuo; Zhan, Weida; Sun, Quan; Hao, Ziqiang

2018-04-01

Differential multi-pulse position modulation (DMPPM) is a new type of modulation technology. There is a fast transmission rate, high bandwidth utilization, high modulation rate characteristics. The study of DMPPM modulation has important scientific value and practical significance. Channel capacity is one of the important indexes to measure the communication capability of communication system, and studying the channel capacity of DMPPM without background noise is the key to analyze the characteristics of DMPPM. The DMPPM theoretical model is established. The symbol structure of DMPPM with guard time slot is analyzed, and the channel capacity expression of DMPPM is deduced. Simulation analysis by MATLAB. The curves of unit channel capacity and capacity efficiency at different pulse and photon counting rates are analyzed. The results show that DMPPM is more advantageous than multi-pulse position modulation (MPPM), and is more suitable for future wireless optical communication system.

Nuclear surface diffuseness revealed in nucleon-nucleus diffraction

NASA Astrophysics Data System (ADS)

Hatakeyama, S.; Horiuchi, W.; Kohama, A.

2018-05-01

The nuclear surface provides useful information on nuclear radius, nuclear structure, as well as properties of nuclear matter. We discuss the relationship between the nuclear surface diffuseness and elastic scattering differential cross section at the first diffraction peak of high-energy nucleon-nucleus scattering as an efficient tool in order to extract the nuclear surface information from limited experimental data involving short-lived unstable nuclei. The high-energy reaction is described by a reliable microscopic reaction theory, the Glauber model. Extending the idea of the black sphere model, we find one-to-one correspondence between the nuclear bulk structure information and proton-nucleus elastic scattering diffraction peak. This implies that we can extract both the nuclear radius and diffuseness simultaneously, using the position of the first diffraction peak and its magnitude of the elastic scattering differential cross section. We confirm the reliability of this approach by using realistic density distributions obtained by a mean-field model.

Role of alpha- and beta-adrenergic receptors in cardiomyocyte differentiation from murine-induced pluripotent stem cells.

PubMed

Li, Xiao-Li; Zeng, Di; Chen, Yan; Ding, Lu; Li, Wen-Ju; Wei, Ting; Ou, Dong-Bo; Yan, Song; Wang, Bin; Zheng, Qiang-Sun

2017-02-01

Induced pluripotent stem cell (iPSC)-derived cardiomyocytes are a promising source of cells for regenerative heart disease therapies, but progress towards their use has been limited by their low differentiation efficiency and high cellular heterogeneity. Previous studies have demonstrated expression of adrenergic receptors (ARs) in stem cells after differentiation; however, roles of ARs in fate specification of stem cells, particularly in cardiomyocyte differentiation and development, have not been characterized. Murine-induced pluripotent stem cells (miPSCs) were cultured in hanging drops to form embryoid bodies, cells of which were then differentiated into cardiomyocytes. To determine whether ARs regulated miPSC differentiation into cardiac lineages, effects of the AR agonist, epinephrine (EPI), on miPSC differentiation and underlying signalling mechanisms, were evaluated. Treatment with EPI, robustly enhanced miPSC cardiac differentiation, as indicated by increased expression levels of cardiac-specific markers, GATA4, Nkx2.5 and Tnnt2. Although β-AR signalling is the foremost signalling pathway in cardiomyocytes, EPI-enhanced cardiac differentiation depended more on α-AR signalling than β-AR signalling. In addition, selective activation of α 1 -AR signalling with specific agonists induced vigorous cardiomyocyte differentiation, whereas selective activation of α 2 - or β-AR signalling induced no or less differentiation, respectively. EPI- and α 1 -AR-dependent cardiomyocyte differentiation from miPSCs occurred through specific promotion of CPC proliferation via the MEK-ERK1/2 pathway and regulation of miPS cell-cycle progression. These results demonstrate that activation of ARs, particularly of α 1 -ARs, promoted miPSC differentiation into cardiac lineages via MEK-ERK1/2 signalling. © 2016 John Wiley & Sons Ltd.

Investigating market efficiency through a forecasting model based on differential equations

NASA Astrophysics Data System (ADS)

de Resende, Charlene C.; Pereira, Adriano C. M.; Cardoso, Rodrigo T. N.; de Magalhães, A. R. Bosco

2017-05-01

A new differential equation based model for stock price trend forecast is proposed as a tool to investigate efficiency in an emerging market. Its predictive power showed statistically to be higher than the one of a completely random model, signaling towards the presence of arbitrage opportunities. Conditions for accuracy to be enhanced are investigated, and application of the model as part of a trading strategy is discussed.

Advanced gearbox technology

NASA Technical Reports Server (NTRS)

Anderson, N. E.; Cedoz, R. W.; Salama, E. E.; Wagner, D. A.

1987-01-01

An advanced 13,000 HP, counterrotating (CR) gearbox was designed and successfully tested to provide a technology base for future designs of geared propfan propulsion systems for both commercial and military aircraft. The advanced technology CR gearbox was designed for high efficiency, low weight, long life, and improved maintainability. The differential planetary CR gearbox features double helical gears, double row cylindrical roller bearings integral with planet gears, tapered roller prop support bearings, and a flexible ring gear and diaphragm to provide load sharing. A new Allison propfan back-to-back gearbox test facility was constructed. Extensive rotating and stationary instrumentation was used to measure temperature, strain, vibration, deflection and efficiency under representative flight operating conditions. The tests verified smooth, efficient gearbox operation. The highly-instrumented advanced CR gearbox was successfully tested to design speed and power (13,000 HP), and to a 115 percent overspeed condition. Measured CR gearbox efficiency was 99.3 percent at the design point based on heat loss to the oil. Tests demonstrated low vibration characteristics of double helical gearing, proper gear tooth load sharing, low stress levels, and the high load capacity of the prop tapered roller bearings. Applied external prop loads did not significantly affect gearbox temperature, vibration, or stress levels. Gearbox hardware was in excellent condition after the tests with no indication of distress.

1,25-dihydroxyvitamin D3 induces CCR10 expression in terminally differentiating human B cells.

PubMed

Shirakawa, Aiko-Konno; Nagakubo, Daisuke; Hieshima, Kunio; Nakayama, Takashi; Jin, Zhe; Yoshie, Osamu

2008-03-01

In the B cell lineage, CCR10 is known to be selectively expressed by plasma cells, especially those secreting IgA. In this study, we examined the regulation of CCR10 expression in terminally differentiating human B cells. As reported previously, IL-21 efficiently induced the differentiation of activated human CD19+ B cells into IgD-CD38+ plasma cells in vitro. A minor proportion of the resulting CD19+IgD-CD38+ cells expressed CCR10 at low levels. 1,25-Dihydroxyvitamin D3 (1,25-(OH)2D3), the active metabolite of vitamine D3, dramatically increased the proportion of CD19+IgD-CD38+ cells expressing high levels of CCR10. The 1,25-(OH)2D3 also increased the number of CCR10+ cells expressing surface IgA, although the majority of CCR10+ cells remained negative for surface IgA. Thus, 1,25-(OH)2D3 alone may not be sufficient for the induction of IgA expression in terminally differentiating human B cells. To further determine whether 1,25-(OH)2D3 directly induces CCR10 expression in terminally differentiating B cells, we next performed the analysis on the human CCR10 promoter. We identified a proximal Ets-1 site and an upstream potential vitamin D response element to be critical for the inducible expression of CCR10 by 1,25-(OH)2D3. We confirmed the specific binding of Ets-1 and 1,25-(OH)2D3-activated vitamin D receptor to the respective sites. In conclusion, 1,25-(OH)2D3 efficiently induces CCR10 expression in terminally differentiating human B cells in vitro. Furthermore, the human CCR10 promoter is cooperatively activated by Ets-1 and vitamin D receptor in the presence of 1,25-(OH)2D3.

Differentiated Staffing and Practice

ERIC Educational Resources Information Center

Christie, Kathy

2005-01-01

The development of the positions of nurse practitioner and physician assistant is a good example of differentiating staffing and practice to meet individual needs in an effective and cost-efficient way. This type of differentiation has been confined to the healthcare industry, principally to health maintenance organizations, but perhaps those in…

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

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

Mueller, C.; Marx, A.; Epp, S. W.

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore » Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

DOE PAGES

Mueller, C.; Marx, A.; Epp, S. W.; ...

2015-08-18

We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore » Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

Suppressive subtractive hybridization approach revealed differential expression of hypersensitive response and reactive oxygen species production genes in tea (Camellia sinensis (L.) O. Kuntze) leaves during Pestalotiopsis thea infection.

PubMed

Senthilkumar, Palanisamy; Thirugnanasambantham, Krishnaraj; Mandal, Abul Kalam Azad

2012-12-01

Tea (Camellia sinensis (L.) O. Kuntze) is an economically important plant cultivated for its leaves. Infection of Pestalotiopsis theae in leaves causes gray blight disease and enormous loss to the tea industry. We used suppressive subtractive hybridization (SSH) technique to unravel the differential gene expression pattern during gray blight disease development in tea. Complementary DNA from P. theae-infected and uninfected leaves of disease tolerant cultivar UPASI-10 was used as tester and driver populations respectively. Subtraction efficiency was confirmed by comparing abundance of β-actin gene. A total of 377 and 720 clones with insert size >250 bp from forward and reverse library respectively were sequenced and analyzed. Basic Local Alignment Search Tool analysis revealed 17 sequences in forward SSH library have high degree of similarity with disease and hypersensitive response related genes and 20 sequences with hypothetical proteins while in reverse SSH library, 23 sequences have high degree of similarity with disease and stress response-related genes and 15 sequences with hypothetical proteins. Functional analysis indicated unknown (61 and 59 %) or hypothetical functions (23 and 18 %) for most of the differentially regulated genes in forward and reverse SSH library, respectively, while others have important role in different cellular activities. Majority of the upregulated genes are related to hypersensitive response and reactive oxygen species production. Based on these expressed sequence tag data, putative role of differentially expressed genes were discussed in relation to disease. We also demonstrated the efficiency of SSH as a tool in enriching gray blight disease related up- and downregulated genes in tea. The present study revealed that many genes related to disease resistance were suppressed during P. theae infection and enhancing these genes by the application of inducers may impart better disease tolerance to the plants.

More efficient rejection of happy than of angry face distractors in visual search.

PubMed

Horstmann, Gernot; Scharlau, Ingrid; Ansorge, Ulrich

2006-12-01

In the present study, we examined whether the detection advantage for negative-face targets in crowds of positive-face distractors over positive-face targets in crowds of negative faces can be explained by differentially efficient distractor rejection. Search Condition A demonstrated more efficient distractor rejection with negative-face targets in positive-face crowds than vice versa. Search Condition B showed that target identity alone is not sufficient to account for this effect, because there was no difference in processing efficiency for positive- and negative-face targets within neutral crowds. Search Condition C showed differentially efficient processing with neutral-face targets among positive- or negative-face distractors. These results were obtained with both a within-participants (Experiment 1) and a between-participants (Experiment 2) design. The pattern of results is consistent with the assumption that efficient rejection of positive (more homogenous) distractors is an important determinant of performance in search among (face) distractors.

Unitary limit in crossed Andreev transport

DOE PAGES

Sadovskyy, I. A.; Lesovik, G. B.; Vinokur, V. M.

2015-10-08

One of the most promising approaches for generating spin- and energy-entangled electron pairs is splitting a Cooper pair into the metal through spatially separated terminals. Utilizing hybrid systems with the energy-dependent barriers at the superconductor/normal metal (NS) interfaces, one can achieve a practically 100% efficiency outcome of entangled electrons. We investigate a minimalistic one-dimensional model comprising a superconductor and two metallic leads and derive an expression for an electron-to-hole transmission probability as a measure of splitting efficiency. We find the conditions for achieving 100% efficiency and present analytical results for the differential conductance and differential noise.

Dendritic cell reprogramming by endogenously produced lactic acid.

PubMed

Nasi, Aikaterini; Fekete, Tünde; Krishnamurthy, Akilan; Snowden, Stuart; Rajnavölgyi, Eva; Catrina, Anca I; Wheelock, Craig E; Vivar, Nancy; Rethi, Bence

2013-09-15

The demand for controlling T cell responses via dendritic cell (DC) vaccines initiated a quest for reliable and feasible DC modulatory strategies that would facilitate cytotoxicity against tumors or tolerance in autoimmunity. We studied endogenous mechanisms in developing monocyte-derived DCs (MoDCs) that can induce inflammatory or suppressor programs during differentiation, and we identified a powerful autocrine pathway that, in a cell concentration-dependent manner, strongly interferes with inflammatory DC differentiation. MoDCs developing at low cell culture density have superior ability to produce inflammatory cytokines, to induce Th1 polarization, and to migrate toward the lymphoid tissue chemokine CCL19. On the contrary, MoDCs originated from dense cultures produce IL-10 but no inflammatory cytokines upon activation. DCs from high-density cultures maintained more differentiation plasticity and can develop to osteoclasts. The cell concentration-dependent pathway was independent of peroxisome proliferator-activated receptor γ (PPARγ), a known endogenous regulator of MoDC differentiation. Instead, it acted through lactic acid, which accumulated in dense cultures and induced an early and long-lasting reprogramming of MoDC differentiation. Our results suggest that the lactic acid-mediated inhibitory pathway could be efficiently manipulated in developing MoDCs to influence the immunogenicity of DC vaccines.

Comparison of Plasma Exosomes by Differential Ultracentrifugation and Solvent Precipitation Methods.

PubMed

Peng, Qiao; Zhang, Jing; Zhou, Gang

2018-06-01

Emerging evidence has identified that exosomes play a pivotal role in intercellular signal transmission. However, the standardized purification techniques to isolate high quality exosomes are still deficient at present. This study was to evaluate reproducibility and efficiency of differential ultracentrifugation and solvent precipitation-based kits by isolating plasma-derived exosomes from oral lichen planus patients. Morphology, exosomal biomarkers, particle size distribution, proteomic components, and protein yield of isolated exosomes were evaluated by transmission electron microscope, western blot, laser diffraction instrument, Coomassie staining, and BCA protein assay kit, respectively. TEM displayed representative cup-shaped morphology of exosomes and western blot identified exosomal biomarkers CD9 and CD63. The size distribution showed that particles by differential ultracentrifugation were mainly from 26.15 nm to 166.5 nm, while some of the particles obtained by solvent precipitation kits were larger than 1,000 nm. In addition, exosomes isolated by solvent precipitation kits showed a significantly higher amount of protein yield due to plasma albumin contamination. Both differential ultracentrifugation and precipitation based kits could successfully isolate plasma exosomes, and exosomes by differential ultracentrifugation were purer and more appropriate for further proteomic analysis.

Scheduled Relaxation Jacobi method: Improvements and applications

NASA Astrophysics Data System (ADS)

Adsuara, J. E.; Cordero-Carrión, I.; Cerdá-Durán, P.; Aloy, M. A.

2016-09-01

Elliptic partial differential equations (ePDEs) appear in a wide variety of areas of mathematics, physics and engineering. Typically, ePDEs must be solved numerically, which sets an ever growing demand for efficient and highly parallel algorithms to tackle their computational solution. The Scheduled Relaxation Jacobi (SRJ) is a promising class of methods, atypical for combining simplicity and efficiency, that has been recently introduced for solving linear Poisson-like ePDEs. The SRJ methodology relies on computing the appropriate parameters of a multilevel approach with the goal of minimizing the number of iterations needed to cut down the residuals below specified tolerances. The efficiency in the reduction of the residual increases with the number of levels employed in the algorithm. Applying the original methodology to compute the algorithm parameters with more than 5 levels notably hinders obtaining optimal SRJ schemes, as the mixed (non-linear) algebraic-differential system of equations from which they result becomes notably stiff. Here we present a new methodology for obtaining the parameters of SRJ schemes that overcomes the limitations of the original algorithm and provide parameters for SRJ schemes with up to 15 levels and resolutions of up to 215 points per dimension, allowing for acceleration factors larger than several hundreds with respect to the Jacobi method for typical resolutions and, in some high resolution cases, close to 1000. Most of the success in finding SRJ optimal schemes with more than 10 levels is based on an analytic reduction of the complexity of the previously mentioned system of equations. Furthermore, we extend the original algorithm to apply it to certain systems of non-linear ePDEs.

Divergence in DNA photorepair efficiency among genotypes from contrasting UV radiation environments in nature.

PubMed

Miner, Brooks E; Kulling, Paige M; Beer, Karlyn D; Kerr, Benjamin

2015-12-01

Populations of organisms routinely face abiotic selection pressures, and a central goal of evolutionary biology is to understand the mechanistic underpinnings of adaptive phenotypes. Ultraviolet radiation (UVR) is one of earth's most pervasive environmental stressors, potentially damaging DNA in any organism exposed to solar radiation. We explored mechanisms underlying differential survival following UVR exposure in genotypes of the water flea Daphnia melanica derived from natural ponds of differing UVR intensity. The UVR tolerance of a D. melanica genotype from a high-UVR habitat depended on the presence of visible and UV-A light wavelengths necessary for photoenzymatic repair of DNA damage, a repair pathway widely shared across the tree of life. We then measured the acquisition and repair of cyclobutane pyrimidine dimers, the primary form of UVR-caused DNA damage, in D. melanica DNA following experimental UVR exposure. We demonstrate that genotypes from high-UVR habitats repair DNA damage faster than genotypes from low-UVR habitats in the presence of visible and UV-A radiation necessary for photoenzymatic repair, but not in dark treatments. Because differences in repair rate only occurred in the presence of visible and UV-A radiation, we conclude that differing rates of DNA repair, and therefore differential UVR tolerance, are a consequence of variation in photoenzymatic repair efficiency. We then rule out a simple gene expression hypothesis for the molecular basis of differing repair efficiency, as expression of the CPD photolyase gene photorepair did not differ among D. melanica lineages, in both the presence and absence of UVR. © 2015 John Wiley & Sons Ltd.

Molecular thermal transistor: Dimension analysis and mechanism

NASA Astrophysics Data System (ADS)

Behnia, S.; Panahinia, R.

2018-04-01

Recently, large challenge has been spent to realize high efficient thermal transistors. Outstanding properties of DNA make it as an excellent nano material in future technologies. In this paper, we introduced a high efficient DNA based thermal transistor. The thermal transistor operates when the system shows an increase in the thermal flux despite of decreasing temperature gradient. This is what called as negative differential thermal resistance (NDTR). Based on multifractal analysis, we could distinguish regions with NDTR state from non-NDTR state. Moreover, Based on dimension spectrum of the system, it is detected that NDTR state is accompanied by ballistic transport regime. The generalized correlation sum (analogous to specific heat) shows that an irregular decrease in the specific heat induces an increase in the mean free path (mfp) of phonons. This leads to the occurrence of NDTR.

Let7a involves in neural stem cell differentiation relating with TLX level

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

Song, Juhyun; Cho, Kyoung Joo; Oh, Yumi

Neural stem cells (NSCs) have the potential for differentiation into neurons known as a groundbreaking therapeutic solution for central nervous system (CNS) diseases. To resolve the therapeutic efficiency of NSCs, recent researchers have focused on the study on microRNA's role in CNS. Some micro RNAs have been reported significant functions in NSC self-renewal and differentiation through the post-transcriptional regulation of neurogenesis genes. MicroRNA-Let7a (Let7a) has known as the regulator of diverse cellular mechanisms including cell differentiation and proliferation. In present study, we investigated whether Let7a regulates NSC differentiation by targeting the nuclear receptor TLX, which is an essential regulator ofmore » NSC self-renewal, proliferation and differentiation. We performed the following experiments: western blot analysis, TaqMan assay, RT-PCR, and immunocytochemistry to confirm the alteration of NSCs. Our data showed that let7a play important roles in controlling NSC fate determination. Thus, manipulating Let-7A and TLX could be a novel strategy to enhance the efficiency of NSC's neuronal differentiation for CNS disorders. - Highlights: • Let7a influences on NSC differentiation and proliferation. • Let7a involves in mainly NSC differentiation rather than proliferation. • Let7a positively regulates the TLX expression.« less

Protection relay of phase-shifting device with thyristor switch for high voltage power transmission lines

NASA Astrophysics Data System (ADS)

Lachugin, V. F.; Panfilov, D. I.; Akhmetov, I. M.; Astashev, M. G.; Shevelev, A. V.

2014-12-01

Problems of functioning of differential current protection systems of phase shifting devices (PSD) with mechanically changed coefficient of transformation of shunt transformer are analyzed. Requirements for devices of protection of PSD with thyristor switch are formulated. Based on use of nonlinear models of series-wound and shunt transformers of PSD modes of operation of major protection during PSD, switching to zero load operation and to operation under load and during short circuit operation were studied for testing PSD with failures. Use of the principle of duplicating by devices of differential current protection (with realization of functions of breaking) of failures of separate pares of PSD with thyristor switch was substantiated. To ensure protection sensitivity to the shunt transformer winding short circuit, in particular, to a short circuit that is not implemented in the current differential protection for PSD with mechanical switch, the differential current protection reacting to the amount of primary ampere-turns of high-voltage and low-voltage winding of this transformer was designed. Studies have shown that the use of differential current cutoff instead of overcurrent protection for the shunt transformer wndings allows one to provide the sensitivity during thyristor failure with the formation of a short circuit. The results of simulation mode for the PSD with switch thyristor designed to be installed as switching point of Voskhod-Tatarskaya-Barabinsk 220 kV transmission line point out the efficiency of the developed solutions that ensure reliable functioning of the PSD.

Development of an efficient fungal DNA extraction method to be used in random amplified polymorphic DNA-PCR analysis to differentiate cyclopiazonic acid mold producers.

PubMed

Sánchez, Beatriz; Rodríguez, Mar; Casado, Eva M; Martín, Alberto; Córdoba, Juan J

2008-12-01

A variety of previously established mechanical and chemical treatments to achieve fungal cell lysis combined with a semiautomatic system operated by a vacuum pump were tested to obtain DNA extract to be directly used in randomly amplified polymorphic DNA (RAPD)-PCR to differentiate cyclopiazonic acid-producing and -nonproducing mold strains. A DNA extraction method that includes digestion with proteinase K and lyticase prior to using a mortar and pestle grinding and a semiautomatic vacuum system yielded DNA of high quality in all the fungal strains and species tested, at concentrations ranging from 17 to 89 ng/microl in 150 microl of the final DNA extract. Two microliters of DNA extracted with this method was directly used for RAPD-PCR using primer (GACA)4. Reproducible RAPD fingerprints showing high differences between producer and nonproducer strains were observed. These differences in the RAPD patterns did not differentiate all the strains tested in clusters by cyclopiazonic acid production but may be very useful to distinguish cyclopiazonic acid producer strains from nonproducer strains by a simple RAPD analysis. Thus, the DNA extracts obtained could be used directly without previous purification and quantification for RAPD analysis to differentiate cyclopiazonic acid producer from nonproducer mold strains. This combined analysis could be adaptable to other toxigenic fungal species to enable differentiation of toxigenic and non-toxigenic molds, a procedure of great interest in food safety.

Differential Expression of Adhesion-Related Proteins and MAPK Pathways Lead to Suitable Osteoblast Differentiation of Human Mesenchymal Stem Cells Subpopulations.

PubMed

Leyva-Leyva, Margarita; López-Díaz, Annia; Barrera, Lourdes; Camacho-Morales, Alberto; Hernandez-Aguilar, Felipe; Carrillo-Casas, Erika M; Arriaga-Pizano, Lourdes; Calderón-Pérez, Jaime; García-Álvarez, Jorge; Orozco-Hoyuela, Gabriel; Piña-Barba, Cristina; Rojas-Martínez, Augusto; Romero-Díaz, Víktor; Lara-Arias, Jorge; Rivera-Bolaños, Nancy; López-Camarillo, César; Moncada-Saucedo, Nidia; Galván-De los Santos, Alejandra; Meza-Urzúa, Fátima; Villarreal-Gómez, Luis; Fuentes-Mera, Lizeth

2015-11-01

Cellular adhesion enables communication between cells and their environment. Adhesion can be achieved throughout focal adhesions and its components influence osteoblast differentiation of human mesenchymal stem cells (hMSCs). Because cell adhesion and osteoblast differentiation are closely related, this article aimed to analyze the expression profiles of adhesion-related proteins during osteoblastic differentiation of two hMSCs subpopulations (CD105(+) and CD105(-)) and propose a strategy for assembling bone grafts based on its adhesion ability. In vitro experiments of osteogenic differentiation in CD105(-) cells showed superior adhesion efficiency and 2-fold increase of α-actinin expression compared with CD105(+) cells at the maturation stage. Interestingly, levels of activated β1-integrin increased in CD105(-) cells during the process. Additionally, the CD105(-) subpopulation showed 3-fold increase of phosphorylated FAK(Y397) compared to CD105(+) cells. Results also indicate that ERK1/2 was activated during CD105(-) bone differentiation and participation of mitogen-activated protein kinase (MAPK)-p38 in CD105(+) differentiation through a focal adhesion kinase (FAK)-independent pathway. In vivo trial demonstrated that grafts containing CD105(-) showed osteocytes embedded in a mineralized matrix, promoted adequate graft integration, increased host vascular infiltration, and efficient intramembranous repairing. In contrast, grafts containing CD105(+) showed deficient endochondral ossification and fibrocartilaginous tissue. Based on the expression of α-actinin, FAKy,(397) and ERK1/2 activation, we define maturation stage as critical for bone graft assembling. By in vitro assays, CD105(-) subpopulation showed superior adhesion efficiency compared to CD105(+) cells. Considering in vitro and in vivo assays, this study suggests that integration of a scaffold with CD105(-) subpopulation at the maturation stage represents an attractive strategy for clinical use in orthopedic bioengineering.

A model and variance reduction method for computing statistical outputs of stochastic elliptic partial differential equations

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

Vidal-Codina, F., E-mail: fvidal@mit.edu; Nguyen, N.C., E-mail: cuongng@mit.edu; Giles, M.B., E-mail: mike.giles@maths.ox.ac.uk

We present a model and variance reduction method for the fast and reliable computation of statistical outputs of stochastic elliptic partial differential equations. Our method consists of three main ingredients: (1) the hybridizable discontinuous Galerkin (HDG) discretization of elliptic partial differential equations (PDEs), which allows us to obtain high-order accurate solutions of the governing PDE; (2) the reduced basis method for a new HDG discretization of the underlying PDE to enable real-time solution of the parameterized PDE in the presence of stochastic parameters; and (3) a multilevel variance reduction method that exploits the statistical correlation among the different reduced basismore » approximations and the high-fidelity HDG discretization to accelerate the convergence of the Monte Carlo simulations. The multilevel variance reduction method provides efficient computation of the statistical outputs by shifting most of the computational burden from the high-fidelity HDG approximation to the reduced basis approximations. Furthermore, we develop a posteriori error estimates for our approximations of the statistical outputs. Based on these error estimates, we propose an algorithm for optimally choosing both the dimensions of the reduced basis approximations and the sizes of Monte Carlo samples to achieve a given error tolerance. We provide numerical examples to demonstrate the performance of the proposed method.« less

Local polynomial chaos expansion for linear differential equations with high dimensional random inputs

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

Chen, Yi; Jakeman, John; Gittelson, Claude

2015-01-08

In this paper we present a localized polynomial chaos expansion for partial differential equations (PDE) with random inputs. In particular, we focus on time independent linear stochastic problems with high dimensional random inputs, where the traditional polynomial chaos methods, and most of the existing methods, incur prohibitively high simulation cost. Furthermore, the local polynomial chaos method employs a domain decomposition technique to approximate the stochastic solution locally. In each subdomain, a subdomain problem is solved independently and, more importantly, in a much lower dimensional random space. In a postprocesing stage, accurate samples of the original stochastic problems are obtained frommore » the samples of the local solutions by enforcing the correct stochastic structure of the random inputs and the coupling conditions at the interfaces of the subdomains. Overall, the method is able to solve stochastic PDEs in very large dimensions by solving a collection of low dimensional local problems and can be highly efficient. In our paper we present the general mathematical framework of the methodology and use numerical examples to demonstrate the properties of the method.« less

LETTER TO THE EDITOR: Iteratively-coupled propagating exterior complex scaling method for electron hydrogen collisions

NASA Astrophysics Data System (ADS)

Bartlett, Philip L.; Stelbovics, Andris T.; Bray, Igor

2004-02-01

A newly-derived iterative coupling procedure for the propagating exterior complex scaling (PECS) method is used to efficiently calculate the electron-impact wavefunctions for atomic hydrogen. An overview of this method is given along with methods for extracting scattering cross sections. Differential scattering cross sections at 30 eV are presented for the electron-impact excitation to the n = 1, 2, 3 and 4 final states, for both PECS and convergent close coupling (CCC), which are in excellent agreement with each other and with experiment. PECS results are presented at 27.2 eV and 30 eV for symmetric and asymmetric energy-sharing triple differential cross sections, which are in excellent agreement with CCC and exterior complex scaling calculations, and with experimental data. At these intermediate energies, the efficiency of the PECS method with iterative coupling has allowed highly accurate partial-wave solutions of the full Schrödinger equation, for L les 50 and a large number of coupled angular momentum states, to be obtained with minimal computing resources.

A moving mesh finite difference method for equilibrium radiation diffusion equations

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

Yang, Xiaobo, E-mail: xwindyb@126.com; Huang, Weizhang, E-mail: whuang@ku.edu; Qiu, Jianxian, E-mail: jxqiu@xmu.edu.cn

2015-10-01

An efficient moving mesh finite difference method is developed for the numerical solution of equilibrium radiation diffusion equations in two dimensions. The method is based on the moving mesh partial differential equation approach and moves the mesh continuously in time using a system of meshing partial differential equations. The mesh adaptation is controlled through a Hessian-based monitor function and the so-called equidistribution and alignment principles. Several challenging issues in the numerical solution are addressed. Particularly, the radiation diffusion coefficient depends on the energy density highly nonlinearly. This nonlinearity is treated using a predictor–corrector and lagged diffusion strategy. Moreover, the nonnegativitymore » of the energy density is maintained using a cutoff method which has been known in literature to retain the accuracy and convergence order of finite difference approximation for parabolic equations. Numerical examples with multi-material, multiple spot concentration situations are presented. Numerical results show that the method works well for radiation diffusion equations and can produce numerical solutions of good accuracy. It is also shown that a two-level mesh movement strategy can significantly improve the efficiency of the computation.« less

Differential pollen placement on an Old World nectar bat increases pollination efficiency

PubMed Central

Stewart, Alyssa B.; Dudash, Michele R.

2016-01-01

Background and Aims Plant species that share pollinators are potentially subject to non-adaptive interspecific pollen transfer, resulting in reduced reproductive success. Mechanisms that increase pollination efficiency between conspecific individuals are therefore highly beneficial. Many nocturnally flowering plant species in Thailand are pollinated by the nectar bat Eonycteris spelaea (Pteropodidae). This study tested the hypothesis that plant species within a community reduce interspecific pollen movement by placing pollen on different areas of the bat’s body. Methods Using flight cage trials, pollen transfer by E. spelaea was compared between conspecific versus heterospecific flowers across four bat-pollinated plant genera. Pollen from four locations on the bat’s body was also quantified to determine if pollen placement varies by plant species. Key Results It was found that E. spelaea transfers significantly more pollen between conspecific than heterospecific flowers, and that diverse floral designs produce significantly different patterns of pollen deposition on E. spelaea. Conclusions In the Old World tropics, differential pollen placement is a mechanism that reduces competition among bat-pollinated plant species sharing a common pollinator. PMID:26482654

Social humanoid robot SARA: development of the wrist mechanism

NASA Astrophysics Data System (ADS)

Penčić, M.; Rackov, M.; Čavić, M.; Kiss, I.; Cioată, V. G.

2018-01-01

This paper presents the development of a wrist mechanism for humanoid robots. The research was conducted within the project which develops social humanoid robot Sara - a mobile anthropomorphic platform for researching the social behaviour of robots. There are two basic ways for the realization of humanoid wrist. The first one is based on biologically inspired structures that have variable stiffness, and the second one on low backlash mechanisms that have high stiffness. Our solution is low backlash differential mechanism that requires small actuators. Based on the kinematic-dynamic requirements, a dynamic model of the robot wrist is formed. A dynamic simulation for several hand positions was performed and the driving torques of the wrist mechanism were determined. The realized wrist has 2 DOFs and enables movements in the direction of flexion/extension 115°, ulnar/radial deviation ±45° and the combination of these two movements. It consists of a differential mechanism with three spur bevel gears, two of which are driving and identical, while the last one is the driven gear to which the robot hand is attached. Power transmission and motion from the actuator to the input links of the differential mechanism is realized with two parallel placed identical gear mechanisms. The wrist mechanism has high carrying capacity and reliability, high efficiency, a compact design and low backlash that provides high positioning accuracy and repeatability of movements, which is essential for motion control.

Partial differential equations constrained combinatorial optimization on an adiabatic quantum computer

NASA Astrophysics Data System (ADS)

Chandra, Rishabh

Partial differential equation-constrained combinatorial optimization (PDECCO) problems are a mixture of continuous and discrete optimization problems. PDECCO problems have discrete controls, but since the partial differential equations (PDE) are continuous, the optimization space is continuous as well. Such problems have several applications, such as gas/water network optimization, traffic optimization, micro-chip cooling optimization, etc. Currently, no efficient classical algorithm which guarantees a global minimum for PDECCO problems exists. A new mapping has been developed that transforms PDECCO problem, which only have linear PDEs as constraints, into quadratic unconstrained binary optimization (QUBO) problems that can be solved using an adiabatic quantum optimizer (AQO). The mapping is efficient, it scales polynomially with the size of the PDECCO problem, requires only one PDE solve to form the QUBO problem, and if the QUBO problem is solved correctly and efficiently on an AQO, guarantees a global optimal solution for the original PDECCO problem.

DWI-associated entire-tumor histogram analysis for the differentiation of low-grade prostate cancer from intermediate-high-grade prostate cancer.

PubMed

Wu, Chen-Jiang; Wang, Qing; Li, Hai; Wang, Xiao-Ning; Liu, Xi-Sheng; Shi, Hai-Bin; Zhang, Yu-Dong

2015-10-01

To investigate diagnostic efficiency of DWI using entire-tumor histogram analysis in differentiating the low-grade (LG) prostate cancer (PCa) from intermediate-high-grade (HG) PCa in comparison with conventional ROI-based measurement. DW images (b of 0-1400 s/mm(2)) from 126 pathology-confirmed PCa (diameter >0.5 cm) in 110 patients were retrospectively collected and processed by mono-exponential model. The measurement of tumor apparent diffusion coefficients (ADCs) was performed with using histogram-based and ROI-based approach, respectively. The diagnostic ability of ADCs from two methods for differentiating LG-PCa (Gleason score, GS ≤ 6) from HG-PCa (GS > 6) was determined by ROC regression, and compared by McNemar's test. There were 49 LG-tumor and 77 HG-tumor at pathologic findings. Histogram-based ADCs (mean, median, 10th and 90th) and ROI-based ADCs (mean) showed dominant relationships with ordinal GS of Pca (ρ = -0.225 to -0.406, p < 0.05). All above imaging indices reflected significant difference between LG-PCa and HG-PCa (all p values <0.01). Histogram 10th ADCs had dominantly high Az (0.738), Youden index (0.415), and positive likelihood ratio (LR+, 2.45) in stratifying tumor GS against mean, median and 90th ADCs, and ROI-based ADCs. Histogram mean, median, and 10th ADCs showed higher specificity (65.3%-74.1% vs. 44.9%, p < 0.01), but lower sensitivity (57.1%-71.3% vs. 84.4%, p < 0.05) than ROI-based ADCs in differentiating LG-PCa from HG-PCa. DWI-associated histogram analysis had higher specificity, Az, Youden index, and LR+ for differentiation of PCa Gleason grade than ROI-based approach.

Rapid differentiation among bacteria that cause gastroenteritis by use of low-resolution Raman spectroscopy and PLS discriminant analysis.

PubMed

Mello, Cesar; Ribeiro, Diórginis; Novaes, Fábio; Poppi, Ronei J

2005-10-01

Use of classical microbiological methods to differentiate bacteria that cause gastroenteritis is cumbersome but usually very efficient. The high cost of reagents and the time required for such identifications, approximately four days, could have serious consequences, however, mainly when the patients are children, the elderly, or adults with low resistance. The search for new methods enabling rapid and reagentless differentiation of these microorganisms is, therefore, extremely relevant. In this work the main microorganisms responsible for gastroenteritis, Escherichia coli, Salmonella choleraesuis, and Shigella flexneri, were studied. For each microorganism sixty different dispersions were prepared in physiological solution. The Raman spectra of these dispersions were recorded using a diode laser operating in the near infrared region. Partial least-squares (PLS) discriminant analysis was used to differentiate among the bacteria by use of their respective Raman spectra. This approach enabled correct classification of 100% of the bacteria evaluated and unknown samples from the clinical environment, in less time ( approximately 10 h), by use of a low-cost, portable Raman spectrometer, which can be easily used in intensive care units and clinical environments.

Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitor Cells in Phenotypic Screening: A Transforming Growth Factor-β Type 1 Receptor Kinase Inhibitor Induces Efficient Cardiac Differentiation.

PubMed

Drowley, Lauren; Koonce, Chad; Peel, Samantha; Jonebring, Anna; Plowright, Alleyn T; Kattman, Steven J; Andersson, Henrik; Anson, Blake; Swanson, Bradley J; Wang, Qing-Dong; Brolen, Gabriella

2016-02-01

Several progenitor cell populations have been reported to exist in hearts that play a role in cardiac turnover and/or repair. Despite the presence of cardiac stem and progenitor cells within the myocardium, functional repair of the heart after injury is inadequate. Identification of the signaling pathways involved in the expansion and differentiation of cardiac progenitor cells (CPCs) will broaden insight into the fundamental mechanisms playing a role in cardiac homeostasis and disease and might provide strategies for in vivo regenerative therapies. To understand and exploit cardiac ontogeny for drug discovery efforts, we developed an in vitro human induced pluripotent stem cell-derived CPC model system using a highly enriched population of KDR(pos)/CKIT(neg)/NKX2.5(pos) CPCs. Using this model system, these CPCs were capable of generating highly enriched cultures of cardiomyocytes under directed differentiation conditions. In order to facilitate the identification of pathways and targets involved in proliferation and differentiation of resident CPCs, we developed phenotypic screening assays. Screening paradigms for therapeutic applications require a robust, scalable, and consistent methodology. In the present study, we have demonstrated the suitability of these cells for medium to high-throughput screens to assess both proliferation and multilineage differentiation. Using this CPC model system and a small directed compound set, we identified activin-like kinase 5 (transforming growth factor-β type 1 receptor kinase) inhibitors as novel and potent inducers of human CPC differentiation to cardiomyocytes. Significance: Cardiac disease is a leading cause of morbidity and mortality, with no treatment available that can result in functional repair. This study demonstrates how differentiation of induced pluripotent stem cells can be used to identify and isolate cell populations of interest that can translate to the adult human heart. Two separate examples of phenotypic screens are discussed, demonstrating the value of this biologically relevant and reproducible technology. In addition, this assay system was able to identify novel and potent inducers of differentiation and proliferation of induced pluripotent stem cell-derived cardiac progenitor cells. ©AlphaMed Press.

High-order fractional partial differential equation transform for molecular surface construction

PubMed Central

Hu, Langhua; Chen, Duan; Wei, Guo-Wei

2013-01-01

Fractional derivative or fractional calculus plays a significant role in theoretical modeling of scientific and engineering problems. However, only relatively low order fractional derivatives are used at present. In general, it is not obvious what role a high fractional derivative can play and how to make use of arbitrarily high-order fractional derivatives. This work introduces arbitrarily high-order fractional partial differential equations (PDEs) to describe fractional hyperdiffusions. The fractional PDEs are constructed via fractional variational principle. A fast fractional Fourier transform (FFFT) is proposed to numerically integrate the high-order fractional PDEs so as to avoid stringent stability constraints in solving high-order evolution PDEs. The proposed high-order fractional PDEs are applied to the surface generation of proteins. We first validate the proposed method with a variety of test examples in two and three-dimensional settings. The impact of high-order fractional derivatives to surface analysis is examined. We also construct fractional PDE transform based on arbitrarily high-order fractional PDEs. We demonstrate that the use of arbitrarily high-order derivatives gives rise to time-frequency localization, the control of the spectral distribution, and the regulation of the spatial resolution in the fractional PDE transform. Consequently, the fractional PDE transform enables the mode decomposition of images, signals, and surfaces. The effect of the propagation time on the quality of resulting molecular surfaces is also studied. Computational efficiency of the present surface generation method is compared with the MSMS approach in Cartesian representation. We further validate the present method by examining some benchmark indicators of macromolecular surfaces, i.e., surface area, surface enclosed volume, surface electrostatic potential and solvation free energy. Extensive numerical experiments and comparison with an established surface model indicate that the proposed high-order fractional PDEs are robust, stable and efficient for biomolecular surface generation. PMID:24364020

Interplay of wavelength, fluence and spot-size in free-electron laser ablation of cornea.

PubMed

Hutson, M Shane; Ivanov, Borislav; Jayasinghe, Aroshan; Adunas, Gilma; Xiao, Yaowu; Guo, Mingsheng; Kozub, John

2009-06-08

Infrared free-electron lasers ablate tissue with high efficiency and low collateral damage when tuned to the 6-microm range. This wavelength-dependence has been hypothesized to arise from a multi-step process following differential absorption by tissue water and proteins. Here, we test this hypothesis at wavelengths for which cornea has matching overall absorption, but drastically different differential absorption. We measure etch depth, collateral damage and plume images and find that the hypothesis is not confirmed. We do find larger etch depths for larger spot sizes--an effect that can lead to an apparent wavelength dependence. Plume imaging at several wavelengths and spot sizes suggests that this effect is due to increased post-pulse ablation at larger spots.

A numerical algorithm for optimal feedback gains in high dimensional linear quadratic regulator problems

NASA Technical Reports Server (NTRS)

Banks, H. T.; Ito, K.

1991-01-01

A hybrid method for computing the feedback gains in linear quadratic regulator problem is proposed. The method, which combines use of a Chandrasekhar type system with an iteration of the Newton-Kleinman form with variable acceleration parameter Smith schemes, is formulated to efficiently compute directly the feedback gains rather than solutions of an associated Riccati equation. The hybrid method is particularly appropriate when used with large dimensional systems such as those arising in approximating infinite-dimensional (distributed parameter) control systems (e.g., those governed by delay-differential and partial differential equations). Computational advantages of the proposed algorithm over the standard eigenvector (Potter, Laub-Schur) based techniques are discussed, and numerical evidence of the efficacy of these ideas is presented.

Quantitative differential phase contrast imaging at high resolution with radially asymmetric illumination.

PubMed

Lin, Yu-Zi; Huang, Kuang-Yuh; Luo, Yuan

2018-06-15

Half-circle illumination-based differential phase contrast (DPC) microscopy has been utilized to recover phase images through a pair of images along multiple axes. Recently, the half-circle based DPC using 12-axis measurements significantly provides a circularly symmetric phase transfer function to improve accuracy for more stable phase recovery. Instead of using half-circle-based DPC, we propose a new scheme of DPC under radially asymmetric illumination to achieve circularly symmetric phase transfer function and enhance the accuracy of phase recovery in a more stable and efficient fashion. We present the design, implementation, and experimental image data demonstrating the ability of our method to obtain quantitative phase images of microspheres, as well as live fibroblast cell samples.

A numerical algorithm for optimal feedback gains in high dimensional LQR problems

NASA Technical Reports Server (NTRS)

Banks, H. T.; Ito, K.

1986-01-01

A hybrid method for computing the feedback gains in linear quadratic regulator problems is proposed. The method, which combines the use of a Chandrasekhar type system with an iteration of the Newton-Kleinman form with variable acceleration parameter Smith schemes, is formulated so as to efficiently compute directly the feedback gains rather than solutions of an associated Riccati equation. The hybrid method is particularly appropriate when used with large dimensional systems such as those arising in approximating infinite dimensional (distributed parameter) control systems (e.g., those governed by delay-differential and partial differential equations). Computational advantage of the proposed algorithm over the standard eigenvector (Potter, Laub-Schur) based techniques are discussed and numerical evidence of the efficacy of our ideas presented.

Efficient spin-filtering, magnetoresistance and negative differential resistance effects of a one-dimensional single-molecule magnet Mn(dmit)2-based device with graphene nanoribbon electrodes

NASA Astrophysics Data System (ADS)

Liu, N.; Liu, J. B.; Yao, K. L.

2017-12-01

We present first-principle spin-dependent quantum transport calculations in a molecular device constructed by one single-molecule magnet Mn(dmit)2 and two graphene nanoribbon electrodes. Our results show that the device could generate perfect spin-filtering performance in a certain bias range both in the parallel configuration (PC) and the antiparallel configuration (APC). At the same time, a magnetoresistance effect, up to a high value of 103%, can be realized. Moreover, visible negative differential resistance phenomenon is obtained for the spin-up current of the PC. These results suggest that our one-dimensional molecular device is a promising candidate for multi-functional spintronics devices.

Magnetic nanoparticles as a new approach to improve the efficacy of gene therapy against differentiated human uterine fibroid cells and tumor-initiating stem cells

PubMed Central

Shalaby, Shahinaz Mahmood; Khater, Mostafa K; Mas Perucho, Aymara; Mohamed, Sara A; Helwa, Inas; Laknaur, Archana; Lebedyeva, Iryna; Liu, Yutao; Diamond, Michael P; Al-Hendy, Ayman A

2016-01-01

Uterine fibroid(s) (UF/UFs) are benign tumors commonly found in women of reproductive age. The long-term outcomes of myomectomies are often hampered by high rates of recurrence (up to 60%). Objective To study whether efficient transduction and subsequent elimination of fibroid tumor initiating stem cells during debulking of tumor cells will aid in completely eradicating the tumor as well as decreasing the likelihood of recurrence. Design We have developed a localized non-surgical adenovirus-based alternative for the treatment of UFs. Combining viral based gene delivery with nanotechnology provides an opportunity to develop more efficient targeted viral gene therapy. Magnetic nanoparticles (MNPs) complexed to adenovirus, in the presence of an external magnetic field, accelerate adenovirus transduction. Setting Research laboratory located in Georgia Regents University, an academic research institution. Patients N/A Interventions MNPs complexed to adenovirus (AD GFP) or (AD LacZ) were used to transfect differentiated human fibroid cells in vitro. Main Outcome Measures rate of transduction and tumor growth inhibition. Results We observed a significant increase in transduction efficiency among differentiated human fibroid cells at 2 different multiplicities of infection (MOI); 1 and 10 respectively, with MNPs as compared to adenovirus-alone. Human fibroid stem cells transfected with AD-LacZ expressed β-Galactosidaze at (MOI) of 1, 10, and 50 at percentages of 19%, 62%, and 90%, respectively, which were significantly enhanced with MNPs. Conclusion When applied with adenovirus herpes simplex thymidine kinase, magnetofection significantly suppressed proliferation and induced apoptosis in both cell types. Through the use of magnetofection, we will prove that a lower viral dose will effectively increase the overall safety profile of suicide gene therapy against fibroid tumors. PMID:27020169

Generation of Functional Human Hepatic Endoderm from Human iPS cells

PubMed Central

Sullivan, Gareth J.; Hay, David C.; Park, In-Hyun; Fletcher, Judy; Hannoun, Zara; Payne, Catherine M.; Dalgetty, Donna; Black, James R.; Ross, James A.; Samuel, Kay; Wang, Gang; Daley, George Q.; Lee, Je-Hyuk; Church, George M.; Forbes, Stuart J.; Iredale, John P.; Wilmut, Ian

2009-01-01

With the advent of induced pluripotent stem cell (iPSC) technology, it is now feasible to generate iPSCs with a defined genotype or disease state. When coupled with direct differentiation of defined lineage, such as hepatic endoderm (HE). iPSC would revolutionise the way we study human liver biology and generate efficient “off the shelf” models of human liver disease. Here we show the `proof of concept' that iPSC lines representing both male and female sexes and two ethnic origins can be differentiated to HE at efficiencies of between 70–90%, using a method mimicking a physiological condition. iPSC-derived HE exhibited hepatic morphology, and expressed the hepatic markers, Albumin and E-Cadherin as assessed by immuno-histochemistry. They also expressed alpha fetal protein (AFP), HNF4a, and a metabolic marker, Cyp7A1, demonstrating a definitive endodermal lineage differentiation. Furthermore, iPSC-derived hepatocytes produced and secreted the plasma proteins, fibrinogen, fibronectin, transthyretin (TTR) and AFP, an essential feature for functional HE. Additionally iPSC-derived HE supported both CYP1A2 and 3A4 metabolism, which is essential for drug and toxicology testing. Conclusion This work is first to demonstrate the efficient generation of hepatic endodermal lineage from human iPSC that exhibits key attributes of hepatocytes, and the potential application of iPSC-derived HE in studying human liver biology. In particular, iPSC from individuals representing highly polymorphic variants in metabolic genes and different ethnic groups will provide pharmaceutical development and toxicology studies a unique opportunity to revolutionise predictive drug toxicology assays and allow the creation of in vitro hepatic disease models. PMID:19877180

Efficient Generation and Editing of Feeder-free IPSCs from Human Pancreatic Cells Using the CRISPR-Cas9 System.

PubMed

Nandal, Anjali; Mallon, Barbara; Telugu, Bhanu P

2017-11-08

Embryonic and induced pluripotent stem cells can self-renew and differentiate into multiple cell types of the body. The pluripotent cells are thus coveted for research in regenerative medicine and are currently in clinical trials for eye diseases, diabetes, heart diseases, and other disorders. The potential to differentiate into specialized cell types coupled with the recent advances in genome editing technologies including the CRISPR/Cas system have provided additional opportunities for tailoring the genome of iPSC for varied applications including disease modeling, gene therapy, and biasing pathways of differentiation, to name a few. Among the available editing technologies, the CRISPR/Cas9 from Streptococcus pyogenes has emerged as a tool of choice for site-specific editing of the eukaryotic genome. The CRISPRs are easily accessible, inexpensive, and highly efficient in engineering targeted edits. The system requires a Cas9 nuclease and a guide sequence (20-mer) specific to the genomic target abutting a 3-nucleotide "NGG" protospacer-adjacent-motif (PAM) for targeting Cas9 to the desired genomic locus, alongside a universal Cas9 binding tracer RNA (together called single guide RNA or sgRNA). Here we present a step-by-step protocol for efficient generation of feeder-independent and footprint-free iPSC and describe methodologies for genome editing of iPSC using the Cas9 ribonucleoprotein (RNP) complexes. The genome editing protocol is effective and can be easily multiplexed by pre-complexing sgRNAs for more than one target with the Cas9 protein and simultaneously delivering into the cells. Finally, we describe a simplified approach for identification and characterization of iPSCs with desired edits. Taken together, the outlined strategies are expected to streamline generation and editing of iPSC for manifold applications.

A poly (lactide-co-glycolide) film loaded with abundant bone morphogenetic protein-2: A substrate promoting osteoblast attachment, proliferation and differentiation in bone tissue engineering.

PubMed

Qu, Xiangyang; Cao, Yujiang; Chen, Cong; Die, Xiaohong; Kang, Quan

2014-12-10

We explored a novel biodegradable poly (lactide-co-glycolide) (PLGA) film loaded with over 80 wt% bone morphogenetic protein (BMP-2), which was regarded as a substrate promoting osteoblast attachment, proliferation and differentiation for application of bone tissue engineering. Using phospholipid as a surfactant, BMP-2 was modified as a complex (PBC) for dispersing in PLGA/dichloromethane solution. The PLGA film loaded with BMP-2 and phospholipid complex (PBC-PF) showed rough and draped morphology with high entrapment efficiency exceeding 80% and good hydrophilicity respectively. The in-vitro release study of BMP-2 showed that about 50% BMP-2 was slowly and continuously released from PBC-PF within 5 weeks and had a short initial burst release only in the last 1.5 days, which was better than serious burst release of PLGA film loaded with pure BMP-2 without phospholipid (BMP-PF) controlling. By comparison with other PLGA films and tissue culture plates, it was confirmed that PBC-PF significantly promoted the attachment, proliferation and differentiation of osteoblasts with higher entrapment efficiency and better sustained release. These advantages illustrated that PBC-PF could be a potential substrate providing long-term requisite growth factors for osteoblasts, which might be applied in bone tissue engineering. This article is protected by copyright. All rights reserved. Copyright © 2014 Wiley Periodicals, Inc., A Wiley Company.

A poly(lactide-co-glycolide) film loaded with abundant bone morphogenetic protein-2: A substrate-promoting osteoblast attachment, proliferation, and differentiation in bone tissue engineering.

PubMed

Qu, Xiangyang; Cao, Yujiang; Chen, Cong; Die, Xiaohong; Kang, Quan

2015-08-01

We explored a novel biodegradable poly(lactide-co-glycolide) (PLGA) film loaded with over 80 wt % bone morphogenetic protein (BMP)-2, which was regarded as a substrate-promoting osteoblast attachment, proliferation, and differentiation for application of bone tissue engineering. Using phospholipid as a surfactant, BMP-2 was modified as a complex (PBC) for dispersing in PLGA/dichloromethane solution. The PLGA film loaded with BMP-2 and phospholipid complex (PBC-PF) showed rough and draped morphology with high entrapment efficiency exceeding 80% and good hydrophilicity, respectively. The in vitro release study of BMP-2 showed that about 50% BMP-2 was slowly and continuously released from PBC-PF within 5 weeks and had a short initial burst release only in the last 1.5 days, which was better than serious burst release of PLGA film loaded with pure BMP-2 without phospholipid (BMP-PF) as control. By comparison with other PLGA films and tissue culture plates, it was confirmed that PBC-PF significantly promoted the attachment, proliferation, and differentiation of osteoblasts with higher entrapment efficiency and better sustained release. These advantages illustrated that PBC-PF could be a potential substrate providing long-term requisite growth factors for osteoblasts, which might be applied in bone tissue engineering. © 2015 Wiley Periodicals, Inc.

Differential effects of ADORA2A gene variations in pre-attentive visual sensory memory subprocesses.

PubMed

Beste, Christian; Stock, Ann-Kathrin; Ness, Vanessa; Epplen, Jörg T; Arning, Larissa

2012-08-01

The ADORA2A gene encodes the adenosine A(2A) receptor that is highly expressed in the striatum where it plays a role in modulating glutamatergic and dopaminergic transmission. Glutamatergic signaling has been suggested to play a pivotal role in cognitive functions related to the pre-attentive processing of external stimuli. Yet, the precise molecular mechanism of these processes is poorly understood. Therefore, we aimed to investigate whether ADORA2A gene variation has modulating effects on visual pre-attentive sensory memory processing. Studying two polymorphisms, rs5751876 and rs2298383, in 199 healthy control subjects who performed a partial-report paradigm, we find that ADORA2A variation is associated with differences in the efficiency of pre-attentive sensory memory sub-processes. We show that especially the initial visual availability of stimulus information is rendered more efficiently in the homozygous rare genotype groups. Processes related to the transfer of information into working memory and the duration of visual sensory (iconic) memory are compromised in the homozygous rare genotype groups. Our results show a differential genotype-dependent modulation of pre-attentive sensory memory sub-processes. Hence, we assume that this modulation may be due to differential effects of increased adenosine A(2A) receptor signaling on glutamatergic transmission and striatal medium spiny neuron (MSN) interaction. Copyright © 2011 Elsevier B.V. and ECNP. All rights reserved.

Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data.

PubMed

Lepre, Jorge; Rice, J Jeremy; Tu, Yuhai; Stolovitzky, Gustavo

2004-05-01

Despite the growing literature devoted to finding differentially expressed genes in assays probing different tissues types, little attention has been paid to the combinatorial nature of feature selection inherent to large, high-dimensional gene expression datasets. New flexible data analysis approaches capable of searching relevant subgroups of genes and experiments are needed to understand multivariate associations of gene expression patterns with observed phenotypes. We present in detail a deterministic algorithm to discover patterns of multivariate gene associations in gene expression data. The patterns discovered are differential with respect to a control dataset. The algorithm is exhaustive and efficient, reporting all existent patterns that fit a given input parameter set while avoiding enumeration of the entire pattern space. The value of the pattern discovery approach is demonstrated by finding a set of genes that differentiate between two types of lymphoma. Moreover, these genes are found to behave consistently in an independent dataset produced in a different laboratory using different arrays, thus validating the genes selected using our algorithm. We show that the genes deemed significant in terms of their multivariate statistics will be missed using other methods. Our set of pattern discovery algorithms including a user interface is distributed as a package called Genes@Work. This package is freely available to non-commercial users and can be downloaded from our website (http://www.research.ibm.com/FunGen).

Lin-28 binds IGF-2 mRNA and participates in skeletal myogenesis by increasing translation efficiency.

PubMed

Polesskaya, Anna; Cuvellier, Sylvain; Naguibneva, Irina; Duquet, Arnaud; Moss, Eric G; Harel-Bellan, Annick

2007-05-01

Lin-28 is a highly conserved, RNA-binding, microRNA-regulated protein that is involved in regulation of developmental timing in Caenorhabditis elegans. In mammals, Lin-28 is stage-specifically expressed in embryonic muscle, neurons, and epithelia, as well as in embryonic carcinoma cells, but is suppressed in most adult tissues, with the notable exception of skeletal and cardiac muscle. The specific function and mechanism of action of Lin-28 are not well understood. Here we used loss-of-function and gain-of-function assays in cultured myoblasts to show that expression of Lin-28 is essential for skeletal muscle differentiation in mice. In order to elucidate the specific function of Lin-28, we used a combination of biochemical and functional assays, which revealed that, in differentiating myoblasts, Lin-28 binds to the polysomes and increases the efficiency of protein synthesis. An important target of Lin-28 is IGF-2, a crucial growth and differentiation factor for muscle tissue. Interaction of Lin-28 with translation initiation complexes in skeletal myoblasts and in the embryonic carcinoma cell line P19 was confirmed by localization of Lin-28 to the stress granules, temporary structures that contain stalled mRNA-protein translation complexes. Our results unravel novel mechanisms of translational regulation in skeletal muscle and suggest that Lin-28 performs the role of "translational enhancer" in embryonic and adult cells and tissues.

Results from Evaluation of Proposed ASME AG-1 Section FI Metal Media Filters - 13063

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

Wilson, John A.; Giffin, Paxton K.; Parsons, Michael S.

High efficiency particulate air (HEPA) filtration technology is commonly used in Department of Energy (DOE) facilities that require control of radioactive particulate matter (PM) emissions due to treatment or management of radioactive materials. Although HEPA technology typically makes use of glass fiber media, metal and ceramic media filters are also capable of filtering efficiencies beyond the required 99.97%. Sintered metal fiber filters are good candidates for use in DOE facilities due to their resistance to corrosive environments and resilience at high temperature and elevated levels of relative humidity. Their strength can protect them from high differential pressure or pressure spikesmore » and allow for back pulse cleaning, extending filter lifetime. Use of these filters has the potential to reduce the cost of filtration in DOE facilities due to life cycle cost savings. ASME AG-1 section FI has not been approved due to a lack of protocols and performance criteria for qualifying section FI filters. The Institute for Clean Energy Technology (ICET) with the aid of the FI project team has developed a Section FI test stand and test plan capable of assisting in the qualification ASME AG-1 section FI filters. Testing done at ICET using the FI test stand evaluates resistance to rated air flow, test aerosol penetration and resistance to heated air of the section FI filters. Data collected during this testing consists of temperature, relative humidity, differential pressure, flow rate, upstream particle concentration, and downstream particle concentration. (authors)« less

Numerical approximations for fractional diffusion equations via a Chebyshev spectral-tau method

NASA Astrophysics Data System (ADS)

Doha, Eid H.; Bhrawy, Ali H.; Ezz-Eldien, Samer S.

2013-10-01

In this paper, a class of fractional diffusion equations with variable coefficients is considered. An accurate and efficient spectral tau technique for solving the fractional diffusion equations numerically is proposed. This method is based upon Chebyshev tau approximation together with Chebyshev operational matrix of Caputo fractional differentiation. Such approach has the advantage of reducing the problem to the solution of a system of algebraic equations, which may then be solved by any standard numerical technique. We apply this general method to solve four specific examples. In each of the examples considered, the numerical results show that the proposed method is of high accuracy and is efficient for solving the time-dependent fractional diffusion equations.

A Comparison of LBG and ADPCM Speech Compression Techniques

NASA Astrophysics Data System (ADS)

Bachu, Rajesh G.; Patel, Jignasa; Barkana, Buket D.

Speech compression is the technology of converting human speech into an efficiently encoded representation that can later be decoded to produce a close approximation of the original signal. In all speech there is a degree of predictability and speech coding techniques exploit this to reduce bit rates yet still maintain a suitable level of quality. This paper is a study and implementation of Linde-Buzo-Gray Algorithm (LBG) and Adaptive Differential Pulse Code Modulation (ADPCM) algorithms to compress speech signals. In here we implemented the methods using MATLAB 7.0. The methods we used in this study gave good results and performance in compressing the speech and listening tests showed that efficient and high quality coding is achieved.

Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation

PubMed Central

Espinosa Angarica, Vladimir

2016-01-01

Pluripotency can be considered a functional characteristic of pluripotent stem cells (PSCs) populations and their niches, rather than a property of individual cells. In this view, individual cells within the population independently adopt a variety of different expression states, maintained by different signaling, transcriptional, and epigenetics regulatory networks. In this review, we propose that generation of integrative network models from single cell data will be essential for getting a better understanding of the regulation of self‐renewal and differentiation. In particular, we suggest that the identification of network stability determinants in these integrative models will provide important insights into the mechanisms mediating the transduction of signals from the niche, and how these signals can trigger differentiation. In this regard, the differential use of these stability determinants in subpopulation‐specific regulatory networks would mediate differentiation into different cell fates. We suggest that this approach could offer a promising avenue for the development of novel strategies for increasing the efficiency and fidelity of differentiation, which could have a strong impact on regenerative medicine. PMID:27321053

Uniform Embryoid Body Production and Enhanced Mesendoderm Differentiation with Murine Embryonic Stem Cells in a Rotary Suspension Bioreactor.

PubMed

Lei, Xiaohua; Deng, Zhili; Duan, Enkui

2016-01-01

Embryonic stem cells (ESCs) are capable of differentiating into almost all cell types in vitro and hold great promise for drug screening, developmental studies and have a huge potential in many therapeutic areas. ESCs can aggregate to form embryoid body (EB) in static suspension culture by spontaneous differentiation, which resembles an intact embryo; while static suspension culture cannot prevent agglomeration of cells and offers little control over the size and shape of EBs, it results in aggregation of EBs into large, irregular masses, which prejudice the efficiency of differentiation of cells. Recently, bioreactor-based platforms have been shown to not only offer a beneficial effect on increasing diffusion of nutrients and oxygen which promotes cell viability and proliferation but also display local biomechanical properties (e.g., low fluid shear stresses and hydrodynamic force) in tissue development and organogenesis. This chapter describes a protocol for using a rotary suspension bioreactor to produce embryoid bodies and process the differentiation of mouse embryonic stem cells (mESCs), and to assess the efficiency of EB differentiation in the bioreactor by real-time PCR and immunostaining.

Let7a involves in neural stem cell differentiation relating with TLX level.

PubMed

Song, Juhyun; Cho, Kyoung Joo; Oh, Yumi; Lee, Jong Eun

2015-07-10

Neural stem cells (NSCs) have the potential for differentiation into neurons known as a groundbreaking therapeutic solution for central nervous system (CNS) diseases. To resolve the therapeutic efficiency of NSCs, recent researchers have focused on the study on microRNA's role in CNS. Some micro RNAs have been reported significant functions in NSC self-renewal and differentiation through the post-transcriptional regulation of neurogenesis genes. MicroRNA-Let7a (Let7a) has known as the regulator of diverse cellular mechanisms including cell differentiation and proliferation. In present study, we investigated whether Let7a regulates NSC differentiation by targeting the nuclear receptor TLX, which is an essential regulator of NSC self-renewal, proliferation and differentiation. We performed the following experiments: western blot analysis, TaqMan assay, RT-PCR, and immunocytochemistry to confirm the alteration of NSCs. Our data showed that let7a play important roles in controlling NSC fate determination. Thus, manipulating Let-7A and TLX could be a novel strategy to enhance the efficiency of NSC's neuronal differentiation for CNS disorders. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Human stem cell neuronal differentiation on silk-carbon nanotube composite

NASA Astrophysics Data System (ADS)

Chen, Chi-Shuo; Soni, Sushant; Le, Catherine; Biasca, Matthew; Farr, Erik; Chen, Eric Y.-T.; Chin, Wei-Chun

2012-02-01

Human embryonic stem cells [hESCs] are able to differentiate into specific lineages corresponding to regulated spatial and temporal signals. This unique attribute holds great promise for regenerative medicine and cell-based therapy for many human diseases such as spinal cord injury [SCI] and multiple sclerosis [MS]. Carbon nanotubes [CNTs] have been successfully used to promote neuronal differentiation, and silk has been widely applied in tissue engineering. This study aims to build silk-CNT composite scaffolds for improved neuron differentiation efficiency from hESCs. Two neuronal markers (β-III tubulin and nestin) were utilized to determine the hESC neuronal lineage differentiation. In addition, axonal lengths were measured to evaluate the progress of neuronal development. The results demonstrated that cells on silk-CNT scaffolds have a higher β-III tubulin and nestin expression, suggesting augmented neuronal differentiation. In addition, longer axons with higher density were found to associate with silk-CNT scaffolds. Our silk-CNT-based composite scaffolds can promote neuronal differentiation of hESCs. The silk-CNT composite scaffolds developed here can serve as efficient supporting matrices for stem cell-derived neuronal transplants, offering a promising opportunity for nerve repair treatments for SCI and MS patients.

Ionization Efficiency in the Dayside Martian Upper Atmosphere

NASA Astrophysics Data System (ADS)

Cui, J.; Wu, X.-S.; Xu, S.-S.; Wang, X.-D.; Wellbrock, A.; Nordheim, T. A.; Cao, Y.-T.; Wang, W.-R.; Sun, W.-Q.; Wu, S.-Q.; Wei, Y.

2018-04-01

Combining the Mars Atmosphere and Volatile Evolution measurements of neutral atmospheric density, solar EUV/X-ray flux, and differential photoelectron intensity made during 240 nominal orbits, we calculate the ionization efficiency, defined as the ratio of the secondary (photoelectron impact) ionization rate to the primary (photon impact) ionization rate, in the dayside Martian upper atmosphere under a range of solar illumination conditions. Both the CO2 and O ionization efficiencies tend to be constant from 160 km up to 250 km, with respective median values of 0.19 ± 0.03 and 0.27 ± 0.04. These values are useful for fast calculation of the ionization rate in the dayside Martian upper atmosphere, without the need to construct photoelectron transport models. No substantial diurnal and solar cycle variations can be identified, except for a marginal trend of reduced ionization efficiency approaching the terminator. These observations are favorably interpreted by a simple scenario with ionization efficiencies, as a first approximation, determined by a comparison between relevant cross sections. Our analysis further reveals a connection between regions with strong crustal magnetic fields and regions with high ionization efficiencies, which are likely indicative of more efficient vertical transport of photoelectrons near magnetic anomalies.

Comparison of two apheresis systems for the collection of CD14+ cells intended to be used in dendritic cell culture.

PubMed

Strasser, Erwin F; Berger, Thomas G; Weisbach, Volker; Zimmermann, Robert; Ringwald, Jürgen; Schuler-Thurner, Beatrice; Zingsem, Jürgen; Eckstein, Reinhold

2003-09-01

Monocytes collected by leukapheresis are increasingly used for dendritic cell (DC) culture in cell factories suitable for DC vaccination in cancer. Using modified MNC programs on two apheresis systems (Cobe Spectra and Fresenius AS.TEC204), leukapheresis components collected from 84 patients with metastatic malignant melanoma and from 31 healthy male donors were investigated. MNCs, monocytes, RBCs, and platelets (PLTs) in donors and components were analyzed by cell counters, WBC differential counts, and flow cytometry. In 5-L collections, Astec showed better results regarding monocyte collection rates (11.0 vs. 7.4 x 10(6)/min, p = 0.04) and efficiencies (collection efficiency, 51.9 vs. 31.9%; p < 0.001). Both devices resulted in monocyte yields at an average of 1 x 10(9) (donors) and 2.5 x 10(9) (patients), whereas Astec components contained high residual RBCs. Compared to components with low residual PLTs, high PLT concentration resulted in higher monocyte loss (48 vs. 20%, p < 0.0001) before DC culture. The Astec is more efficient in 5-L MNC collections compared to the Spectra. Components with high residual PLTs result in high MNC loss by purification procedures. Thus, optimizing MNC programs is essential to obtain components with high MNC yields and low residual cells as prerequisite for high DC yields.

A high-order Lagrangian-decoupling method for the incompressible Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Ho, Lee-Wing; Maday, Yvon; Patera, Anthony T.; Ronquist, Einar M.

1989-01-01

A high-order Lagrangian-decoupling method is presented for the unsteady convection-diffusion and incompressible Navier-Stokes equations. The method is based upon: (1) Lagrangian variational forms that reduce the convection-diffusion equation to a symmetric initial value problem; (2) implicit high-order backward-differentiation finite-difference schemes for integration along characteristics; (3) finite element or spectral element spatial discretizations; and (4) mesh-invariance procedures and high-order explicit time-stepping schemes for deducing function values at convected space-time points. The method improves upon previous finite element characteristic methods through the systematic and efficient extension to high order accuracy, and the introduction of a simple structure-preserving characteristic-foot calculation procedure which is readily implemented on modern architectures. The new method is significantly more efficient than explicit-convection schemes for the Navier-Stokes equations due to the decoupling of the convection and Stokes operators and the attendant increase in temporal stability. Numerous numerical examples are given for the convection-diffusion and Navier-Stokes equations for the particular case of a spectral element spatial discretization.

High-power laser phosphor light source with liquid cooling for digital cinema applications

NASA Astrophysics Data System (ADS)

Li, Kenneth

2014-02-01

Laser excited phosphor has been used to excite phosphor material, producing high intensity light output with smaller etendue than that of LEDs with the same long lifetime. But due to the high intensity of the laser light, phosphor with organic binder burns at low power, which requires the phosphor to be deposited on a rotating wheel in practical applications. Phosphor with inorganic binders, commonly known as ceramic phosphor, on the other hand, does not burn, but efficiency goes down as temperature goes up under high power excitation. This paper describes cooling schemes in sealed chambers such that the phosphor materials using organic or inorganic binders can be liquid cooled for high efficiency operations. Confined air bubbles are introduced into the sealed chamber accommodating the differential thermal expansion of the liquid and the chamber. For even higher power operation suitable for digital cinema, a suspension of phosphor in liquid is described suitable for screen brightness of over 30,000 lumens. The aging issues of phosphor can also be solved by using replaceable phosphor cartridges.

The Effect of Traditional Chinese Formula Danchaiheji on the Differentiation of Regulatory Dendritic Cells

PubMed Central

Wang, Xiaodong; Tong, Jingzhi; Li, Keqiu; Jing, Yaqing

2016-01-01

Recently, regulatory dendritic cells (DCregs), a newly described dendritic cell subset with potent immunomodulatory function, have attracted increased attention for their utility in treating immune response-related diseases, such as graft-versus-host disease, hypersensitivity, and autoimmune diseases. Danchaiheji (DCHJ) is a traditional Chinese formula that has been used for many years in the clinic. However, whether DCHJ can program dendritic cells towards a regulatory phenotype and the underlying mechanism behind this process remain unknown. Herein, we investigate the effects of traditional Chinese DCHJ on DCregs differentiation and a mouse model of skin transplantation. The current study demonstrates that DCHJ can induce dendritic cells to differentiate into DCregs, which are represented by high CD11b and low CD86 and HLA-DR expression as well as the secretion of IL-10 and TGF-β. In addition, DCHJ inhibited DC migration and T cell proliferation, which correlated with increased IDO expression. Furthermore, DCHJ significantly prolonged skin graft survival time in a mouse model of skin transplantation without any liver or kidney toxicity. The traditional Chinese formula DCHJ has the potential to be a potent immunosuppressive agent with high efficiency and nontoxicity. PMID:27525028

Generation of high-yield insulin producing cells from human bone marrow mesenchymal stem cells.

PubMed

Jafarian, Arefeh; Taghikhani, Mohammad; Abroun, Saeid; Pourpak, Zahra; Allahverdi, Amir; Soleimani, Masoud

2014-07-01

Allogenic islet transplantation is a most efficient approach for treatment of diabetes mellitus. However, the scarcity of islets and long term need for an immunosuppressant limits its application. Recently, cell replacement therapies that generate of unlimited sources of β cells have been developed to overcome these limitations. In this study we have described a stage specific differentiation protocol for the generation of insulin producing islet-like clusters from human bone marrow mesenchymal stem cells (hBM-MSCs). This specific stepwise protocol induced differentiation of hMSCs into definitive endoderm, pancreatic endoderm and pancreatic endocrine cells that expressed of sox17, foxa2, pdx1, ngn3, nkx2.2, insulin, glucagon, somatostatin, pancreatic polypeptide, and glut2 transcripts respectively. In addition, immunocytochemical analysis confirmed protein expression of the above mentioned genes. Western blot analysis discriminated insulin from proinsulin in the final differentiated cells. In derived insulin producing cells (IPCs), secreted insulin and C-peptide was in a glucose dependent manner. We have developed a protocol that generates effective high-yield human IPCs from hBM-MSCs in vitro. These finding suggest that functional IPCs generated by this procedure can be used as a cell-based approach for insulin dependent diabetes mellitus.

DVS-SOFTWARE: An Effective Tool for Applying Highly Parallelized Hardware To Computational Geophysics

NASA Astrophysics Data System (ADS)

Herrera, I.; Herrera, G. S.

2015-12-01

Most geophysical systems are macroscopic physical systems. The behavior prediction of such systems is carried out by means of computational models whose basic models are partial differential equations (PDEs) [1]. Due to the enormous size of the discretized version of such PDEs it is necessary to apply highly parallelized super-computers. For them, at present, the most efficient software is based on non-overlapping domain decomposition methods (DDM). However, a limiting feature of the present state-of-the-art techniques is due to the kind of discretizations used in them. Recently, I. Herrera and co-workers using 'non-overlapping discretizations' have produced the DVS-Software which overcomes this limitation [2]. The DVS-software can be applied to a great variety of geophysical problems and achieves very high parallel efficiencies (90%, or so [3]). It is therefore very suitable for effectively applying the most advanced parallel supercomputers available at present. In a parallel talk, in this AGU Fall Meeting, Graciela Herrera Z. will present how this software is being applied to advance MOD-FLOW. Key Words: Parallel Software for Geophysics, High Performance Computing, HPC, Parallel Computing, Domain Decomposition Methods (DDM)REFERENCES [1]. Herrera Ismael and George F. Pinder, Mathematical Modelling in Science and Engineering: An axiomatic approach", John Wiley, 243p., 2012. [2]. Herrera, I., de la Cruz L.M. and Rosas-Medina A. "Non Overlapping Discretization Methods for Partial, Differential Equations". NUMER METH PART D E, 30: 1427-1454, 2014, DOI 10.1002/num 21852. (Open source) [3]. Herrera, I., & Contreras Iván "An Innovative Tool for Effectively Applying Highly Parallelized Software To Problems of Elasticity". Geofísica Internacional, 2015 (In press)

940nm QCW diode laser bars with 70% efficiency at 1 kW output power at 203K: analysis of remaining limits and path to higher efficiency and power at 200K and 300K

NASA Astrophysics Data System (ADS)

Frevert, C.; Bugge, F.; Knigge, S.; Ginolas, A.; Erbert, G.; Crump, P.

2016-03-01

Both high-energy-class laser facilities and commercial high-energy pulsed laser sources require reliable optical pumps with the highest pulse power and electro-optical efficiency. Although commercial quasi-continuous wave (QCW) diode laser bars reach output powers of 300…500 W further improvements are urgently sought to lower the cost per Watt, improve system performance and reduce overall system complexity. Diode laser bars operating at temperatures of around 200 K show significant advances in performance, and are particularly attractive in systems that use cryogenically cooled solid state lasers. We present the latest results on 940 nm, passively cooled, 4 mm long QCW diode bars which operate under pulse conditions of 1.2 ms, 10 Hz at an output power of 1 kW with efficiency of 70% at 203 K: a two-fold increase in power compared to 300 K, without compromising efficiency. We discuss how custom low-temperature design of the vertical layers can mitigate the limiting factors such as series resistance while sustaining high power levels. We then focus on the remaining obstacles to higher efficiency and power, and use a detailed study of multiple vertical structures to demonstrate that the properties of the active region are a major performance limit. Specifically, one key limit to series resistance is transport in the layers around the active region and the differential internal efficiency is closely correlated to the threshold current. Tailoring the barriers around the active region and reducing transparency current density thus promise bars with increased performance at temperatures of 200 K as well as 300 K.

Development of an Automatic Differentiation Version of the FPX Rotor Code

NASA Technical Reports Server (NTRS)

Hu, Hong

1996-01-01

The ADIFOR2.0 automatic differentiator is applied to the FPX rotor code along with the grid generator GRGN3. The FPX is an eXtended Full-Potential CFD code for rotor calculations. The automatic differentiation version of the code is obtained, which provides both non-geometry and geometry sensitivity derivatives. The sensitivity derivatives via automatic differentiation are presented and compared with divided difference generated derivatives. The study shows that automatic differentiation method gives accurate derivative values in an efficient manner.

The Effect of Thermal Cycling on Crystal-Liquid Separation During Lunar Magma Ocean Differentiation

NASA Technical Reports Server (NTRS)

Mills, Ryan D.

2013-01-01

Differentiation of magma oceans likely involves a mixture of fractional and equilibrium crystallization [1]. The existence of: 1) large volumes of anorthosite in the lunar highlands and 2) the incompatible- rich (KREEP) reservoir suggests that fractional crystallization may have dominated during differentiation of the Moon. For this to have occurred, crystal fractionation must have been remarkably efficient. Several authors [e.g. 2, 3] have hypothesized that equilibrium crystallization would have dominated early in differentiation of magma oceans because of crystal entrainment during turbulent convection. However, recent numerical modeling [4] suggests that crystal settling could have occurred throughout the entire solidification history of the lunar magma ocean if crystals were large and crystal fraction was low. These results indicate that the crystal size distribution could have played an important role in differentiation of the lunar magma ocean. Here, I suggest that thermal cycling from tidal heating during lunar magma ocean crystallization caused crystals to coarsen, leading to efficient crystal-liquid separation.

An Efficient Spectral Method for Ordinary Differential Equations with Rational Function Coefficients

NASA Technical Reports Server (NTRS)

Coutsias, Evangelos A.; Torres, David; Hagstrom, Thomas

1994-01-01

We present some relations that allow the efficient approximate inversion of linear differential operators with rational function coefficients. We employ expansions in terms of a large class of orthogonal polynomial families, including all the classical orthogonal polynomials. These families obey a simple three-term recurrence relation for differentiation, which implies that on an appropriately restricted domain the differentiation operator has a unique banded inverse. The inverse is an integration operator for the family, and it is simply the tridiagonal coefficient matrix for the recurrence. Since in these families convolution operators (i.e. matrix representations of multiplication by a function) are banded for polynomials, we are able to obtain a banded representation for linear differential operators with rational coefficients. This leads to a method of solution of initial or boundary value problems that, besides having an operation count that scales linearly with the order of truncation N, is computationally well conditioned. Among the applications considered is the use of rational maps for the resolution of sharp interior layers.

Mouse embryonic stem cell-derived cells reveal niches that support neuronal differentiation in the adult rat brain.

PubMed

Maya-Espinosa, Guadalupe; Collazo-Navarrete, Omar; Millán-Aldaco, Diana; Palomero-Rivero, Marcela; Guerrero-Flores, Gilda; Drucker-Colín, René; Covarrubias, Luis; Guerra-Crespo, Magdalena

2015-02-01

A neurogenic niche can be identified by the proliferation and differentiation of its naturally residing neural stem cells. However, it remains unclear whether "silent" neurogenic niches or regions suitable for neural differentiation, other than the areas of active neurogenesis, exist in the adult brain. Embryoid body (EB) cells derived from embryonic stem cells (ESCs) are endowed with a high potential to respond to specification and neuralization signals of the embryo. Hence, to identify microenvironments in the postnatal and adult rat brain with the capacity to support neuronal differentiation, we transplanted dissociated EB cells to conventional neurogenic and non-neurogenic regions. Our results show a neuronal differentiation pattern of EB cells that was dependent on the host region. Efficient neuronal differentiation of EB cells occurred within an adjacent region to the rostral migratory stream. EB cell differentiation was initially patchy and progressed toward an even distribution along the graft by 15-21 days post-transplantation, giving rise mostly to GABAergic neurons. EB cells in the striatum displayed a lower level of neuronal differentiation and derived into a significant number of astrocytes. Remarkably, when EB cells were transplanted to the striatum of adult rats after a local ischemic stroke, increased number of neuroblasts and neurons were observed. Unexpectedly, we determined that the adult substantia nigra pars compacta, considered a non-neurogenic area, harbors a robust neurogenic environment. Therefore, neurally uncommitted cells derived from ESCs can detect regions that support neuronal differentiation within the adult brain, a fundamental step for the development of stem cell-based replacement therapies. © 2014 AlphaMed Press.

Resveratrol Ameliorates the Maturation Process of β-Cell-Like Cells Obtained from an Optimized Differentiation Protocol of Human Embryonic Stem Cells

PubMed Central

Pezzolla, Daniela; López-Beas, Javier; Lachaud, Christian C.; Domínguez-Rodríguez, Alejandro; Smani, Tarik; Hmadcha, Abdelkrim; Soria, Bernat

2015-01-01

Human embryonic stem cells (hESCs) retain the extraordinary capacity to differentiate into different cell types of an adult organism, including pancreatic β-cells. For this particular lineage, although a lot of effort has been made in the last ten years to achieve an efficient and reproducible differentiation protocol, it was not until recently that this aim was roughly accomplished. Besides, several studies evidenced the impact of resveratrol (RSV) on insulin secretion, even though the mechanism by which this polyphenol potentiates glucose-stimulated insulin secretion (GSIS) is still not clear. The aim of this study was to optimize an efficient differentiation protocol that mimics in vivo pancreatic organogenesis and to investigate whether RSV may improve the final maturation step to obtain functional insulin-secreting cells. Our results indicate that treatment of hESCs (HS-181) with activin-A induced definitive endoderm differentiation as detected by the expression of SOX17 and FOXA2. Addition of retinoic acid (RA), Noggin and Cyclopamine promoted pancreatic differentiation as indicated by the expression of the early pancreatic progenitor markers ISL1, NGN3 and PDX1. Moreover, during maturation in suspension culture, differentiating cells assembled in islet-like clusters, which expressed specific endocrine markers such as PDX1, SST, GCG and INS. Similar results were confirmed with the human induced Pluripotent Stem Cell (hiPSC) line MSUH-001. Finally, differentiation protocols incorporating RSV treatment yielded numerous insulin-positive cells, induced significantly higher PDX1 expression and were able to transiently normalize glycaemia when transplanted in streptozotocin (STZ) induced diabetic mice thus promoting its survival. In conclusion, our strategy allows the efficient differentiation of hESCs into pancreatic endoderm capable of generating β-cell-like cells and demonstrates that RSV improves the maturation process. PMID:25774684

Study on Temperature and Synthetic Compensation of Piezo-Resistive Differential Pressure Sensors by Coupled Simulated Annealing and Simplex Optimized Kernel Extreme Learning Machine

PubMed Central

Li, Ji; Hu, Guoqing; Zhou, Yonghong; Zou, Chong; Peng, Wei; Alam SM, Jahangir

2017-01-01

As a high performance-cost ratio solution for differential pressure measurement, piezo-resistive differential pressure sensors are widely used in engineering processes. However, their performance is severely affected by the environmental temperature and the static pressure applied to them. In order to modify the non-linear measuring characteristics of the piezo-resistive differential pressure sensor, compensation actions should synthetically consider these two aspects. Advantages such as nonlinear approximation capability, highly desirable generalization ability and computational efficiency make the kernel extreme learning machine (KELM) a practical approach for this critical task. Since the KELM model is intrinsically sensitive to the regularization parameter and the kernel parameter, a searching scheme combining the coupled simulated annealing (CSA) algorithm and the Nelder-Mead simplex algorithm is adopted to find an optimal KLEM parameter set. A calibration experiment at different working pressure levels was conducted within the temperature range to assess the proposed method. In comparison with other compensation models such as the back-propagation neural network (BP), radius basis neural network (RBF), particle swarm optimization optimized support vector machine (PSO-SVM), particle swarm optimization optimized least squares support vector machine (PSO-LSSVM) and extreme learning machine (ELM), the compensation results show that the presented compensation algorithm exhibits a more satisfactory performance with respect to temperature compensation and synthetic compensation problems. PMID:28422080

Study on Temperature and Synthetic Compensation of Piezo-Resistive Differential Pressure Sensors by Coupled Simulated Annealing and Simplex Optimized Kernel Extreme Learning Machine.

PubMed

Li, Ji; Hu, Guoqing; Zhou, Yonghong; Zou, Chong; Peng, Wei; Alam Sm, Jahangir

2017-04-19

As a high performance-cost ratio solution for differential pressure measurement, piezo-resistive differential pressure sensors are widely used in engineering processes. However, their performance is severely affected by the environmental temperature and the static pressure applied to them. In order to modify the non-linear measuring characteristics of the piezo-resistive differential pressure sensor, compensation actions should synthetically consider these two aspects. Advantages such as nonlinear approximation capability, highly desirable generalization ability and computational efficiency make the kernel extreme learning machine (KELM) a practical approach for this critical task. Since the KELM model is intrinsically sensitive to the regularization parameter and the kernel parameter, a searching scheme combining the coupled simulated annealing (CSA) algorithm and the Nelder-Mead simplex algorithm is adopted to find an optimal KLEM parameter set. A calibration experiment at different working pressure levels was conducted within the temperature range to assess the proposed method. In comparison with other compensation models such as the back-propagation neural network (BP), radius basis neural network (RBF), particle swarm optimization optimized support vector machine (PSO-SVM), particle swarm optimization optimized least squares support vector machine (PSO-LSSVM) and extreme learning machine (ELM), the compensation results show that the presented compensation algorithm exhibits a more satisfactory performance with respect to temperature compensation and synthetic compensation problems.

New numerical approximation of fractional derivative with non-local and non-singular kernel: Application to chaotic models

NASA Astrophysics Data System (ADS)

Toufik, Mekkaoui; Atangana, Abdon

2017-10-01

Recently a new concept of fractional differentiation with non-local and non-singular kernel was introduced in order to extend the limitations of the conventional Riemann-Liouville and Caputo fractional derivatives. A new numerical scheme has been developed, in this paper, for the newly established fractional differentiation. We present in general the error analysis. The new numerical scheme was applied to solve linear and non-linear fractional differential equations. We do not need a predictor-corrector to have an efficient algorithm, in this method. The comparison of approximate and exact solutions leaves no doubt believing that, the new numerical scheme is very efficient and converges toward exact solution very rapidly.

Discontinuous pH gradient-mediated separation of TiO2-enriched phosphopeptides

PubMed Central

Park, Sung-Soo; Maudsley, Stuart

2010-01-01

Global profiling of phosphoproteomes has proven a great challenge due to the relatively low stoichiometry of protein phosphorylation and poor ionization efficiency in mass spectrometers. Effective, physiologically-relevant, phosphoproteome research relies on the efficient phosphopeptide enrichment from complex samples. Immobilized metal affinity chromatography and titanium dioxide chromatography (TOC) can greatly assist selective phosphopeptide enrichment. However, the complexity of resultant enriched samples is often still high, suggesting that further separation of enriched phosphopeptides is required. We have developed a pH-gradient elution technique for enhanced phosphopeptide identification in conjunction with TOC. Using this process, we have demonstrated its superiority to the traditional ‘one-pot’ strategies for differential protein identification. Our technique generated a highly specific separation of phosphopeptides by an applied pH-gradient between 9.2 and 11.3. The most efficient elution range for high-resolution phosphopeptide separation was between pH 9.2 and 9.4. High-resolution separation of multiply-phosphorylated peptides was primarily achieved using elution ranges > pH 9.4. Investigation of phosphopeptide sequences identified in each pH fraction indicated that phosphopeptides with phosphorylated residues proximal to acidic residues, including glutamic acid, aspartic acid, and other phosphorylated residues, were preferentially eluted at higher pH values. PMID:20946866

High Repetition Rate Pulsed 2-Micron Laser Transmitter for Coherent CO2 DIAL Measurement

NASA Technical Reports Server (NTRS)

Singh, Uprendra N.; Bai, Yingxin; Yu, Jirong; Petros, Mulugeta; Petzar, Paul J.; Trieu, Bo C.; Lee, Hyung

2009-01-01

A high repetition rate, highly efficient, Q-switched 2-micron laser system as the transmitter of a coherent differential absorption lidar for CO2 measurement has been developed at NASA Langley Research Center. Such a laser transmitter is a master-slave laser system. The master laser operates in a single frequency, either on-line or off-line of a selected CO2 absorption line. The slave laser is a Q-switched ring-cavity Ho:YLF laser which is pumped by a Tm:fiber laser. The repetition rate can be adjusted from a few hundred Hz to 10 kHz. The injection seeding success rate is from 99.4% to 99.95%. For 1 kHz operation, the output pulse energy is 5.5mJ with the pulse length of approximately 50 ns. The optical-to-optical efficiency is 39% when the pump power is 14.5W. The measured standard deviation of the laser frequency jitter is about 3 MHz.

Energy efficient engine high-pressure turbine single crystal vane and blade fabrication technology report

NASA Technical Reports Server (NTRS)

Giamei, A. F.; Salkeld, R. W.; Hayes, C. W.

1981-01-01

The objective of the High-Pressure Turbine Fabrication Program was to demonstrate the application and feasibility of Pratt & Whitney Aircraft-developed two-piece, single crystal casting and bonding technology on the turbine blade and vane configurations required for the high-pressure turbine in the Energy Efficient Engine. During the first phase of the program, casting feasibility was demonstrated. Several blade and vane halves were made for the bonding trials, plus solid blades and vanes were successfully cast for materials evaluation tests. Specimens exhibited the required microstructure and chemical composition. Bonding feasibility was demonstrated in the second phase of the effort. Bonding yields of 75 percent for the vane and 30 percent for the blade were achieved, and methods for improving these yield percentages were identified. A bond process was established for PWA 1480 single crystal material which incorporated a transient liquid phase interlayer. Bond properties were substantiated and sensitivities determined. Tooling die materials were identified, and an advanced differential thermal expansion tooling concept was incorporated into the bond process.

A parametric finite element method for solid-state dewetting problems with anisotropic surface energies

NASA Astrophysics Data System (ADS)

Bao, Weizhu; Jiang, Wei; Wang, Yan; Zhao, Quan

2017-02-01

We propose an efficient and accurate parametric finite element method (PFEM) for solving sharp-interface continuum models for solid-state dewetting of thin films with anisotropic surface energies. The governing equations of the sharp-interface models belong to a new type of high-order (4th- or 6th-order) geometric evolution partial differential equations about open curve/surface interface tracking problems which include anisotropic surface diffusion flow and contact line migration. Compared to the traditional methods (e.g., marker-particle methods), the proposed PFEM not only has very good accuracy, but also poses very mild restrictions on the numerical stability, and thus it has significant advantages for solving this type of open curve evolution problems with applications in the simulation of solid-state dewetting. Extensive numerical results are reported to demonstrate the accuracy and high efficiency of the proposed PFEM.

Efficient parallel architecture for highly coupled real-time linear system applications

NASA Technical Reports Server (NTRS)

Carroll, Chester C.; Homaifar, Abdollah; Barua, Soumavo

1988-01-01

A systematic procedure is developed for exploiting the parallel constructs of computation in a highly coupled, linear system application. An overall top-down design approach is adopted. Differential equations governing the application under consideration are partitioned into subtasks on the basis of a data flow analysis. The interconnected task units constitute a task graph which has to be computed in every update interval. Multiprocessing concepts utilizing parallel integration algorithms are then applied for efficient task graph execution. A simple scheduling routine is developed to handle task allocation while in the multiprocessor mode. Results of simulation and scheduling are compared on the basis of standard performance indices. Processor timing diagrams are developed on the basis of program output accruing to an optimal set of processors. Basic architectural attributes for implementing the system are discussed together with suggestions for processing element design. Emphasis is placed on flexible architectures capable of accommodating widely varying application specifics.

Considerations for higher efficiency and productivity in research activities.

PubMed

Forero, Diego A; Moore, Jason H

2016-01-01

There are several factors that are known to affect research productivity; some of them imply the need for large financial investments and others are related to work styles. There are some articles that provide suggestions for early career scientists (PhD students and postdocs) but few publications are oriented to professors about scientific leadership. As academic mentoring might be useful at all levels of experience, in this note we suggest several key considerations for higher efficiency and productivity in academic and research activities. More research is needed into the main work style features that differentiate highly productive scientists and research groups, as some of them could be innate and others could be transferable. As funding agencies, universities and research centers invest large amounts of money in order to have a better scientific productivity, a deeper understanding of these factors will be of high academic and societal impact.

The paradox of physicians and administrators in health care organizations.

PubMed

Peirce, J C

2000-01-01

Rapidly changing times in health care challenge both physicians and health care administrators to manage the paradox of providing orderly, high quality, and efficient care while bringing forth innovations to address present unmet problems and surprises that emerge. Health care has grown throughout the past several centuries through differentiation and integration, becoming a highly complex biological system with the hospital as the central attractive force--or "strange attractor"--during this century. The theoretical model of complex adaptive systems promises more effective strategic direction in addressing these chaotic times where the new strange attractor moves beyond the hospital.

A modular approach to large-scale design optimization of aerospace systems

NASA Astrophysics Data System (ADS)

Hwang, John T.

Gradient-based optimization and the adjoint method form a synergistic combination that enables the efficient solution of large-scale optimization problems. Though the gradient-based approach struggles with non-smooth or multi-modal problems, the capability to efficiently optimize up to tens of thousands of design variables provides a valuable design tool for exploring complex tradeoffs and finding unintuitive designs. However, the widespread adoption of gradient-based optimization is limited by the implementation challenges for computing derivatives efficiently and accurately, particularly in multidisciplinary and shape design problems. This thesis addresses these difficulties in two ways. First, to deal with the heterogeneity and integration challenges of multidisciplinary problems, this thesis presents a computational modeling framework that solves multidisciplinary systems and computes their derivatives in a semi-automated fashion. This framework is built upon a new mathematical formulation developed in this thesis that expresses any computational model as a system of algebraic equations and unifies all methods for computing derivatives using a single equation. The framework is applied to two engineering problems: the optimization of a nanosatellite with 7 disciplines and over 25,000 design variables; and simultaneous allocation and mission optimization for commercial aircraft involving 330 design variables, 12 of which are integer variables handled using the branch-and-bound method. In both cases, the framework makes large-scale optimization possible by reducing the implementation effort and code complexity. The second half of this thesis presents a differentiable parametrization of aircraft geometries and structures for high-fidelity shape optimization. Existing geometry parametrizations are not differentiable, or they are limited in the types of shape changes they allow. This is addressed by a novel parametrization that smoothly interpolates aircraft components, providing differentiability. An unstructured quadrilateral mesh generation algorithm is also developed to automate the creation of detailed meshes for aircraft structures, and a mesh convergence study is performed to verify that the quality of the mesh is maintained as it is refined. As a demonstration, high-fidelity aerostructural analysis is performed for two unconventional configurations with detailed structures included, and aerodynamic shape optimization is applied to the truss-braced wing, which finds and eliminates a shock in the region bounded by the struts and the wing.

Time-dependent jet flow and noise computations

NASA Technical Reports Server (NTRS)

Berman, C. H.; Ramos, J. I.; Karniadakis, G. E.; Orszag, S. A.

1990-01-01

Methods for computing jet turbulence noise based on the time-dependent solution of Lighthill's (1952) differential equation are demonstrated. A key element in this approach is a flow code for solving the time-dependent Navier-Stokes equations at relatively high Reynolds numbers. Jet flow results at Re = 10,000 are presented here. This code combines a computationally efficient spectral element technique and a new self-consistent turbulence subgrid model to supply values for Lighthill's turbulence noise source tensor.

Highly efficient Cas9-mediated transcriptional programming

DOE PAGES

Chavez, Alejandro; Scheiman, Jonathan; Vora, Suhani; ...

2015-03-02

The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. Here we describe an improved transcriptional regulator through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease-null Cas9. Here, we demonstrate its utility in activating endogenous coding and non-coding genes, targeting several genes simultaneously and stimulating neuronal differentiation of human induced pluripotent stem cells (iPSCs).

Evaluation of the protective effects of curcuminoid (curcumin and bisdemethoxycurcumin)-loaded liposomes against bone turnover in a cell-based model of osteoarthritis.

PubMed

Yeh, Chih-Chang; Su, Yu-Han; Lin, Yu-Jhe; Chen, Pin-Jyun; Shi, Chung-Sheng; Chen, Cheng-Nan; Chang, Hsin-I

2015-01-01

Curcumin (Cur) and bisdemethoxycurcumin (BDMC), extracted from Curcuma longa, are poorly water-soluble polyphenol compounds that have shown anti-inflammatory potential for the treatment of osteoarthritis. To increase cellular uptake of Cur and BDMC in bone tissue, soybean phosphatidylcholines were used for liposome formulation. In this study, curcuminoid (Cur and BDMC)-loaded liposomes were characterized in terms of particle size, encapsulation efficiency, liposome stability, and cellular uptake. The results show that there is about 70% entrapment efficiency of Cur and BDMC in liposomes and that particle sizes are stable after liposome formation. Both types of liposome can inhibit macrophage inflammation and osteoclast differential activities. In comparison with free drugs (Cur and BDMC), curcuminoid-loaded liposomes were less cytotoxic and expressed high cellular uptake of the drugs. Of note is that Cur-loaded liposomes can prevent liposome-dependent inhibition of osteoblast differentiation and mineralization, but BDMC-loaded liposomes could not. With interleukin (IL)-1β stimulation, curcuminoid-loaded liposomes can successfully downregulate the expression of inflammatory markers on osteoblasts, and show a high osteoprotegerin (OPG)/receptor activator of nuclear factor κB ligand (RANKL) ratio to prevent osteoclastogenesis. In the present study, we demonstrated that Cur and BDMC can be successfully encapsulated in liposomes and can reduce osteoclast activity and maintain osteoblast functions. Therefore, curcuminoid-loaded liposomes may slow osteoarthritis progression.

A Tutorial on RxODE: Simulating Differential Equation Pharmacometric Models in R.

PubMed

Wang, W; Hallow, K M; James, D A

2016-01-01

This tutorial presents the application of an R package, RxODE, that facilitates quick, efficient simulations of ordinary differential equation models completely within R. Its application is illustrated through simulation of design decision effects on an adaptive dosing regimen. The package provides an efficient, versatile way to specify dosing scenarios and to perform simulation with variability with minimal custom coding. Models can be directly translated to Rshiny applications to facilitate interactive, real-time evaluation/iteration on simulation scenarios.

Human Stem Cells Can Differentiate in Post-implantation Mouse Embryos.

PubMed

Tam, Patrick P L

2016-01-07

The potency of human pluripotent stem cells (hPSCs) to differentiate into germ layer derivatives is conventionally assessed by teratoma induction and in vitro differentiation. In this issue of Cell Stem Cell, Mascetti and Pedersen (2016) demonstrate that the human-mouse post-implantation chimera offers an efficient avenue to test the germ layer differentiation potential of hPSCs in mouse embryos ex vivo. Copyright © 2016 Elsevier Inc. All rights reserved.

A fully defined and scalable 3D culture system for human pluripotent stem cell expansion and differentiation

NASA Astrophysics Data System (ADS)

Lei, Yuguo; Schaffer, David V.

2013-12-01

Human pluripotent stem cells (hPSCs), including human embryonic stem cells and induced pluripotent stem cells, are promising for numerous biomedical applications, such as cell replacement therapies, tissue and whole-organ engineering, and high-throughput pharmacology and toxicology screening. Each of these applications requires large numbers of cells of high quality; however, the scalable expansion and differentiation of hPSCs, especially for clinical utilization, remains a challenge. We report a simple, defined, efficient, scalable, and good manufacturing practice-compatible 3D culture system for hPSC expansion and differentiation. It employs a thermoresponsive hydrogel that combines easy manipulation and completely defined conditions, free of any human- or animal-derived factors, and entailing only recombinant protein factors. Under an optimized protocol, the 3D system enables long-term, serial expansion of multiple hPSCs lines with a high expansion rate (∼20-fold per 5-d passage, for a 1072-fold expansion over 280 d), yield (∼2.0 × 107 cells per mL of hydrogel), and purity (∼95% Oct4+), even with single-cell inoculation, all of which offer considerable advantages relative to current approaches. Moreover, the system enabled 3D directed differentiation of hPSCs into multiple lineages, including dopaminergic neuron progenitors with a yield of ∼8 × 107 dopaminergic progenitors per mL of hydrogel and ∼80-fold expansion by the end of a 15-d derivation. This versatile system may be useful at numerous scales, from basic biological investigation to clinical development.

Artificial masculinization in tilapia involves androgen receptor activation.

PubMed

Golan, Matan; Levavi-Sivan, Berta

2014-10-01

Estrogens have a pivotal role in natural female sexual differentiation of tilapia while lack of steroids results in testicular development. Despite the fact that androgens do not participate in natural sex differentiation, synthetic androgens, mainly 17-α-methyltestosterone (MT) are effective in the production of all-male fish in aquaculture. The sex inversion potency of synthetic androgens may arise from their androgenic activity or else as inhibitors of aromatase activity. The current study is an attempt to differentiate between the two alleged activities in order to evaluate their contribution to the sex inversion process and aid the search for novel sex inversion agents. In the present study, MT inhibited aromatase activity, when applied in vitro as did the non-aromatizable androgen dihydrotestosterone (DHT). In comparison, exposure to fadrozole, a specific aromatase inhibitor, was considerably more effective. Androgenic activity of MT was evaluated by exposure of Sciaenochromis fryeri fry to the substance and testing for the appearance of blue color. Flutamide, an androgen antagonist, administered concomitantly with MT, reduced the appearance of the blue color and the sex inversion potency of MT in a dose-dependent manner. In tilapia, administration of MT, fadrozole or DHT resulted in efficient sex inversion while flutamide reduced the sex inversion potency of all three compounds. In the case of MT and DHT the decrease in sex inversion efficiency caused by flutamide is most likely due to the direct blocking of the androgen binding to its cognate receptor. The negative effect of flutamide on the efficiency of the fadrozole treatment may indicate that the masculinizing activity of fadrozole may be attributed to excess, un-aromatized, androgens accumulated in the differentiating gonad. The present study shows that when androgen receptors are blocked, there is a reduction in the efficiency of sex inversion treatments. Our results suggest that in contrast to natural sex differentiation, during sex inversion treatments, androgens, either endogenous or exogenous, participate in inducing testicular differentiation. Copyright © 2014 Elsevier Inc. All rights reserved.

Model-order reduction of lumped parameter systems via fractional calculus

NASA Astrophysics Data System (ADS)

Hollkamp, John P.; Sen, Mihir; Semperlotti, Fabio

2018-04-01

This study investigates the use of fractional order differential models to simulate the dynamic response of non-homogeneous discrete systems and to achieve efficient and accurate model order reduction. The traditional integer order approach to the simulation of non-homogeneous systems dictates the use of numerical solutions and often imposes stringent compromises between accuracy and computational performance. Fractional calculus provides an alternative approach where complex dynamical systems can be modeled with compact fractional equations that not only can still guarantee analytical solutions, but can also enable high levels of order reduction without compromising on accuracy. Different approaches are explored in order to transform the integer order model into a reduced order fractional model able to match the dynamic response of the initial system. Analytical and numerical results show that, under certain conditions, an exact match is possible and the resulting fractional differential models have both a complex and frequency-dependent order of the differential operator. The implications of this type of approach for both model order reduction and model synthesis are discussed.

Multiple Active Contours Guided by Differential Evolution for Medical Image Segmentation

PubMed Central

Cruz-Aceves, I.; Avina-Cervantes, J. G.; Lopez-Hernandez, J. M.; Rostro-Gonzalez, H.; Garcia-Capulin, C. H.; Torres-Cisneros, M.; Guzman-Cabrera, R.

2013-01-01

This paper presents a new image segmentation method based on multiple active contours guided by differential evolution, called MACDE. The segmentation method uses differential evolution over a polar coordinate system to increase the exploration and exploitation capabilities regarding the classical active contour model. To evaluate the performance of the proposed method, a set of synthetic images with complex objects, Gaussian noise, and deep concavities is introduced. Subsequently, MACDE is applied on datasets of sequential computed tomography and magnetic resonance images which contain the human heart and the human left ventricle, respectively. Finally, to obtain a quantitative and qualitative evaluation of the medical image segmentations compared to regions outlined by experts, a set of distance and similarity metrics has been adopted. According to the experimental results, MACDE outperforms the classical active contour model and the interactive Tseng method in terms of efficiency and robustness for obtaining the optimal control points and attains a high accuracy segmentation. PMID:23983809

Elasticity of human embryonic stem cells as determined by atomic force microscopy.

PubMed

Kiss, Robert; Bock, Henry; Pells, Steve; Canetta, Elisabetta; Adya, Ashok K; Moore, Andrew J; De Sousa, Paul; Willoughby, Nicholas A

2011-10-01

The expansive growth and differentiation potential of human embryonic stem cells (hESCs) make them a promising source of cells for regenerative medicine. However, this promise is off set by the propensity for spontaneous or uncontrolled differentiation to result in heterogeneous cell populations. Cell elasticity has recently been shown to characterize particular cell phenotypes, with undifferentiated and differentiated cells sometimes showing significant differences in their elasticities. In this study, we determined the Young's modulus of hESCs by atomic force microscopy using a pyramidal tip. Using this method we are able to take point measurements of elasticity at multiple locations on a single cell, allowing local variations due to cell structure to be identified. We found considerable differences in the elasticity of the analyzed hESCs, reflected by a broad range of Young's modulus (0.05-10 kPa). This surprisingly high variation suggests that elasticity could serve as the basis of a simple and efficient large scale purification/separation technique to discriminate subpopulations of hESCs.

The Effects of Simulated Microgravity on Gene Expression in Human Bone Marrow MSC's Under Osteogenic Differentiation

NASA Astrophysics Data System (ADS)

Buravkova, L. B.; Gershovich, J. G.; Gershovich, P. M.; Grigoriev, A. I.

2013-02-01

In this work it was found that the expression level of 144 genes significantly changed in human mesenchymal stem cells during their osteogenic differentiation after 20 days of exposure to simulated microgravity: the expression of 30 genes significantly increased (from 1.7 to 11.9 fold), and 114 - decreased (from 0.2 to 0.6 fold). Most of the revealed genes were attributed to the 11 major groups corresponding to its biological role in the cells. Additional group was formed from the genes which did not belong to these categories, or did not have a description in the known databases (such as Pubmed). The greatest number of genes with altered expression was found in the group “Matrix and Adhesion", while the lowest - in the "Apoptosis and the response to external stimuli" group. These findings suggest that cultured hMSCs, placed in non-standard conditions, maintain a high level of viability, but have significantly altered functional properties which could affect their efficiency to differentiate towards osteogenic direction.

The regulation of health care providers' payments when horizontal and vertical differentiation matter.

PubMed

Bardey, David; Canta, Chiara; Lozachmeur, Jean-Marie

2012-09-01

This paper analyzes the regulation of payment schemes for health care providers competing in both quality and product differentiation of their services. The regulator uses two instruments: a prospective payment per patient and a cost reimbursement rate. When the regulator can only use a prospective payment, the optimal price involves a trade-off between the level of quality provision and the level of horizontal differentiation. If this pure prospective payment leads to underprovision of quality and overdifferentiation, a mixed reimbursement scheme allows the regulator to improve the allocation efficiency. This is true for a relatively low level of patients' transportation costs. We also show that if the regulator cannot commit to the level of the cost reimbursement rate, the resulting allocation can dominate the one with full commitment. This occurs when the transportation cost is low or high enough, and the full commitment solution either implies full or zero cost reimbursement. Copyright © 2012 Elsevier B.V. All rights reserved.

Regulatory T Cells in Skin Facilitate Epithelial Stem Cell Differentiation.

PubMed

Ali, Niwa; Zirak, Bahar; Rodriguez, Robert Sanchez; Pauli, Mariela L; Truong, Hong-An; Lai, Kevin; Ahn, Richard; Corbin, Kaitlin; Lowe, Margaret M; Scharschmidt, Tiffany C; Taravati, Keyon; Tan, Madeleine R; Ricardo-Gonzalez, Roberto R; Nosbaum, Audrey; Bertolini, Marta; Liao, Wilson; Nestle, Frank O; Paus, Ralf; Cotsarelis, George; Abbas, Abul K; Rosenblum, Michael D

2017-06-01

The maintenance of tissue homeostasis is critically dependent on the function of tissue-resident immune cells and the differentiation capacity of tissue-resident stem cells (SCs). How immune cells influence the function of SCs is largely unknown. Regulatory T cells (Tregs) in skin preferentially localize to hair follicles (HFs), which house a major subset of skin SCs (HFSCs). Here, we mechanistically dissect the role of Tregs in HF and HFSC biology. Lineage-specific cell depletion revealed that Tregs promote HF regeneration by augmenting HFSC proliferation and differentiation. Transcriptional and phenotypic profiling of T regs and HFSCs revealed that skin-resident Tregs preferentially express high levels of the Notch ligand family member, Jagged 1 (Jag1). Expression of Jag1 on Tregs facilitated HFSC function and efficient HF regeneration. Taken together, our work demonstrates that Tregs in skin play a major role in HF biology by promoting the function of HFSCs. Copyright © 2017 Elsevier Inc. All rights reserved.

Design of electrospun nanofibrous mats for osteogenic differentiation of mesenchymal stem cells.

PubMed

Wang, Shige; Hu, Fei; Li, Jingchao; Zhang, Shuping; Shen, Mingwu; Huang, Mingxian; Shi, Xiangyang

2017-05-26

The clinical translation potential of mesenchymal stem cells (MSCs) in regenerative medicine has been greatly exploited. With the merits of high surface area to volume ratio, facile control of components, well retained topography, and the capacity to mimic the native extracellular matrix (ECM), nanofibers have received a great deal of attention as bone tissue engineering scaffolds. Electrospinning has been considered as an efficient approach for scale-up fabrication of nanofibrous materials. Electrospun nanofibers are capable of stimulating cell-matrix interaction to form a cell niche, directing cellular behavior, and promoting the MSCs adhesion and proliferation. In this review, we give a comprehensive literature survey on the mechanisms of electrospun nanofibers in supporting the MSCs differentiation. Specifically, the influences of biological and physical osteogenic inductive cues on the MSCs osteogenic differentiation are reviewed. Along with the significant advances in the field, current research challenges and future perspectives are also discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

Imaging structural covariance in the development of intelligence.

PubMed

Khundrakpam, Budhachandra S; Lewis, John D; Reid, Andrew; Karama, Sherif; Zhao, Lu; Chouinard-Decorte, Francois; Evans, Alan C

2017-01-01

Verbal and non-verbal intelligence in children is highly correlated, and thus, it has been difficult to differentiate their neural substrates. Nevertheless, recent studies have shown that verbal and non-verbal intelligence can be dissociated and focal cortical regions corresponding to each have been demonstrated. However, the pattern of structural covariance corresponding to verbal and non-verbal intelligence remains unexplored. In this study, we used 586 longitudinal anatomical MRI scans of subjects aged 6-18 years, who had concurrent intelligence quotient (IQ) testing on the Wechsler Abbreviated Scale of Intelligence. Structural covariance networks (SCNs) were constructed using interregional correlations in cortical thickness for low-IQ (Performance IQ=100±8, Verbal IQ=100±7) and high-IQ (PIQ=121±8, VIQ=120±9) groups. From low- to high-VIQ group, we observed constrained patterns of anatomical coupling among cortical regions, complemented by observations of higher global efficiency and modularity, and lower local efficiency in high-VIQ group, suggesting a shift towards a more optimal topological organization. Analysis of nodal topological properties (regional efficiency and participation coefficient) revealed greater involvement of left-hemispheric language related regions including inferior frontal and superior temporal gyri for high-VIQ group. From low- to high-PIQ group, we did not observe significant differences in anatomical coupling patterns, global and nodal topological properties. Our findings indicate that people with higher verbal intelligence have structural brain differences from people with lower verbal intelligence - not only in localized cortical regions, but also in the patterns of anatomical coupling among widely distributed cortical regions, possibly resulting to a system-level reorganization that might lead to a more efficient organization in high-VIQ group. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Mouse decellularised liver scaffold improves human embryonic and induced pluripotent stem cells differentiation into hepatocyte-like cells

PubMed Central

Scottoni, Federico; Crowley, Claire; Fiadeiro, Rebeca; Maghsoudlou, Panagiotis; Pellegata, Alessandro Filippo; Mazzacuva, Francesca; Gjinovci, Asllan; Lyne, Anne-Marie; Zulini, Justine; Little, Daniel; Mosaku, Olukunbi; Kelly, Deirdre; De Coppi, Paolo; Gissen, Paul

2017-01-01

Liver transplantation is the definitive treatment of liver failure but donor organ shortage limits its availability. Stem cells are highly expandable and have the potential to differentiate into any specialist cell. Use of patient-derived induced Pluripotent Stem Cells (hiPSCs) has the additional advantage for organ regeneration therapies by removing the need for immunosuppression. We compared hepatocyte differentiation of human embryonic stem cells (hESCs) and hiPSCs in a mouse decellularised liver scaffold (3D) with standard in vitro protocol (2D). Mouse livers were decellularised preserving micro-architecture, blood vessel network and extracellular matrix. hESCs and hiPSCs were primed towards the definitive endoderm. Cells were then seeded either in 3D or 2D cultures and the hepatocyte differentiation was continued. Both hESCs and hiPSCs differentiated more efficiently in 3D than in 2D, with higher and earlier expression of mature hepatocyte marker albumin, lipid and glycogen synthesis associated with a decrease in expression of fetal hepatocyte marker alpha-fetoprotein. Thus we conclude that stem cell hepatocyte differentiation in 3D culture promotes faster cell maturation. This finding suggests that optimised 3D protocols could allow generation of mature liver cells not achieved so far in standard 2D conditions and lead to improvement in cell models of liver disease and regenerative medicine applications. PMID:29261712

Optimization of gear ratio and power distribution for a multimotor powertrain of an electric vehicle

NASA Astrophysics Data System (ADS)

Urbina Coronado, Pedro Daniel; Orta Castañón, Pedro; Ahuett-Garza, Horacio

2018-02-01

The architecture and design of the propulsion system of electric vehicles are highly important for the reduction of energy losses. This work presents a powertrain composed of four electric motors in which each motor is connected with a different gear ratio to the differential of the rear axle. A strategy to reduce energy losses is proposed, in which two phases are applied. Phase 1 uses a divide-and-conquer approach to increase the overall output efficiency by obtaining the optimal torque distribution for the electric motors. Phase 2 applies a genetic algorithm to find the optimal value of the gear ratios, in which each individual of each generation applies Phase 1. The results show an optimized efficiency map for the output torque and speed of the powertrain. The increase in efficiency and the reduction of energy losses are validated by the use of numerical experiments in various driving cycles.

Efficient Construction of Discrete Adjoint Operators on Unstructured Grids by Using Complex Variables

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.; Kleb, William L.

2005-01-01

A methodology is developed and implemented to mitigate the lengthy software development cycle typically associated with constructing a discrete adjoint solver for aerodynamic simulations. The approach is based on a complex-variable formulation that enables straightforward differentiation of complicated real-valued functions. An automated scripting process is used to create the complex-variable form of the set of discrete equations. An efficient method for assembling the residual and cost function linearizations is developed. The accuracy of the implementation is verified through comparisons with a discrete direct method as well as a previously developed handcoded discrete adjoint approach. Comparisons are also shown for a large-scale configuration to establish the computational efficiency of the present scheme. To ultimately demonstrate the power of the approach, the implementation is extended to high temperature gas flows in chemical nonequilibrium. Finally, several fruitful research and development avenues enabled by the current work are suggested.

Efficient Construction of Discrete Adjoint Operators on Unstructured Grids Using Complex Variables

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.; Kleb, William L.

2005-01-01

A methodology is developed and implemented to mitigate the lengthy software development cycle typically associated with constructing a discrete adjoint solver for aerodynamic simulations. The approach is based on a complex-variable formulation that enables straightforward differentiation of complicated real-valued functions. An automated scripting process is used to create the complex-variable form of the set of discrete equations. An efficient method for assembling the residual and cost function linearizations is developed. The accuracy of the implementation is verified through comparisons with a discrete direct method as well as a previously developed handcoded discrete adjoint approach. Comparisons are also shown for a large-scale configuration to establish the computational efficiency of the present scheme. To ultimately demonstrate the power of the approach, the implementation is extended to high temperature gas flows in chemical nonequilibrium. Finally, several fruitful research and development avenues enabled by the current work are suggested.

Increase in the Shockley–Read–Hall recombination rate in InGaN/GaN QWs as the main mechanism of the efficiency droop in LEDs at high injection levels

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

Bochkareva, N. I.; Rebane, Yu. T.; Shreter, Yu. G., E-mail: y.shreter@mail.ioffe.ru

It is shown that the efficiency droop observed as the current through a GaN-based light-emitting diode increases is due to a decrease in the Shockley–Read–Hall nonradiative lifetime. The lifetime decreases with increasing current because a steadily growing number of traps in the density-of-states tails of InGaN/GaN quantum wells become nonradiative recombination centers upon the approach of quasi-Fermi levels to the band edges. This follows from the correlation between the efficiency droop and the appearance of negative differential capacitance, observed in the study. The correlation appears due to slow trap recharging via the trap-assisted tunneling of electrons through the n-type barriermore » of the quantum well and to the inductive nature of the diode-current variation with forward bias.« less

Development of a model to assess environmental performance, concerning HSE-MS principles.

PubMed

Abbaspour, M; Hosseinzadeh Lotfi, F; Karbassi, A R; Roayaei, E; Nikoomaram, H

2010-06-01

The main objective of the present study was to develop a valid and appropriate model to evaluate companies' efficiency and environmental performance, concerning health, safety, and environmental management system principles. The proposed model overcomes the shortcomings of the previous models developed in this area. This model has been designed on the basis of a mathematical method known as Data Envelopment Analysis (DEA). In order to differentiate high-performing companies from weak ones, one of DEA nonradial models named as enhanced Russell graph efficiency measure has been applied. Since some of the environmental performance indicators cannot be controlled by companies' managers, it was necessary to develop the model in a way that it could be applied when discretionary and/or nondiscretionary factors were involved. The model, then, has been modified on a real case that comprised 12 oil and gas general contractors. The results showed the relative efficiency, inefficiency sources, and the rank of contractors.

Melatonin enhances neural stem cell differentiation and engraftment by increasing mitochondrial function.

PubMed

Mendivil-Perez, Miguel; Soto-Mercado, Viviana; Guerra-Librero, Ana; Fernandez-Gil, Beatriz I; Florido, Javier; Shen, Ying-Qiang; Tejada, Miguel A; Capilla-Gonzalez, Vivian; Rusanova, Iryna; Garcia-Verdugo, José M; Acuña-Castroviejo, Darío; López, Luis Carlos; Velez-Pardo, Carlos; Jimenez-Del-Rio, Marlene; Ferrer, José M; Escames, Germaine

2017-09-01

Neural stem cells (NSCs) are regarded as a promising therapeutic approach to protecting and restoring damaged neurons in neurodegenerative diseases (NDs) such as Parkinson's disease and Alzheimer's disease (PD and AD, respectively). However, new research suggests that NSC differentiation is required to make this strategy effective. Several studies have demonstrated that melatonin increases mature neuronal markers, which reflects NSC differentiation into neurons. Nevertheless, the possible involvement of mitochondria in the effects of melatonin during NSC differentiation has not yet been fully established. We therefore tested the impact of melatonin on NSC proliferation and differentiation in an attempt to determine whether these actions depend on modulating mitochondrial activity. We measured proliferation and differentiation markers, mitochondrial structural and functional parameters as well as oxidative stress indicators and also evaluated cell transplant engraftment. This enabled us to show that melatonin (25 μM) induces NSC differentiation into oligodendrocytes and neurons. These effects depend on increased mitochondrial mass/DNA/complexes, mitochondrial respiration, and membrane potential as well as ATP synthesis in NSCs. It is also interesting to note that melatonin prevented oxidative stress caused by high levels of mitochondrial activity. Finally, we found that melatonin enriches NSC engraftment in the ND mouse model following transplantation. We concluded that a combined therapy involving transplantation of NSCs pretreated with pharmacological doses of melatonin could efficiently restore neuronal cell populations in PD and AD mouse models depending on mitochondrial activity promotion. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Efficient and rapid derivation of primitive neural stem cells and generation of brain subtype neurons from human pluripotent stem cells.

PubMed

Yan, Yiping; Shin, Soojung; Jha, Balendu Shekhar; Liu, Qiuyue; Sheng, Jianting; Li, Fuhai; Zhan, Ming; Davis, Janine; Bharti, Kapil; Zeng, Xianmin; Rao, Mahendra; Malik, Nasir; Vemuri, Mohan C

2013-11-01

Human pluripotent stem cells (hPSCs), including human embryonic stem cells and human induced pluripotent stem cells, are unique cell sources for disease modeling, drug discovery screens, and cell therapy applications. The first step in producing neural lineages from hPSCs is the generation of neural stem cells (NSCs). Current methods of NSC derivation involve the time-consuming, labor-intensive steps of an embryoid body generation or coculture with stromal cell lines that result in low-efficiency derivation of NSCs. In this study, we report a highly efficient serum-free pluripotent stem cell neural induction medium that can induce hPSCs into primitive NSCs (pNSCs) in 7 days, obviating the need for time-consuming, laborious embryoid body generation or rosette picking. The pNSCs expressed the neural stem cell markers Pax6, Sox1, Sox2, and Nestin; were negative for Oct4; could be expanded for multiple passages; and could be differentiated into neurons, astrocytes, and oligodendrocytes, in addition to the brain region-specific neuronal subtypes GABAergic, dopaminergic, and motor neurons. Global gene expression of the transcripts of pNSCs was comparable to that of rosette-derived and human fetal-derived NSCs. This work demonstrates an efficient method to generate expandable pNSCs, which can be further differentiated into central nervous system neurons and glia with temporal, spatial, and positional cues of brain regional heterogeneity. This method of pNSC derivation sets the stage for the scalable production of clinically relevant neural cells for cell therapy applications in good manufacturing practice conditions.

Primary Spinal OPC Culture System from Adult Zebrafish to Study Oligodendrocyte Differentiation In Vitro.

PubMed

Kroehne, Volker; Tsata, Vasiliki; Marrone, Lara; Froeb, Claudia; Reinhardt, Susanne; Gompf, Anne; Dahl, Andreas; Sterneckert, Jared; Reimer, Michell M

2017-01-01

Endogenous oligodendrocyte progenitor cells (OPCs) are a promising target to improve functional recovery after spinal cord injury (SCI) by remyelinating denuded, and therefore vulnerable, axons. Demyelination is the result of a primary insult and secondary injury, leading to conduction blocks and long-term degeneration of the axons, which subsequently can lead to the loss of their neurons. In response to SCI, dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes (OLs). Therefore, researchers strive to control OPC responses, and utilize small molecule screening approaches in order to identify mechanisms of OPC activation, proliferation, migration and differentiation. In zebrafish, OPCs remyelinate axons of the optic tract after lysophosphatidylcholine (LPC)-induced demyelination back to full thickness myelin sheaths. In contrast to zebrafish, mammalian OPCs are highly vulnerable to excitotoxic stress, a cause of secondary injury, and remyelination remains insufficient. Generally, injury induced remyelination leads to shorter internodes and thinner myelin sheaths in mammals. In this study, we show that myelin sheaths are lost early after a complete spinal transection injury, but are re-established within 14 days after lesion. We introduce a novel, easy-to-use, inexpensive and highly reproducible OPC culture system based on dormant spinal OPCs from adult zebrafish that enables in vitro analysis. Zebrafish OPCs are robust, can easily be purified with high viability and taken into cell culture. This method enables to examine why zebrafish OPCs remyelinate better than their mammalian counterparts, identify cell intrinsic responses, which could lead to pro-proliferating or pro-differentiating strategies, and to test small molecule approaches. In this methodology paper, we show efficient isolation of OPCs from adult zebrafish spinal cord and describe culture conditions that enable analysis up to 10 days in vitro . Finally, we demonstrate that zebrafish OPCs differentiate into Myelin Basic Protein (MBP)-expressing OLs when co-cultured with human motor neurons differentiated from induced pluripotent stem cells (iPSCs). This shows that the basic mechanisms of oligodendrocyte differentiation are conserved across species and that understanding the regulation of zebrafish OPCs can contribute to the development of new treatments to human diseases.

Supplementation with IL-6 and Muscle Cell Culture Conditioned Media Enhances Myogenic Differentiation of Adipose Tissue-Derived Stem Cells through STAT3 Activation.

PubMed

Seo, Eunhui; Kang, Hwansu; Lim, Oh-Kyung; Jun, Hee-Sook

2018-05-24

Mature skeletal muscle cells cannot be expanded in culture systems. Therefore, it is difficult to construct an in vitro model for muscle diseases. To establish an efficient protocol for myogenic differentiation of human adipose tissue-derived stem cells (hADSCs), we investigated whether addition of IL-6 and/or myocyte-conditioned media (CM) to conventional differentiation media can shorten the differentiation period. hADSCs were differentiated to myocytes using the conventional protocol or modified with the addition of 25 pg/mL IL-6 and/or C2C12 CM (25% v / v ). The expression of MyoD and myogenine mRNA was significantly higher at 5⁻6 days after differentiation using the modified protocol than with the conventional protocol. mRNA and protein expression of myosin heavy chain, a marker of myotubes, was significantly upregulated at 28 and 42 days of differentiation using the modified protocol, and the level achieved after a 4-week differentiation period was similar to that achieved at 6 weeks using the conventional protocol. The expression of p-STAT3 was significantly increased when the modified protocol was used. Similarly, addition of colivelin, a STAT3 activator, instead of IL-6 and C2C12 CM, promoted the myogenic differentiation of ADSCs. The modified protocol improved differentiation efficiency and reduced the time required for differentiation of myocytes. It might be helpful to save cost and time when preparing myocytes for cell therapies and drug discovery.

Raman spectroscopy of skin neoplasms

NASA Astrophysics Data System (ADS)

Moryatov, A. A.; Kozlov, S. V.; Kaganov, O. I.; Orlov, A. E.; Zaharov, V. P.; Batrachenko, I. A.; Artemiev, D. N.; Blinov, N. V.

2017-09-01

Skin melanoma is spread inhomogeneously worldwide, particularly in Samara region there are high figures of skin neoplasms sick rate as well—18.6%. Research goal: to develop a new method of early non-invasive differential diagnostics of skin neoplasms. Registration of Raman spectrum was implemented in the distance of 3-4 mm, the spectrum registration from pathologically changed zone was subsequently conducted, then from healthy skin zone. The test time for 1 patient was no longer than 3-5 min. In a range of experiments ex vivo there were the following results: melanoma—24, basal cell cancer—25, squamosus cell sarcinoma—7, nevus pigmentosis—9, other malignant neoplasms—6; in vivo: melanoma—9, basal cell cancer—8, nevus pigmentosis—2, other benign neoplasms—2. The first results of the research dedicated to studying permissive opportunities of Raman spectroscopy, with successive two-phase analysis of received parameters display high efficiency of method of differential diagnostic for skin melanoma and other malignant neoplasms, pigment and benign skin neoplasms. Safety and rapidity of the research reveal a high potential of the technique.

Reduced-order modelling of parameter-dependent, linear and nonlinear dynamic partial differential equation models.

PubMed

Shah, A A; Xing, W W; Triantafyllidis, V

2017-04-01

In this paper, we develop reduced-order models for dynamic, parameter-dependent, linear and nonlinear partial differential equations using proper orthogonal decomposition (POD). The main challenges are to accurately and efficiently approximate the POD bases for new parameter values and, in the case of nonlinear problems, to efficiently handle the nonlinear terms. We use a Bayesian nonlinear regression approach to learn the snapshots of the solutions and the nonlinearities for new parameter values. Computational efficiency is ensured by using manifold learning to perform the emulation in a low-dimensional space. The accuracy of the method is demonstrated on a linear and a nonlinear example, with comparisons with a global basis approach.

Reduced-order modelling of parameter-dependent, linear and nonlinear dynamic partial differential equation models

PubMed Central

Xing, W. W.; Triantafyllidis, V.

2017-01-01

In this paper, we develop reduced-order models for dynamic, parameter-dependent, linear and nonlinear partial differential equations using proper orthogonal decomposition (POD). The main challenges are to accurately and efficiently approximate the POD bases for new parameter values and, in the case of nonlinear problems, to efficiently handle the nonlinear terms. We use a Bayesian nonlinear regression approach to learn the snapshots of the solutions and the nonlinearities for new parameter values. Computational efficiency is ensured by using manifold learning to perform the emulation in a low-dimensional space. The accuracy of the method is demonstrated on a linear and a nonlinear example, with comparisons with a global basis approach. PMID:28484327

Low-power G m-C filter employing current-reuse differential difference amplifiers

DOE PAGES

Mincey, John S.; Briseno-Vidrios, Carlos; Silva-Martinez, Jose; ...

2016-08-10

This study deals with the design of low-power, high performance, continuous-time filters. The proposed OTA architecture employs current-reuse differential difference amplifiers in order to produce more power efficient Gm-C filter solutions. To demonstrate this, a 6th order low-pass Butterworth filter was designed in 0.18 m CMOS achieving a 65-MHz -3-dB frequency, an in-band input-referred third-order intercept point of 12.0 dBm, and an input referred noise density of 40 nV/Hz1=2, while only consuming 8.07 mW from a 1.8 V supply and occupying a total chip area of 0.21 mm2 with a power consumption of only 1.19 mW per pole.

Transcriptome-Based Differentiation of Closely-Related Miscanthus Lines

DOE PAGES

Chouvarine, Philippe; Cooksey, Amanda M.; McCarthy, Fiona M.; ...

2012-01-10

Distinguishing between individuals is critical to those conducting animal/plant breeding, food safety/quality research, diagnostic and clinical testing, and evolutionary biology studies. Classical genetic identification studies are based on marker polymorphisms, but polymorphism-based techniques are time and labor intensive and often cannot distinguish between closely related individuals. Illumina sequencing technologies provide the detailed sequence data required for rapid and efficient differentiation of related species, lines/cultivars, and individuals in a cost-effective manner. Here we describe the use of Illumina high-throughput exome sequencing, coupled with SNP mapping, as a rapid means of distinguishing between related cultivars of the lignocellulosic bioenergy crop giant miscanthusmore » (Miscanthus6giganteus). We provide the first exome sequence database for Miscanthus species complete with Gene Ontology (GO) functional annotations."« less

Computing generalized Langevin equations and generalized Fokker-Planck equations.

PubMed

Darve, Eric; Solomon, Jose; Kia, Amirali

2009-07-07

The Mori-Zwanzig formalism is an effective tool to derive differential equations describing the evolution of a small number of resolved variables. In this paper we present its application to the derivation of generalized Langevin equations and generalized non-Markovian Fokker-Planck equations. We show how long time scales rates and metastable basins can be extracted from these equations. Numerical algorithms are proposed to discretize these equations. An important aspect is the numerical solution of the orthogonal dynamics equation which is a partial differential equation in a high dimensional space. We propose efficient numerical methods to solve this orthogonal dynamics equation. In addition, we present a projection formalism of the Mori-Zwanzig type that is applicable to discrete maps. Numerical applications are presented from the field of Hamiltonian systems.

Low-power G m-C filter employing current-reuse differential difference amplifiers

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

Mincey, John S.; Briseno-Vidrios, Carlos; Silva-Martinez, Jose

This study deals with the design of low-power, high performance, continuous-time filters. The proposed OTA architecture employs current-reuse differential difference amplifiers in order to produce more power efficient Gm-C filter solutions. To demonstrate this, a 6th order low-pass Butterworth filter was designed in 0.18 m CMOS achieving a 65-MHz -3-dB frequency, an in-band input-referred third-order intercept point of 12.0 dBm, and an input referred noise density of 40 nV/Hz1=2, while only consuming 8.07 mW from a 1.8 V supply and occupying a total chip area of 0.21 mm2 with a power consumption of only 1.19 mW per pole.

[Correlations of 18F-Fluorodeoxyglucose Positron Emission Tomography/Magnetic Resonance Imaging Parameters with the Pathological Differentiation of Head and Neck Squamous Cell Carcinoma and Their Diagnostic Efficiencies].

PubMed

Dang, Hao Dan; Chen, Yu; Shi, Xiao Hua; Hou, Bo; Xing, Hai Qun; Zhang, Tao; Chen, Xing Ming; Zhang, Zhu Hua; Xue, Hua Dan; Jin, Zheng Yu

2018-04-28

Objective To evaluate the correlation of the positron emission tomography/magnetic resonance imaging (PET/MR) parameters with the pathological differentiation of head and neck squamous cell carcinoma(HNSCC) and the diagnostic efficiencies of PET/MR parameters. Methods Patients with clinical suspicion of HNSCC were included and underwent PET/MR scan. HNSCC was pathologically confirmed in all these patients. The PET/MR examination included PET and MR sequences of diffusion-weighted imaging (DWI) and T2-and T1-weighted imaging. The multiple parameters of PET/MR included the mean values of apparent diffusion coefficient(ADC mean ) and the maximum and mean values of standardized uptake value (SUV max and SUV mean ) were measured and estimated. The correlations of all the parameters and distribution between the different tumor differentiation groups were analyzed. Logistic regression was utilized to build the model as the PET/MR combined parameter for predicting the differentiation by multiple parameters of PET/MR. The receiver operating characteristic curve was calculated for each parameter and the combination. Results Totally 23 patients were included in this study:9 patients (9 males and 0 female) had well-differentiated tumor,with an average age of (61.0±6.8)years;14 cases had moderately-differentiated (n=10) or poorly-differentiated tumors (n=4),with an average age of (62.0±9.1) years. All the patients were males. There was statistical correlation between SUV mean and SUV max (P<0.001);however,ADC mean showed no statistical correlation with SUV max and with SUV mean (P=0.42,P=0.13). ADC mean and SUV mean showed significant difference between well-differentiated group and moderately-poorly-differentiated group (P=0.005,P=0.007). Compared with the individual parameters,the combination of PET/MR parameters with SUV mean and ADC mean had higher efficacy in predicting tumor differentiation,with an area under curve of 0.84. Conclusions The distributions of ADC mean ,SUV max and SUV mean differ among HNSCC with different pathological differentiation. Compared with the individual parameters,the combination of the PET/MR parameters has higher efficiency in predicting tumor differentiation.

Rho kinase inhibitor Y-27632 promotes the differentiation of human bone marrow mesenchymal stem cells into keratinocyte-like cells in xeno-free conditioned medium.

PubMed

Li, Zhenzhen; Han, Shichao; Wang, Xingqin; Han, Fu; Zhu, Xiongxiang; Zheng, Zhao; Wang, Hongtao; Zhou, Qin; Wang, Yunchuan; Su, Linlin; Shi, Jihong; Tang, Chaowu; Hu, Dahai

2015-03-11

Bone marrow mesenchymal stem cells (BMSCs), which have the ability to self-renew and to differentiate into multiple cell types, have recently become a novel strategy for cell-based therapies. The differentiation of BMSCs into keratinocytes may be beneficial for patients with burns, disease, or trauma. However, the currently available cells are exposed to animal materials during their cultivation and induction. These xeno-contaminations severely limit their clinical outcomes. Previous studies have shown that the Rho kinase (ROCK) inhibitor Y-27632 can promote induction efficiency and regulate the self-renewal and differentiation of stem cells. In the present study, we attempted to establish a xeno-free system for the differentiation of BMSCs into keratinocytes and to investigate whether Y-27632 can facilitate this differentiation. BMSCs isolated from patients were cultured by using a xeno-free system and characterised by using flow cytometric analysis and adipogenic and osteogenic differentiation assays. Human primary keratinocytes were also isolated from patients. Then, the morphology, population doubling time, and β-galactosidase staining level of these cells were evaluated in the presence or absence of Y-27632 to determine the effects of Y-27632 on the state of the keratinocytes. Keratinocyte-like cells (KLCs) were detected at different time points by immunocytofluorescence analysis. Moreover, the efficiency of BMSC differentiation under different conditions was measured by quantitative real-time-polymerase chain reaction (RT-PCR) and Western blot analyses. The ROCK inhibitor Y-27632 promoted the proliferation and lifespan of human primary keratinocytes. In addition, we showed that keratinocyte-specific markers could be detected in BMSCs cultured in a xeno-free system using keratinocyte-conditioned medium (KCM) independent of the presence of Y-27632. However, the efficiency of the differentiation of BMSCs into KLCs was significantly higher in the presence of Y-27632 using immunofluorescence, quantitative RT-PCR, and Western blot analyses. This study demonstrated that Y-27632 could promote the proliferation and survival of human primary keratinocytes in a xeno-free culture system. In addition, we found that BMSCs have the ability to differentiate into KLCs in KCM and that Y-27632 can facilitate this differentiation. Our results suggest that BMSCs are capable of differentiating into KLCs in vitro and that the ROCK pathway may play a critical role in this process.

Precision cut lung slices as an efficient tool for in vitro lung physio-pharmacotoxicology studies.

PubMed

Morin, Jean-Paul; Baste, Jean-Marc; Gay, Arnaud; Crochemore, Clément; Corbière, Cécile; Monteil, Christelle

2013-01-01

1.We review the specific approaches for lung tissue slices preparation and incubation systems and the research application fields in which lung slices proved to be a very efficient alternative to animal experimentation for biomechanical, physiological, pharmacological and toxicological approaches. 2.Focus is made on air-liquid interface dynamic organ culture systems that allow direct tissue exposure to complex aerosol and that best mimic in vivo lung tissue physiology. 3.A compilation of research applications in the fields of vascular and airway reactivity, mucociliary transport, polyamine transport, xenobiotic biotransformation, chemicals toxicology and complex aerosols supports the concept that precision cut lung slices are a very efficient tool maintaining highly differentiated functions similar to in vivo lung organ when kept under dynamic organ culture. They also have been successfully used for lung gene transfer efficiency assessment, for lung viral infection efficiency assessment, for studies of tissue preservation media and tissue post-conditioning to optimize lung tissue viability before grafting. 4.Taken all together, the reviewed studies point to a great interest for precision cut lung slices as an efficient and valuable alternative to in vivo lung organ experimentation.

Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations.

PubMed

Wu, Shuang; Liu, Zhi-Ping; Qiu, Xing; Wu, Hulin

2014-01-01

The immune response to viral infection is regulated by an intricate network of many genes and their products. The reverse engineering of gene regulatory networks (GRNs) using mathematical models from time course gene expression data collected after influenza infection is key to our understanding of the mechanisms involved in controlling influenza infection within a host. A five-step pipeline: detection of temporally differentially expressed genes, clustering genes into co-expressed modules, identification of network structure, parameter estimate refinement, and functional enrichment analysis, is developed for reconstructing high-dimensional dynamic GRNs from genome-wide time course gene expression data. Applying the pipeline to the time course gene expression data from influenza-infected mouse lungs, we have identified 20 distinct temporal expression patterns in the differentially expressed genes and constructed a module-based dynamic network using a linear ODE model. Both intra-module and inter-module annotations and regulatory relationships of our inferred network show some interesting findings and are highly consistent with existing knowledge about the immune response in mice after influenza infection. The proposed method is a computationally efficient, data-driven pipeline bridging experimental data, mathematical modeling, and statistical analysis. The application to the influenza infection data elucidates the potentials of our pipeline in providing valuable insights into systematic modeling of complicated biological processes.

Non-photosynthetic plastids as hosts for metabolic engineering.

PubMed

Mellor, Silas Busck; Behrendorff, James B Y H; Nielsen, Agnieszka Zygadlo; Jensen, Poul Erik; Pribil, Mathias

2018-04-13

Using plants as hosts for production of complex, high-value compounds and therapeutic proteins has gained increasing momentum over the past decade. Recent advances in metabolic engineering techniques using synthetic biology have set the stage for production yields to become economically attractive, but more refined design strategies are required to increase product yields without compromising development and growth of the host system. The ability of plant cells to differentiate into various tissues in combination with a high level of cellular compartmentalization represents so far the most unexploited plant-specific resource. Plant cells contain organelles called plastids that retain their own genome, harbour unique biosynthetic pathways and differentiate into distinct plastid types upon environmental and developmental cues. Chloroplasts, the plastid type hosting the photosynthetic processes in green tissues, have proven to be suitable for high yield protein and bio-compound production. Unfortunately, chloroplast manipulation often affects photosynthetic efficiency and therefore plant fitness. In this respect, plastids of non-photosynthetic tissues, which have focused metabolisms for synthesis and storage of particular classes of compounds, might prove more suitable for engineering the production and storage of non-native metabolites without affecting plant fitness. This review provides the current state of knowledge on the molecular mechanisms involved in plastid differentiation and focuses on non-photosynthetic plastids as alternative biotechnological platforms for metabolic engineering. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

DEVELOPMENTS IN GRworkbench

NASA Astrophysics Data System (ADS)

Moylan, Andrew; Scott, Susan M.; Searle, Anthony C.

2006-02-01

The software tool GRworkbench is an ongoing project in visual, numerical General Relativity at The Australian National University. Recently, GRworkbench has been significantly extended to facilitate numerical experimentation in analytically-defined space-times. The numerical differential geometric engine has been rewritten using functional programming techniques, enabling objects which are normally defined as functions in the formalism of differential geometry and General Relativity to be directly represented as function variables in the C++ code of GRworkbench. The new functional differential geometric engine allows for more accurate and efficient visualisation of objects in space-times and makes new, efficient computational techniques available. Motivated by the desire to investigate a recent scientific claim using GRworkbench, new tools for numerical experimentation have been implemented, allowing for the simulation of complex physical situations.

Synovial fluid progenitors expressing CD90+ from normal but not osteoarthritic joints undergo chondrogenic differentiation without micro-mass culture.

PubMed

Krawetz, Roman J; Wu, Yiru Elizabeth; Martin, Liam; Rattner, Jerome B; Matyas, John R; Hart, David A

2012-01-01

Mesenchymal progenitor cells (MPCs) can differentiate into osteoblasts, adipocytes, and chondrocytes, and are in part responsible for maintaining tissue integrity. Recently, a progenitor cell population has been found within the synovial fluid that shares many similarities with bone marrow MPCs. These synovial fluid MPCs (sfMPCs) share the ability to differentiate into bone and fat, with a bias for cartilage differentiation. In this study, sfMPCs were isolated from human and canine synovial fluid collected from normal individuals and those with osteoarthritis (human: clinician-diagnosed, canine: experimental) to compare the differentiation potential of CD90+ vs. CD90- sfMPCs, and to determine if CD90 (Thy-1) is a predictive marker of synovial fluid progenitors with chondrogenic capacity in vitro. sfMPCs were derived from synovial fluid from normal and OA knee joints. These cells were induced to differentiate into chondrocytes and analyzed using quantitative PCR, immunofluorescence, and electron microscopy. The CD90+ subpopulation of sfMPCs had increased chondrogenic potential compared to the CD90- population. Furthermore, sfMPCs derived from healthy joints did not require a micro-mass step for efficient chondrogenesis. Whereas sfMPCs from OA synovial fluid retain the ability to undergo chondrogenic differentiation, they require micro-mass culture conditions. Overall, this study has demonstrated an increased chondrogenic potential within the CD90+ fraction of human and canine sfMPCs and that this population of cells derived from healthy normal joints do not require a micro-mass step for efficient chondrogenesis, while sfMPCs obtained from OA knee joints do not differentiate efficiently into chondrocytes without the micro-mass procedure. These results reveal a fundamental shift in the chondrogenic ability of cells isolated from arthritic joint fluids, and we speculate that the mechanism behind this change of cell behavior is exposure to the altered milieu of the OA joint fluid, which will be examined in further studies.

High transduction efficiency of circulating first trimester fetal mesenchymal stem cells: potential targets for in utero ex vivo gene therapy.

PubMed

Campagnoli, Cesare; Bellantuono, Ilaria; Kumar, Sailesh; Fairbairn, Leslie J; Roberts, Irene; Fisk, Nicholas M

2002-08-01

We recently reported the existence of fetal mesenchymal stem cells in first trimester fetal blood. Here we demonstrate that fetal mesenchymal stem cells from as early as eight weeks of gestation can be retrovirally transduced with 99% efficiency without selection. Circulating fetal mesenchymal stem cells are known to readily expand and differentiate into multiple tissue types both in vitro and in vivo, and might be suitable vehicles for prenatal gene delivery. With advances in early fetal blood sampling techniques, we suggest that genetic disorders causing irreversible damage before birth could be treated in utero in the late first/early second trimester by genetically manipulated autologous fetal stem cells.

An Investigation of Differential Deposition for Figure Corrections in Full-Shell Grazing-Incidents X-Ray Optics

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail V.; Kilaru, Kirenmayee; Ramsey, Brian D.

2009-01-01

We are investigating differential deposition as a way of correcting small figure errors inside full-shell grazing-incidence x-ray optics. The optics in our study are fabricated using the electroformed-nickel-replication technique, and the figure errors arise from fabrication errors in the mandrel, from which the shells are replicated, as well as errors induced during the electroforming process. Combined, these give sub-micron-scale figure deviations which limit the angular resolution of the optics to approx. 10 arcsec. Sub-micron figure errors can be corrected by selectively depositing (physical vapor deposition) material inside the shell. The requirements for this filler material are that it must not degrade the ultra-smooth surface finish necessary for efficient x-ray reflection (approx. 5 A rms), and must not be highly stressed. In addition, a technique must be found to produce well controlled and defined beams within highly constrained geometries, as some of our mirror shells are less than 3 cm in diameter.

An Efficient Platform for Astrocyte Differentiation from Human Induced Pluripotent Stem Cells.

PubMed

Tcw, Julia; Wang, Minghui; Pimenova, Anna A; Bowles, Kathryn R; Hartley, Brigham J; Lacin, Emre; Machlovi, Saima I; Abdelaal, Rawan; Karch, Celeste M; Phatnani, Hemali; Slesinger, Paul A; Zhang, Bin; Goate, Alison M; Brennand, Kristen J

2017-08-08

Growing evidence implicates the importance of glia, particularly astrocytes, in neurological and psychiatric diseases. Here, we describe a rapid and robust method for the differentiation of highly pure populations of replicative astrocytes from human induced pluripotent stem cells (hiPSCs), via a neural progenitor cell (NPC) intermediate. We evaluated this protocol across 42 NPC lines (derived from 30 individuals). Transcriptomic analysis demonstrated that hiPSC-astrocytes from four individuals are highly similar to primary human fetal astrocytes and characteristic of a non-reactive state. hiPSC-astrocytes respond to inflammatory stimulants, display phagocytic capacity, and enhance microglial phagocytosis. hiPSC-astrocytes also possess spontaneous calcium transient activity. Our protocol is a reproducible, straightforward (single medium), and rapid (<30 days) method to generate populations of hiPSC-astrocytes that can be used for neuron-astrocyte and microglia-astrocyte co-cultures for the study of neuropsychiatric disorders. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

The discriminatory power of ribotyping as automatable technique for differentiation of bacteria.

PubMed

Schumann, Peter; Pukall, Rüdiger

2013-09-01

Since the introduction of ribonucleic acid gene restriction patterns as taxonomic tools in 1986, ribotyping has become an established method for systematics, epidemiological, ecological and population studies of microorganisms. In the last 25 years, several modifications have improved the convenience, reproducibility and turn-around time of this technique. The technological development culminated in the automation of ribotyping which allowed for high-throughput applications e.g. in the quality control of food production, pharmaceutical industry and culture collections. The capability of the fully automated RiboPrinter(®) System for the differentiation of bacteria below the species level is compared with the discriminatory power of traditional ribotyping, of molecular fingerprint techniques like PFGE, MLST and MLVA as well as of MALDI-TOF mass spectrometry. While automated RiboPrinting is advantageous with respect to standardization, ease and speed, PCR ribotyping has proved being a highly discriminatory, flexible, robust and cost-efficient routine technique which makes inter-laboratory comparison and build of ribotype databases possible, too. Copyright © 2013 Elsevier GmbH. All rights reserved.

The large discretization step method for time-dependent partial differential equations

NASA Technical Reports Server (NTRS)

Haras, Zigo; Taasan, Shlomo

1995-01-01

A new method for the acceleration of linear and nonlinear time dependent calculations is presented. It is based on the Large Discretization Step (LDS) approximation, defined in this work, which employs an extended system of low accuracy schemes to approximate a high accuracy discrete approximation to a time dependent differential operator. Error bounds on such approximations are derived. These approximations are efficiently implemented in the LDS methods for linear and nonlinear hyperbolic equations, presented here. In these algorithms the high and low accuracy schemes are interpreted as the same discretization of a time dependent operator on fine and coarse grids, respectively. Thus, a system of correction terms and corresponding equations are derived and solved on the coarse grid to yield the fine grid accuracy. These terms are initialized by visiting the fine grid once in many coarse grid time steps. The resulting methods are very general, simple to implement and may be used to accelerate many existing time marching schemes.

Are Strong Zonal Winds in Giant Planets Caused by Density-Stratification?

NASA Astrophysics Data System (ADS)

Verhoeven, J.; Stellmach, S.

2012-12-01

One of the most striking features of giant planets like Jupiter and Saturn are the zonal wind patterns observed on their surfaces. The mechanism that drives this differential rotation is still not clearly identified and is currently strongly debated in the astro- and geophysics community. Different mechanisms have been proposed over the last decades. Here, a recently discovered mechanism based on background density stratification (Glatzmaier et al., 2009) is investigated. This mechanism has the potential to overcome known difficulties of previous explanations and its efficiency has been demonstrated in 2-d simulations covering equatorial planes. By performing highly resolved numerical simulations in a local Cartesian geometry, we are able to test the efficiency and functionality of this mechanism in turbulent, rotating convection in three spatial dimensions. The choice of a Cartesian model geometry naturally excludes other known mechanisms capable of producing differential rotation, thus allowing us to investigate the role of density stratification in isolation. Typically, the dynamics can be classified into two main regimes: A regime exhibiting strong zonal winds for weak to moderate thermal driving and a regime where zonal winds are largely absent in the case of a strong thermal forcing. Our results indicate that previous 2-d results must be handled with care and can only explain parts of the full 3-d behavior. We show that the density-stratification mechanism tends to operate in a more narrow parameter range in 3-d as compared to 2-d simulations. The dynamics of the regime transition is shown to differ in both cases, which renders scaling laws derived from two-dimensional studies questionable. Based on our results, we provide estimates for the importance of the density-stratification mechanism for giant planets like Jupiter (strong density stratification), for systems like the Earth's core (weak density stratification) and compare its efficiency with other suggested mechanisms for driving differential rotation. Gary A. Glatzmaier, Martha Evonuk and Tamara M. Rogers (2009), Differential rotation in giant planets maintained by density-stratified turbulent convection. Geophysical and Astrophysical Fluid Dynamics, Vol. 103, No. 1, 31-51.

Design for high-power, single-lobe, grating-surface-emitting quantum cascade lasers enabled by plasmon-enhanced absorption of antisymmetric modes

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

Sigler, C.; Kirch, J. D.; Mawst, L. J.

2014-03-31

Resonant coupling of the transverse-magnetic polarized (guided) optical mode of a quantum-cascade laser (QCL) to the antisymmetric surface-plasmon modes of 2nd-order distributed-feedback (DFB) metal/semiconductor gratings results in strong antisymmetric-mode absorption. In turn, lasing in the symmetric mode, that is, surface emission in a single-lobe far-field beam pattern, is strongly favored over controllable ranges in grating duty cycle and tooth height. By using core-region characteristics of a published 4.6 μm-emitting QCL, grating-coupled surface-emitting (SE) QCLs are analyzed and optimized for highly efficient single-lobe operation. For infinite-length devices, it is found that when the antisymmetric mode is resonantly absorbed, the symmetric mode hasmore » negligible absorption loss (∼0.1 cm{sup −1}) while still being efficiently outcoupled, through the substrate, by the DFB grating. For finite-length devices, 2nd-order distributed Bragg reflector (DBR) gratings are used on both sides of the DFB grating to prevent uncontrolled reflections from cleaved facets. Equations for the threshold-current density and the differential quantum efficiency of SE DFB/DBR QCLs are derived. For 7 mm-long, 8.0 μm-wide, 4.6 μm-emitting devices, with an Ag/InP grating of ∼39% duty cycle, and ∼0.22 μm tooth height, threshold currents as low as 0.45 A are projected. Based on experimentally obtained internal efficiency values from high-performance QCLs, slope efficiencies as high as 3.4 W/A are projected; thus, offering a solution for watt-range, single-lobe CW operation from SE, mid-infrared QCLs.« less

Derivation and characterization of Chinese human embryonic stem cell line with high potential to differentiate into pancreatic and hepatic cells.

PubMed

Shi, Cheng; Shen, Huan; Jiang, Wei; Song, Zhi-Hua; Wang, Cheng-Yan; Wei, Li-Hui

2011-04-01

Human embryonic stem cells have prospective uses in regenerative medicine and drug screening. Every human embryonic stem cell line has its own genetic background, which determines its specific ability for differentiation as well as susceptibility to drugs. It is necessary to compile many human embryonic stem cell lines with various backgrounds for future clinical use, especially in China due to its large population. This study contributes to isolating new Chinese human embryonic stem cell lines with clarified directly differentiation ability. Donated embryos that exceeded clinical use in our in vitro fertilization-embryo transfer (IVF-ET) center were collected to establish human embryonic stem cells lines with informed consent. The classic growth factors of basic fibroblast growth factor (bFGF) and recombinant human leukaemia inhibitory factor (hLIF) for culturing embryonic stem cells were used to capture the stem cells from the plated embryos. Mechanical and enzymetic methods were used to propagate the newly established human embryonic stem cells line. The new cell line was checked for pluripotent characteristics with detecting the expression of stemness genes and observing spontaneous differentiation both in vitro and in vivo. Finally similar step-wise protocols from definitive endoderm to target specific cells were used to check the cell line's ability to directly differentiate into pancreatic and hepatic cells. We generated a new Chinese human embryonic stem cells line, CH1. This cell line showed the same characteristics as other reported Chinese human embryonic stem cells lines: normal morphology, karyotype and pluripotency in vitro and in vivo. The CH1 cells could be directly differentiated towards pancreatic and hepatic cells with equal efficiency compared to the H1 cell line. This newly established Chinese cell line, CH1, which is pluripotent and has high potential to differentiate into pancreatic and hepatic cells, will provide a useful tool for embryo development research, along with clinical treatments for diabetes and some hepatic diseases.

Arrested neural and advanced mesenchymal differentiation of glioblastoma cells-comparative study with neural progenitors

PubMed Central

2009-01-01

Background Although features of variable differentiation in glioblastoma cell cultures have been reported, a comparative analysis of differentiation properties of normal neural GFAP positive progenitors, and those shown by glioblastoma cells, has not been performed. Methods Following methods were used to compare glioblastoma cells and GFAP+NNP (NHA): exposure to neural differentiation medium, exposure to adipogenic and osteogenic medium, western blot analysis, immunocytochemistry, single cell assay, BrdU incorporation assay. To characterize glioblastoma cells EGFR amplification analysis, LOH/MSI analysis, and P53 nucleotide sequence analysis were performed. Results In vitro differentiation of cancer cells derived from eight glioblastomas was compared with GFAP-positive normal neural progenitors (GFAP+NNP). Prior to exposure to differentiation medium, both types of cells showed similar multilineage phenotype (CD44+/MAP2+/GFAP+/Vimentin+/Beta III-tubulin+/Fibronectin+) and were positive for SOX-2 and Nestin. In contrast to GFAP+NNP, an efficient differentiation arrest was observed in all cell lines isolated from glioblastomas. Nevertheless, a subpopulation of cells isolated from four glioblastomas differentiated after serum-starvation with varying efficiency into derivatives indistinguishable from the neural derivatives of GFAP+NNP. Moreover, the cells derived from a majority of glioblastomas (7 out of 8), as well as GFAP+NNP, showed features of mesenchymal differentiation when exposed to medium with serum. Conclusion Our results showed that stable co-expression of multilineage markers by glioblastoma cells resulted from differentiation arrest. According to our data up to 95% of glioblastoma cells can present in vitro multilineage phenotype. The mesenchymal differentiation of glioblastoma cells is advanced and similar to mesenchymal differentiation of normal neural progenitors GFAP+NNP. PMID:19216795

CRISPR screen identifies the NCOR/HDAC3 complex as a major suppressor of differentiation in rhabdomyosarcoma

PubMed Central

Phelps, Michael P.; Bailey, Jenna N.; Vleeshouwer-Neumann, Terra

2016-01-01

Dysregulated gene expression resulting from abnormal epigenetic alterations including histone acetylation and deacetylation has been demonstrated to play an important role in driving tumor growth and progression. However, the mechanisms by which specific histone deacetylases (HDACs) regulate differentiation in solid tumors remains unclear. Using pediatric rhabdomyosarcoma (RMS) as a paradigm to elucidate the mechanism blocking differentiation in solid tumors, we identified HDAC3 as a major suppressor of myogenic differentiation from a high-efficiency Clustered regularly interspaced short palindromic repeats (CRISPR)-based phenotypic screen of class I and II HDAC genes. Detailed characterization of the HDAC3-knockout phenotype in vitro and in vivo using a tamoxifen-inducible CRISPR targeting strategy demonstrated that HDAC3 deacetylase activity and the formation of a functional complex with nuclear receptor corepressors (NCORs) were critical in restricting differentiation in RMS. The NCOR/HDAC3 complex specifically functions by blocking myoblast determination protein 1 (MYOD1)-mediated activation of myogenic differentiation. Interestingly, there was also a transient up-regulation of growth-promoting genes upon initial HDAC3 targeting, revealing a unique cancer-specific response to the forced transition from a neoplastic state to terminal differentiation. Our study applied modifications of CRISPR/CRISPR-associated endonuclease 9 (Cas9) technology to interrogate the function of essential cancer genes and pathways and has provided insights into cancer cell adaptation in response to altered differentiation status. Because current pan-HDAC inhibitors have shown disappointing results in clinical trials of solid tumors, therapeutic targets specific to HDAC3 function represent a promising option for differentiation therapy in malignant tumors with dysregulated HDAC3 activity. PMID:27956629

Isolation of genes negatively or positively co-expressed with human recombination activating gene 1 (RAG1) by differential display PCR (DD RT-PCR).

PubMed

Verkoczy, L K; Berinstein, N L

1998-10-01

Differential display PCR (DD RT-PCR) has been extensively used for analysis of differential gene expression, but continues to be hampered by technical limitations that impair its effectiveness. In order to isolate novel genes co-expressing with human RAG1, we have developed an effective, multi-tiered screening/purification approach which effectively complements the standard DD RT-PCR methodology. In 'primary' screens, standard DD RT-PCR was used, detecting 22 reproducible differentially expressed amplicons between clonally related cell variants with differential constitutive expression of RAG mRNAs. 'Secondary' screens used differential display (DD) amplicons as probes in low and high stringency northern blotting. Eight of 22 independent DD amplicons detected nine independent differentially expressed transcripts. 'Tertiary' screens used reconfirmed amplicons as probes in northern analysis of multiple RAG-and RAG+sources. Reconfirmed DD amplicons detected six independent RAG co-expressing transcripts. All DD amplicons reconfirmed by northern blot were a heterogeneous mixture of cDNAs, necessitating further purification to isolate single cDNAs prior to subcloning and sequencing. To effectively select the appropriate cDNAs from DD amplicons, we excised and eluted the cDNA(s) directly from regions of prior northern blots in which differentially expressed transcripts were detected. Sequences of six purified cDNA clones specifically detecting RAG co-expressing transcripts included matches to portions of the human RAG2 and BSAP regions and to four novel partial cDNAs (three with homologies to human ESTs). Overall, our results also suggest that even when using clonally related variants from the same cell line in addition to all appropriate internal controls previously reported, further screening and purification steps are still required in order to efficiently and specifically isolate differentially expressed genes by DD RT-PCR.

CRISPR screen identifies the NCOR/HDAC3 complex as a major suppressor of differentiation in rhabdomyosarcoma.

PubMed

Phelps, Michael P; Bailey, Jenna N; Vleeshouwer-Neumann, Terra; Chen, Eleanor Y

2016-12-27

Dysregulated gene expression resulting from abnormal epigenetic alterations including histone acetylation and deacetylation has been demonstrated to play an important role in driving tumor growth and progression. However, the mechanisms by which specific histone deacetylases (HDACs) regulate differentiation in solid tumors remains unclear. Using pediatric rhabdomyosarcoma (RMS) as a paradigm to elucidate the mechanism blocking differentiation in solid tumors, we identified HDAC3 as a major suppressor of myogenic differentiation from a high-efficiency Clustered regularly interspaced short palindromic repeats (CRISPR)-based phenotypic screen of class I and II HDAC genes. Detailed characterization of the HDAC3-knockout phenotype in vitro and in vivo using a tamoxifen-inducible CRISPR targeting strategy demonstrated that HDAC3 deacetylase activity and the formation of a functional complex with nuclear receptor corepressors (NCORs) were critical in restricting differentiation in RMS. The NCOR/HDAC3 complex specifically functions by blocking myoblast determination protein 1 (MYOD1)-mediated activation of myogenic differentiation. Interestingly, there was also a transient up-regulation of growth-promoting genes upon initial HDAC3 targeting, revealing a unique cancer-specific response to the forced transition from a neoplastic state to terminal differentiation. Our study applied modifications of CRISPR/CRISPR-associated endonuclease 9 (Cas9) technology to interrogate the function of essential cancer genes and pathways and has provided insights into cancer cell adaptation in response to altered differentiation status. Because current pan-HDAC inhibitors have shown disappointing results in clinical trials of solid tumors, therapeutic targets specific to HDAC3 function represent a promising option for differentiation therapy in malignant tumors with dysregulated HDAC3 activity.

Hidden physics models: Machine learning of nonlinear partial differential equations

NASA Astrophysics Data System (ADS)

Raissi, Maziar; Karniadakis, George Em

2018-03-01

While there is currently a lot of enthusiasm about "big data", useful data is usually "small" and expensive to acquire. In this paper, we present a new paradigm of learning partial differential equations from small data. In particular, we introduce hidden physics models, which are essentially data-efficient learning machines capable of leveraging the underlying laws of physics, expressed by time dependent and nonlinear partial differential equations, to extract patterns from high-dimensional data generated from experiments. The proposed methodology may be applied to the problem of learning, system identification, or data-driven discovery of partial differential equations. Our framework relies on Gaussian processes, a powerful tool for probabilistic inference over functions, that enables us to strike a balance between model complexity and data fitting. The effectiveness of the proposed approach is demonstrated through a variety of canonical problems, spanning a number of scientific domains, including the Navier-Stokes, Schrödinger, Kuramoto-Sivashinsky, and time dependent linear fractional equations. The methodology provides a promising new direction for harnessing the long-standing developments of classical methods in applied mathematics and mathematical physics to design learning machines with the ability to operate in complex domains without requiring large quantities of data.

Natural killer cell-based adoptive immunotherapy eradicates and drives differentiation of chemoresistant bladder cancer stem-like cells.

PubMed

Ferreira-Teixeira, Margarida; Paiva-Oliveira, Daniela; Parada, Belmiro; Alves, Vera; Sousa, Vitor; Chijioke, Obinna; Münz, Christian; Reis, Flávio; Rodrigues-Santos, Paulo; Gomes, Célia

2016-10-21

High-grade non-muscle invasive bladder cancer (NMIBC) has a high risk of recurrence and progression to muscle-invasive forms, which seems to be largely related to the presence of tumorigenic stem-like cell populations that are refractory to conventional therapies. Here, we evaluated the therapeutic potential of Natural Killer (NK) cell-based adoptive immunotherapy against chemoresistant bladder cancer stem-like cells (CSCs) in a pre-clinical relevant model, using NK cells from healthy donors and NMIBC patients. Cytokine-activated NK cells from healthy donors and from high-grade NMIBC patients were phenotypically characterized and assayed in vitro against stem-like and bulk differentiated bladder cancer cells. Stem-like cells were isolated from two bladder cancer cell lines using the sphere-forming assay. The in vivo therapeutic efficacy was evaluated in mice bearing a CSC-induced orthotopic bladder cancer. Animals were treated by intravesical instillation of interleukin-activated NK cells. Tumor response was evaluated longitudinally by non-invasive bioluminescence imaging. NK cells from healthy donors upon activation with IL-2 and IL-15 kills indiscriminately both stem-like and differentiated tumor cells via stress ligand recognition. In addition to cell killing, NK cells shifted CSCs towards a more differentiated phenotype, rendering them more susceptible to cisplatin, highlighting the benefits of a possible combined therapy. On the contrary, NK cells from NMIBC patients displayed a low density on NK cytotoxicity receptors, adhesion molecules and a more immature phenotype, losing their ability to kill and drive differentiation of CSCs. The local administration, via the transurethral route, of activated NK cells from healthy donors provides an efficient tumor infiltration and a subsequent robust tumoricidal activity against bladder cancer with high selective cytolytic activity against CSCs, leading to a dramatic reduction in tumor burden from 80 % to complete remission. Although pre-clinical, our results strongly suggest that an immunotherapeutic strategy using allogeneic activated NK cells from healthy donors is effective and should be exploited as a complementary therapeutic strategy in high-risk NMIBC patients to prevent tumor recurrence and progression.

Genetic Modification of Human Pancreatic Progenitor Cells Through Modified mRNA.

PubMed

Lu, Song; Chow, Christie C; Zhou, Junwei; Leung, Po Sing; Tsui, Stephen K; Lui, Kathy O

2016-01-01

In this chapter, we describe a highly efficient genetic modification strategy for human pancreatic progenitor cells using modified mRNA-encoding GFP and Neurogenin-3. The properties of modified mRNA offer an invaluable platform to drive protein expression, which has broad applicability in pathway regulation, directed differentiation, and lineage specification. This approach can also be used to regulate expression of other pivotal transcription factors during pancreas development and might have potential therapeutic values in regenerative medicine.

A Metric to Quantify Shared Visual Attention in Two-Person Teams

NASA Technical Reports Server (NTRS)

Gontar, Patrick; Mulligan, Jeffrey B.

2015-01-01

Critical tasks in high-risk environments are often performed by teams, the members of which must work together efficiently. In some situations, the team members may have to work together to solve a particular problem, while in others it may be better for them to divide the work into separate tasks that can be completed in parallel. We hypothesize that these two team strategies can be differentiated on the basis of shared visual attention, measured by gaze tracking.

Oxygen-controlled automated neural differentiation of mouse embryonic stem cells.

PubMed

Mondragon-Teran, Paul; Tostoes, Rui; Mason, Chris; Lye, Gary J; Veraitch, Farlan S

2013-03-01

Automation and oxygen tension control are two tools that provide significant improvements to the reproducibility and efficiency of stem cell production processes. the aim of this study was to establish a novel automation platform capable of controlling oxygen tension during both the cell-culture and liquid-handling steps of neural differentiation processes. We built a bespoke automation platform, which enclosed a liquid-handling platform in a sterile, oxygen-controlled environment. An airtight connection was used to transfer cell culture plates to and from an automated oxygen-controlled incubator. Our results demonstrate that our system yielded comparable cell numbers, viabilities, metabolism profiles and differentiation efficiencies when compared with traditional manual processes. Interestingly, eliminating exposure to ambient conditions during the liquid-handling stage resulted in significant improvements in the yield of MAP2-positive neural cells, indicating that this level of control can improve differentiation processes. This article describes, for the first time, an automation platform capable of maintaining oxygen tension control during both the cell-culture and liquid-handling stages of a 2D embryonic stem cell differentiation process.

Modeling to Optimize Terminal Stem Cell Differentiation

PubMed Central

Gallicano, G. Ian

2013-01-01

Embryonic stem cell (ESC), iPCs, and adult stem cells (ASCs) all are among the most promising potential treatments for heart failure, spinal cord injury, neurodegenerative diseases, and diabetes. However, considerable uncertainty in the production of ESC-derived terminally differentiated cell types has limited the efficiency of their development. To address this uncertainty, we and other investigators have begun to employ a comprehensive statistical model of ESC differentiation for determining the role of intracellular pathways (e.g., STAT3) in ESC differentiation and determination of germ layer fate. The approach discussed here applies the Baysian statistical model to cell/developmental biology combining traditional flow cytometry methodology and specific morphological observations with advanced statistical and probabilistic modeling and experimental design. The final result of this study is a unique tool and model that enhances the understanding of how and when specific cell fates are determined during differentiation. This model provides a guideline for increasing the production efficiency of therapeutically viable ESCs/iPSCs/ASC derived neurons or any other cell type and will eventually lead to advances in stem cell therapy. PMID:24278782

The diversity of (13)C isotope discrimination in a Quercus robur full-sib family is associated with differences in intrinsic water use efficiency, transpiration efficiency, and stomatal conductance.

PubMed

Roussel, Magali; Dreyer, Erwin; Montpied, Pierre; Le-Provost, Grégoire; Guehl, Jean-Marc; Brendel, Oliver

2009-01-01

(13)C discrimination in organic matter with respect to atmospheric CO(2) (Delta(13)C) is under tight genetic control in many plant species, including the pedunculate oak (Quercus robur L.) full-sib progeny used in this study. Delta(13)C is expected to reflect intrinsic water use efficiency, but this assumption requires confirmation due to potential interferences with mesophyll conductance to CO(2), or post-photosynthetic discrimination. In order to dissect the observed Delta(13)C variability in this progeny, six genotypes that have previously been found to display extreme phenotypic values of Delta(13)C [either very high ('high Delta') or low ('low Delta') phenotype] were selected, and transpiration efficiency (TE; accumulated biomass/transpired water), net CO(2) assimilation rate (A), stomatal conductance for water vapour (g(s)), and intrinsic water use efficiency (W(i)=A/g(s)) were compared with Delta(13)C in bulk leaf matter, wood, and cellulose in wood. As expected, 'high Delta' displayed higher values of Delta(13)C not only in bulk leaf matter, but also in wood and cellulose. This confirmed the stability of the genotypic differences in Delta(13)C recorded earlier. 'High Delta' also displayed lower TE, lower W(i), and higher g(s). A small difference was detected in photosynthetic capacity but none in mesophyll conductance to CO(2). 'High Delta' and 'low Delta' displayed very similar leaf anatomy, except for higher stomatal density in 'high Delta'. Finally, diurnal courses of leaf gas exchange revealed a higher g(s) in 'high Delta' in the morning than in the afternoon when the difference decreased. The gene ERECTA, involved in the control of water use efficiency, leaf differentiation, and stomatal density, displayed higher expression levels in 'low Delta'. In this progeny, the variability of Delta(13)C correlated closely with that of W(i) and TE. Genetic differences of Delta(13)C and W(i) can be ascribed to differences in stomatal conductance and stomatal density but not in photosynthetic capacity.

Differential pollen placement on an Old World nectar bat increases pollination efficiency.

PubMed

Stewart, Alyssa B; Dudash, Michele R

2016-01-01

Plant species that share pollinators are potentially subject to non-adaptive interspecific pollen transfer, resulting in reduced reproductive success. Mechanisms that increase pollination efficiency between conspecific individuals are therefore highly beneficial. Many nocturnally flowering plant species in Thailand are pollinated by the nectar bat Eonycteris spelaea (Pteropodidae). This study tested the hypothesis that plant species within a community reduce interspecific pollen movement by placing pollen on different areas of the bat's body. Using flight cage trials, pollen transfer by E. spelaea was compared between conspecific versus heterospecific flowers across four bat-pollinated plant genera. Pollen from four locations on the bat's body was also quantified to determine if pollen placement varies by plant species. It was found that E. spelaea transfers significantly more pollen between conspecific than heterospecific flowers, and that diverse floral designs produce significantly different patterns of pollen deposition on E. spelaea. In the Old World tropics, differential pollen placement is a mechanism that reduces competition among bat-pollinated plant species sharing a common pollinator. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacao L., the chocolate tree.

PubMed

Maximova, Siela N; Florez, Sergio; Shen, Xiangling; Niemenak, Nicolas; Zhang, Yufan; Curtis, Wayne; Guiltinan, Mark J

2014-07-16

Theobroma cacao L. is a tropical fruit tree, the seeds of which are used to create chocolate. In vitro somatic embryogenesis (SE) of cacao is a propagation system useful for rapid mass-multiplication to accelerate breeding programs and to provide plants directly to farmers. Two major limitations of cacao SE remain: the efficiency of embryo production is highly genotype dependent and the lack of full cotyledon development results in low embryo to plant conversion rates. With the goal to better understand SE development and to improve the efficiency of SE conversion we examined gene expression differences between zygotic and somatic embryos using a whole genome microarray. The expression of 28,752 genes was determined at 4 developmental time points during zygotic embryogenesis (ZE) and 2 time points during cacao somatic embryogenesis (SE). Within the ZE time course, 10,288 differentially expressed genes were enriched for functions related to responses to abiotic and biotic stimulus, metabolic and cellular processes. A comparison ZE and SE expression profiles identified 10,175 differentially expressed genes. Many TF genes, putatively involved in ethylene metabolism and response, were more strongly expressed in SEs as compared to ZEs. Expression levels of genes involved in fatty acid metabolism, flavonoid biosynthesis and seed storage protein genes were also differentially expressed in the two types of embryos. Large numbers of genes were differentially regulated during various stages of both ZE and SE development in cacao. The relatively higher expression of ethylene and flavonoid related genes during SE suggests that the developing tissues may be experiencing high levels of stress during SE maturation caused by the in vitro environment. The expression of genes involved in the synthesis of auxin, polyunsaturated fatty acids and secondary metabolites was higher in SEs relative to ZEs despite lack of lipid and metabolite accumulation. These differences in gene transcript levels associated with critical processes during seed development are consistent with the fact that somatic embryos do not fully develop the large storage cotyledons found in zygotic embryos. These results provide insight towards design of improved protocols for cacao somatic embryogenesis.

Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacao L., the chocolate tree

PubMed Central

2014-01-01

Background Theobroma cacao L. is a tropical fruit tree, the seeds of which are used to create chocolate. In vitro somatic embryogenesis (SE) of cacao is a propagation system useful for rapid mass-multiplication to accelerate breeding programs and to provide plants directly to farmers. Two major limitations of cacao SE remain: the efficiency of embryo production is highly genotype dependent and the lack of full cotyledon development results in low embryo to plant conversion rates. With the goal to better understand SE development and to improve the efficiency of SE conversion we examined gene expression differences between zygotic and somatic embryos using a whole genome microarray. Results The expression of 28,752 genes was determined at 4 developmental time points during zygotic embryogenesis (ZE) and 2 time points during cacao somatic embryogenesis (SE). Within the ZE time course, 10,288 differentially expressed genes were enriched for functions related to responses to abiotic and biotic stimulus, metabolic and cellular processes. A comparison ZE and SE expression profiles identified 10,175 differentially expressed genes. Many TF genes, putatively involved in ethylene metabolism and response, were more strongly expressed in SEs as compared to ZEs. Expression levels of genes involved in fatty acid metabolism, flavonoid biosynthesis and seed storage protein genes were also differentially expressed in the two types of embryos. Conclusions Large numbers of genes were differentially regulated during various stages of both ZE and SE development in cacao. The relatively higher expression of ethylene and flavonoid related genes during SE suggests that the developing tissues may be experiencing high levels of stress during SE maturation caused by the in vitro environment. The expression of genes involved in the synthesis of auxin, polyunsaturated fatty acids and secondary metabolites was higher in SEs relative to ZEs despite lack of lipid and metabolite accumulation. These differences in gene transcript levels associated with critical processes during seed development are consistent with the fact that somatic embryos do not fully develop the large storage cotyledons found in zygotic embryos. These results provide insight towards design of improved protocols for cacao somatic embryogenesis. PMID:25030026

Can differentiated care models solve the crisis in HIV treatment financing? Analysis of prospects for 38 countries in sub-Saharan Africa.

PubMed

Barker, Catherine; Dutta, Arin; Klein, Kate

2017-07-21

Rapid scale-up of antiretroviral therapy (ART) in the context of financial and health system constraints has resulted in calls to maximize efficiency in ART service delivery. Adopting differentiated care models (DCMs) for ART could potentially be more cost-efficient and improve outcomes. However, no study comprehensively projects the cost savings across countries. We model the potential reduction in facility-level costs and number of health workers needed when implementing two types of DCMs while attempting to reach 90-90-90 targets in 38 sub-Saharan African countries from 2016 to 2020. We estimated the costs of three service delivery models: (1) undifferentiated care, (2) differentiated care by patient age and stability, and (3) differentiated care by patient age, stability, key vs. general population status, and urban vs. rural location. Frequency of facility visits, type and frequency of laboratory testing, and coverage of community ART support vary by patient subgroup. For each model, we estimated the total costs of antiretroviral drugs, laboratory commodities, and facility-level personnel and overhead. Certain groups under four-criteria differentiation require more intensive inputs. Community-based ART costs were included in the DCMs. We take into account underlying uncertainty in the projected numbers on ART and unit costs. Total five-year facility-based ART costs for undifferentiated care are estimated to be US$23.33 billion (95% confidence interval [CI]: $23.3-$23.5 billion). An estimated 17.5% (95% CI: 17.4%-17.7%) and 16.8% (95% CI: 16.7%-17.0%) could be saved from 2016 to 2020 from implementing the age and stability DCM and four-criteria DCM, respectively, with annual cost savings increasing over time. DCMs decrease the full-time equivalent (FTE) health workforce requirements for ART. An estimated 46.4% (95% CI: 46.1%-46.7%) fewer FTE health workers are needed in 2020 for the age and stability DCM compared with undifferentiated care. Adopting DCMs can result in significant efficiency gains in terms of reduced costs and health workforce needs, even with the costs of scaling up community-based ART support under DCMs. Efficiency gains remained flat with increased differentiation. More evidence is needed on how to translate analyzed efficiency gains into implemented cost reductions at the facility level.

A simple and efficient method for deriving neurospheres from bone marrow stromal cells

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

Yang Qin; Mu Jun; Li Qi

2008-08-08

Bone marrow stromal cells (MSCs) can be differentiated into neuronal and glial-like cell types under appropriate experimental conditions. However, previously reported methods are complicated and involve the use of toxic reagents. Here, we present a simplified and nontoxic method for efficient conversion of rat MSCs into neurospheres that express the neuroectodermal marker nestin. These neurospheres can proliferate and differentiate into neuron, astrocyte, and oligodendrocyte phenotypes. We thus propose that MSCs are an emerging model cell for the treatment of a variety of neurological diseases.

Bioinspired Nanocomplex for Spatiotemporal Imaging of Sequential mRNA Expression in Differentiating Neural Stem Cells

PubMed Central

2015-01-01

Messenger RNA plays a pivotal role in regulating cellular activities. The expression dynamics of specific mRNA contains substantial information on the intracellular milieu. Unlike the imaging of stationary mRNAs, real-time intracellular imaging of the dynamics of mRNA expression is of great value for investigating mRNA biology and exploring specific cellular cascades. In addition to advanced imaging methods, timely extracellular stimulation is another key factor in regulating the mRNA expression repertoire. The integration of effective stimulation and imaging into a single robust system would significantly improve stimulation efficiency and imaging accuracy, producing fewer unwanted artifacts. In this study, we developed a multifunctional nanocomplex to enable self-activating and spatiotemporal imaging of the dynamics of mRNA sequential expression during the neural stem cell differentiation process. This nanocomplex showed improved enzymatic stability, fast recognition kinetics, and high specificity. With a mechanism regulated by endogenous cell machinery, this nanocomplex realized the successive stimulating motif release and the dynamic imaging of chronological mRNA expression during neural stem cell differentiation without the use of transgenetic manipulation. The dynamic imaging montage of mRNA expression ultimately facilitated genetic heterogeneity analysis. In vivo lateral ventricle injection of this nanocomplex enabled endogenous neural stem cell activation and labeling at their specific differentiation stages. This nanocomplex is highly amenable as an alternative tool to explore the dynamics of intricate mRNA activities in various physiological and pathological conditions. PMID:25494492

Bioinspired nanocomplex for spatiotemporal imaging of sequential mRNA expression in differentiating neural stem cells.

PubMed

Wang, Zhe; Zhang, Ruili; Wang, Zhongliang; Wang, He-Fang; Wang, Yu; Zhao, Jun; Wang, Fu; Li, Weitao; Niu, Gang; Kiesewetter, Dale O; Chen, Xiaoyuan

2014-12-23

Messenger RNA plays a pivotal role in regulating cellular activities. The expression dynamics of specific mRNA contains substantial information on the intracellular milieu. Unlike the imaging of stationary mRNAs, real-time intracellular imaging of the dynamics of mRNA expression is of great value for investigating mRNA biology and exploring specific cellular cascades. In addition to advanced imaging methods, timely extracellular stimulation is another key factor in regulating the mRNA expression repertoire. The integration of effective stimulation and imaging into a single robust system would significantly improve stimulation efficiency and imaging accuracy, producing fewer unwanted artifacts. In this study, we developed a multifunctional nanocomplex to enable self-activating and spatiotemporal imaging of the dynamics of mRNA sequential expression during the neural stem cell differentiation process. This nanocomplex showed improved enzymatic stability, fast recognition kinetics, and high specificity. With a mechanism regulated by endogenous cell machinery, this nanocomplex realized the successive stimulating motif release and the dynamic imaging of chronological mRNA expression during neural stem cell differentiation without the use of transgenetic manipulation. The dynamic imaging montage of mRNA expression ultimately facilitated genetic heterogeneity analysis. In vivo lateral ventricle injection of this nanocomplex enabled endogenous neural stem cell activation and labeling at their specific differentiation stages. This nanocomplex is highly amenable as an alternative tool to explore the dynamics of intricate mRNA activities in various physiological and pathological conditions.

Solving Ordinary Differential Equations

NASA Technical Reports Server (NTRS)

Krogh, F. T.

1987-01-01

Initial-value ordinary differential equation solution via variable order Adams method (SIVA/DIVA) package is collection of subroutines for solution of nonstiff ordinary differential equations. There are versions for single-precision and double-precision arithmetic. Requires fewer evaluations of derivatives than other variable-order Adams predictor/ corrector methods. Option for direct integration of second-order equations makes integration of trajectory problems significantly more efficient. Written in FORTRAN 77.

Gaussian decomposition of high-resolution melt curve derivatives for measuring genome-editing efficiency

PubMed Central

Zaboikin, Michail; Freter, Carl

2018-01-01

We describe a method for measuring genome editing efficiency from in silico analysis of high-resolution melt curve data. The melt curve data derived from amplicons of genome-edited or unmodified target sites were processed to remove the background fluorescent signal emanating from free fluorophore and then corrected for temperature-dependent quenching of fluorescence of double-stranded DNA-bound fluorophore. Corrected data were normalized and numerically differentiated to obtain the first derivatives of the melt curves. These were then mathematically modeled as a sum or superposition of minimal number of Gaussian components. Using Gaussian parameters determined by modeling of melt curve derivatives of unedited samples, we were able to model melt curve derivatives from genetically altered target sites where the mutant population could be accommodated using an additional Gaussian component. From this, the proportion contributed by the mutant component in the target region amplicon could be accurately determined. Mutant component computations compared well with the mutant frequency determination from next generation sequencing data. The results were also consistent with our earlier studies that used difference curve areas from high-resolution melt curves for determining the efficiency of genome-editing reagents. The advantage of the described method is that it does not require calibration curves to estimate proportion of mutants in amplicons of genome-edited target sites. PMID:29300734

Cycling capacity recovery effect: A coulombic efficiency and post-mortem study

NASA Astrophysics Data System (ADS)

Wilhelm, Jörn; Seidlmayer, Stefan; Keil, Peter; Schuster, Jörg; Kriele, Armin; Gilles, Ralph; Jossen, Andreas

2017-10-01

The analysis of lithium-ion battery aging relies on correct differentiation between irreversible and reversible capacity changes. Anode overhang regions have been observed to influence Coulombic Efficiency (CE) measurements through lithium diffusion into and out of these areas, complicating precise capacity determination. This work presents an analysis of the extent of graphite anode overhang lithiation after calendar storage by means of local X-ray diffraction (XRD), CE measurements, and color change analysis. We found LiC12 lithiation of the anode overhang area after 20 month storage at 40 °C at high state of charge (SoC) and partial lithiation (LiC18) at medium SoC storage at 40 °C and 25 °C. Graphite color changes in the overhang areas are observed and consistent with the state of lithiation measured by XRD. Coulombic efficiencies greater than unity and increasing capacity during 1200 h of cycling are detected for high SoC storage cells. The capacity difference between high and low storage SoC batteries decreases by up to 40 mAh (3.6% of nominal capacity) after cycling compared to tests directly after storage. Consequently, the size of the anode overhang areas as well as the battery storage temperature and duration need to be considered in CE analysis and state of health assessment.

Differentially categorized structural brain hubs are involved in different microstructural, functional, and cognitive characteristics and contribute to individual identification.

PubMed

Wang, Xindi; Lin, Qixiang; Xia, Mingrui; He, Yong

2018-04-01

Very little is known regarding whether structural hubs of human brain networks that enable efficient information communication may be classified into different categories. Using three multimodal neuroimaging data sets, we construct individual structural brain networks and further identify hub regions based on eight widely used graph-nodal metrics, followed by comprehensive characteristics and reproducibility analyses. We show the three categories of structural hubs in the brain network, namely, aggregated, distributed, and connector hubs. Spatially, these distinct categories of hubs are primarily located in the default-mode system and additionally in the visual and limbic systems for aggregated hubs, in the frontoparietal system for distributed hubs, and in the sensorimotor and ventral attention systems for connector hubs. These categorized hubs exhibit various distinct characteristics to support their differentiated roles, involving microstructural organization, wiring costs, topological vulnerability, functional modular integration, and cognitive flexibility; moreover, these characteristics are better in the hubs than nonhubs. Finally, all three categories of hubs display high across-session spatial similarities and act as structural fingerprints with high predictive rates (100%, 100%, and 84.2%) for individual identification. Collectively, we highlight three categories of brain hubs with differential microstructural, functional and, cognitive associations, which shed light on topological mechanisms of the human connectome. © 2018 Wiley Periodicals, Inc.

Pluripotent stem cell-derived radial glia-like cells as stable intermediate for efficient generation of human oligodendrocytes.

PubMed

Gorris, Raphaela; Fischer, Julia; Erwes, Kim Lina; Kesavan, Jaideep; Peterson, Daniel A; Alexander, Michael; Nöthen, Markus M; Peitz, Michael; Quandel, Tamara; Karus, Michael; Brüstle, Oliver

2015-12-01

Neural precursor cells (NPCs) derived from human pluripotent stem cells (hPSCs) represent an attractive tool for the in vitro generation of various neural cell types. However, the developmentally early NPCs emerging during hPSC differentiation typically show a strong propensity for neuronal differentiation, with more limited potential for generating astrocytes and, in particular, for generating oligodendrocytes. This phenomenon corresponds well to the consecutive and protracted generation of neurons and GLIA during normal human development. To obtain a more gliogenic NPC type, we combined growth factor-mediated expansion with pre-exposure to the differentiation-inducing agent retinoic acid and subsequent immunoisolation of CD133-positive cells. This protocol yields an adherent and self-renewing population of hindbrain/spinal cord radial glia (RG)-like neural precursor cells (RGL-NPCs) expressing typical neural stem cell markers such as nestin, ASCL1, SOX2, and PAX6 as well as RG markers BLBP, GLAST, vimentin, and GFAP. While RGL-NPCs maintain the ability for tripotential differentiation into neurons, astrocytes, and oligodendrocytes, they exhibit greatly enhanced propensity for oligodendrocyte generation. Under defined differentiation conditions promoting the expression of the major oligodendrocyte fate-determinants OLIG1/2, NKX6.2, NKX2.2, and SOX10, RGL-NPCs efficiently convert into NG2-positive oligodendroglial progenitor cells (OPCs) and are subsequently capable of in vivo myelination. Representing a stable intermediate between PSCs and OPCs, RGL-NPCs expedite the generation of PSC-derived oligodendrocytes with O4-, 4860-, and myelin basic protein (MBP)-positive cells that already appear within 7 weeks following growth factor withdrawal-induced differentiation. Thus, RGL-NPCs may serve as robust tool for time-efficient generation of human oligodendrocytes from embryonic and induced pluripotent stem cells. © 2015 Wiley Periodicals, Inc.

[Contrastive study on conventional ultrasound, compression elastography and acoustic radiation force impulse imaging in the differential diagnosis of benign and malignant breast tumors].

PubMed

Zhang, Lu; Zhou, Ping; Deng, Jin; Tian, Shuangming; Qian, Ying; Wu, Xiaomin; Ma, Shuhua; Li, Jiale

2014-12-01

To evaluate the diagnostic performance of conventional ultrasound, compression elastography (CE) and acoustic radiation force impulse imaging (ARFI) in differential diagnosis of benign and malignant breast tumors. A total of 98 patients with liver lesions were included in the study. The images of conventional ultrasound, CE and the values of virtual touch tissue quantification (VTQ) of breast lesions were obtained. The diagnostic performance of conventional ultrasound, CE and ARFI were assessed by using pathology as the gold standard, and then evaluate the diagnosis efficiency of these three approaches in differential diagnosing benign and malignant breast tumors. The specificity, sensitivity and accuracy in the diagnosis of malignant breast tumors for conventional ultrasound were 80.0%, 81.1% and 81.7%, respectively, whereas for CE elastic score were 85.7%, 86.7% and 86.3%, respectively. With a cutoff value of 3.71 for the SR, the sensitivity, specificity, accuracy in diagnosis of malignant breast tumors were 97.1%, 83.3% and 88.4%, respectively. With a cutoff value of 3.78 m/s for VTQ, the sensitivity, specificity, accuracy in diagnosis of malignant breast tumors were 94.3%, 91.7% and 92.6%, respectively. The difference in diagnosis efficiency among ARFI, CE and conventional ultrasound in differential diagnosis of benign and malignant breast tumors was significant (P< 0.05). Conventional ultrasound, CE and ARFI are all useful for the differential diagnosis of benign and malignant breast tumors. But the diagnosis efficiency of ARFI is superior to CE and conventional ultrasound. The three approaches can help each other in differential diagnosis of benign and malignant breast tumors.

Improving multilevel Monte Carlo for stochastic differential equations with application to the Langevin equation

PubMed Central

Müller, Eike H.; Scheichl, Rob; Shardlow, Tony

2015-01-01

This paper applies several well-known tricks from the numerical treatment of deterministic differential equations to improve the efficiency of the multilevel Monte Carlo (MLMC) method for stochastic differential equations (SDEs) and especially the Langevin equation. We use modified equations analysis as an alternative to strong-approximation theory for the integrator, and we apply this to introduce MLMC for Langevin-type equations with integrators based on operator splitting. We combine this with extrapolation and investigate the use of discrete random variables in place of the Gaussian increments, which is a well-known technique for the weak approximation of SDEs. We show that, for small-noise problems, discrete random variables can lead to an increase in efficiency of almost two orders of magnitude for practical levels of accuracy. PMID:27547075

Improving multilevel Monte Carlo for stochastic differential equations with application to the Langevin equation.

PubMed

Müller, Eike H; Scheichl, Rob; Shardlow, Tony

2015-04-08

This paper applies several well-known tricks from the numerical treatment of deterministic differential equations to improve the efficiency of the multilevel Monte Carlo (MLMC) method for stochastic differential equations (SDEs) and especially the Langevin equation. We use modified equations analysis as an alternative to strong-approximation theory for the integrator, and we apply this to introduce MLMC for Langevin-type equations with integrators based on operator splitting. We combine this with extrapolation and investigate the use of discrete random variables in place of the Gaussian increments, which is a well-known technique for the weak approximation of SDEs. We show that, for small-noise problems, discrete random variables can lead to an increase in efficiency of almost two orders of magnitude for practical levels of accuracy.

High-efficient Nd:YAG microchip laser for optical surface scanning

NASA Astrophysics Data System (ADS)

Šulc, Jan; Jelínková, Helena; Nejezchleb, Karel; Škoda, Václav

2017-12-01

A CW operating, compact, high-power, high-efficient diode pumped 1064nm laser, based on Nd:YAG active medium, was developed for optical surface scanning and mapping applications. To enhance the output beam quality, laser stability, and compactness, a microchip configuration was used. In this arrangement the resonator mirrors were deposited directly on to the laser crystal faces. The Nd-doping concentration was 1 at.% Nd/Y. The Nd:YAG crystal was 5mm long. The laser resonator without pumping radiation recuperation was investigated {the output coupler was transparent for pumping radiation. For the generated laser radiation the output coupler reflectivity was 95%@1064 nm. The diameter of the samples was 5 mm. For the laser pumping two arrangements were investigated. Firstly, a fibre coupled laser diode operating at wavelength 808nm was used in CW mode. The 400 ¹m fiber was delivering up to 14W of pump power amplitude to the microchip laser. The maximum CW output power of 7.2W @ 1064nm in close to TEM00 beam was obtained for incident pumping power 13.7W @ 808 nm. The differential efficiency in respect to the incident pump power reached 56 %. Secondly, a single-emitter, 1W laser diode operating at 808nm was used for Nd:YAG microchip pumping. The laser pumping was directly coupled into the microchip laser using free-space lens optics. Slope efficiency up to 70% was obtained in stable, high-quality, 1064nm laser beam with CW power up to 350mW. The system was successfully used for scanning of super-Gaussian laser mirrors reflectivity profile.

High-throughput full-length single-cell mRNA-seq of rare cells.

PubMed

Ooi, Chin Chun; Mantalas, Gary L; Koh, Winston; Neff, Norma F; Fuchigami, Teruaki; Wong, Dawson J; Wilson, Robert J; Park, Seung-Min; Gambhir, Sanjiv S; Quake, Stephen R; Wang, Shan X

2017-01-01

Single-cell characterization techniques, such as mRNA-seq, have been applied to a diverse range of applications in cancer biology, yielding great insight into mechanisms leading to therapy resistance and tumor clonality. While single-cell techniques can yield a wealth of information, a common bottleneck is the lack of throughput, with many current processing methods being limited to the analysis of small volumes of single cell suspensions with cell densities on the order of 107 per mL. In this work, we present a high-throughput full-length mRNA-seq protocol incorporating a magnetic sifter and magnetic nanoparticle-antibody conjugates for rare cell enrichment, and Smart-seq2 chemistry for sequencing. We evaluate the efficiency and quality of this protocol with a simulated circulating tumor cell system, whereby non-small-cell lung cancer cell lines (NCI-H1650 and NCI-H1975) are spiked into whole blood, before being enriched for single-cell mRNA-seq by EpCAM-functionalized magnetic nanoparticles and the magnetic sifter. We obtain high efficiency (> 90%) capture and release of these simulated rare cells via the magnetic sifter, with reproducible transcriptome data. In addition, while mRNA-seq data is typically only used for gene expression analysis of transcriptomic data, we demonstrate the use of full-length mRNA-seq chemistries like Smart-seq2 to facilitate variant analysis of expressed genes. This enables the use of mRNA-seq data for differentiating cells in a heterogeneous population by both their phenotypic and variant profile. In a simulated heterogeneous mixture of circulating tumor cells in whole blood, we utilize this high-throughput protocol to differentiate these heterogeneous cells by both their phenotype (lung cancer versus white blood cells), and mutational profile (H1650 versus H1975 cells), in a single sequencing run. This high-throughput method can help facilitate single-cell analysis of rare cell populations, such as circulating tumor or endothelial cells, with demonstrably high-quality transcriptomic data.

Production of Functional Glucagon-Secreting α-Cells From Human Embryonic Stem Cells

PubMed Central

Rezania, Alireza; Riedel, Michael J.; Wideman, Rhonda D.; Karanu, Francis; Ao, Ziliang; Warnock, Garth L.; Kieffer, Timothy J.

2011-01-01

OBJECTIVE Differentiation of human embryonic stem (hES) cells to fully developed cell types holds great therapeutic promise. Despite significant progress, the conversion of hES cells to stable, fully differentiated endocrine cells that exhibit physiologically regulated hormone secretion has not yet been achieved. Here we describe an efficient differentiation protocol for the in vitro conversion of hES cells to functional glucagon-producing α- cells. RESEARCH DESIGN AND METHODS Using a combination of small molecule screening and empirical testing, we developed a six-stage differentiation protocol for creating functional α-cells. An extensive in vitro and in vivo characterization of the differentiated cells was performed. RESULTS A high rate of synaptophysin expression (>75%) and robust expression of glucagon and the α-cell transcription factor ARX was achieved. After a transient polyhormonal state in which cells coexpress glucagon and insulin, maturation in vitro or in vivo resulted in depletion of insulin and other β-cell markers with concomitant enrichment of α-cell markers. After transplantation, these cells secreted fully processed, biologically active glucagon in response to physiologic stimuli including prolonged fasting and amino acid challenge. Moreover, glucagon release from transplanted cells was sufficient to reduce demand for pancreatic glucagon, resulting in a significant decrease in pancreatic α-cell mass. CONCLUSIONS These results indicate that fully differentiated pancreatic endocrine cells can be created via stepwise differentiation of hES cells. These cells may serve as a useful screening tool for the identification of compounds that modulate glucagon secretion as well as those that promote the transdifferentiation of α-cells to β-cells. PMID:20971966

Functionalizing Ascl1 with Novel Intracellular Protein Delivery Technology for Promoting Neuronal Differentiation of Human Induced Pluripotent Stem Cells.

PubMed

Robinson, Meghan; Chapani, Parv; Styan, Tara; Vaidyanathan, Ranjani; Willerth, Stephanie Michelle

2016-08-01

Pluripotent stem cells can become any cell type found in the body. Accordingly, one of the major challenges when working with pluripotent stem cells is producing a highly homogenous population of differentiated cells, which can then be used for downstream applications such as cell therapies or drug screening. The transcription factor Ascl1 plays a key role in neural development and previous work has shown that Ascl1 overexpression using viral vectors can reprogram fibroblasts directly into neurons. Here we report on how a recombinant version of the Ascl1 protein functionalized with intracellular protein delivery technology (Ascl1-IPTD) can be used to rapidly differentiate human induced pluripotent stem cells (hiPSCs) into neurons. We first evaluated a range of Ascl1-IPTD concentrations to determine the most effective amount for generating neurons from hiPSCs cultured in serum free media. Next, we looked at the frequency of Ascl1-IPTD supplementation in the media on differentiation and found that one time supplementation is sufficient enough to trigger the neural differentiation process. Ascl1-IPTD was efficiently taken up by the hiPSCs and enabled rapid differentiation into TUJ1-positive and NeuN-positive populations with neuronal morphology after 8 days. After 12 days of culture, hiPSC-derived neurons produced by Ascl1-IPTD treatment exhibited greater neurite length and higher numbers of branch points compared to neurons derived using a standard neural progenitor differentiation protocol. This work validates Ascl1-IPTD as a powerful tool for engineering neural tissue from pluripotent stem cells.

Molecular Validation of Chondrogenic Differentiation and Hypoxia Responsiveness of Platelet-Lysate Expanded Adipose Tissue-Derived Human Mesenchymal Stromal Cells.

PubMed

Galeano-Garces, Catalina; Camilleri, Emily T; Riester, Scott M; Dudakovic, Amel; Larson, Dirk R; Qu, Wenchun; Smith, Jay; Dietz, Allan B; Im, Hee-Jeong; Krych, Aaron J; Larson, A Noelle; Karperien, Marcel; van Wijnen, Andre J

2017-07-01

To determine the optimal environmental conditions for chondrogenic differentiation of human adipose tissue-derived mesenchymal stromal/stem cells (AMSCs). In this investigation we specifically investigate the role of oxygen tension and 3-dimensional (3D) culture systems. Both AMSCs and primary human chondrocytes were cultured for 21 days in chondrogenic media under normoxic (21% oxygen) or hypoxic (2% oxygen) conditions using 2 distinct 3D culture methods (high-density pellets and poly-ε-caprolactone [PCL] scaffolds). Histologic analysis of chondro-pellets and the expression of chondrocyte-related genes as measured by reverse transcriptase quantitative polymerase chain reaction were used to evaluate the efficiency of differentiation. AMSCs are capable of expressing established cartilage markers including COL2A1, ACAN, and DCN when grown in chondrogenic differentiation media as determined by gene expression and histologic analysis of cartilage markers. Expression of several cartilage-related genes was enhanced by low oxygen tension, including ACAN and HAPLN1. The pellet culture environment also promoted the expression of hypoxia-inducible cartilage markers compared with cells grown on 3D scaffolds. Cell type-specific effects of low oxygen and 3D environments indicate that mesenchymal cell fate and differentiation potential is remarkably sensitive to oxygen. Genetic programming of AMSCs to a chondrocytic phenotype is effective under hypoxic conditions as evidenced by increased expression of cartilage-related biomarkers and biosynthesis of a glycosaminoglycan-positive matrix. Lower local oxygen levels within cartilage pellets may be a significant driver of chondrogenic differentiation.

Efficient generation of smooth muscle cells from adipose-derived stromal cells by 3D mechanical stimulation can substitute the use of growth factors in vascular tissue engineering.

PubMed

Parvizi, Mojtaba; Bolhuis-Versteeg, Lydia A M; Poot, André A; Harmsen, Martin C

2016-07-01

Occluding artery disease causes a high demand for bioartificial replacement vessels. We investigated the combined use of biodegradable and creep-free poly (1,3-trimethylene carbonate) (PTMC) with smooth muscle cells (SMC) derived by biochemical or mechanical stimulation of adipose tissue-derived stromal cells (ASC) to engineer bioartificial arteries. Biochemical induction of cultured ASC to SMC was done with TGF-β1 for 7d. Phenotype and function were assessed by qRT-PCR, immunodetection and collagen contraction assays. The influence of mechanical stimulation on non-differentiated and pre-differentiated ASC, loaded in porous tubular PTMC scaffolds, was assessed after culturing under pulsatile flow for 14d. Assays included qRT-PCR, production of extracellular matrix and scanning electron microscopy. ASC adhesion and TGF-β1-driven differentiation to contractile SMC on PTMC did not differ from tissue culture polystyrene controls. Mesenchymal and SMC markers were increased compared to controls. Interestingly, pre-differentiated ASC had only marginal higher contractility than controls. Moreover, in 3D PTMC scaffolds, mechanical stimulation yielded well-aligned ASC-derived SMC which deposited ECM. Under the same conditions, pre-differentiated ASC-derived SMC maintained their SMC phenotype. Our results show that mechanical stimulation can replace TGF-β1 pre-stimulation to generate SMC from ASC and that pre-differentiated ASC keep their SMC phenotype with increased expression of SMC markers. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Successful immortalization of mesenchymal progenitor cells derived from human placenta and the differentiation abilities of immortalized cells

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

Zhang Xiaohong; Soda, Yasushi; Takahashi, Kenji

2006-12-29

We reported previously that mesenchymal progenitor cells derived from chorionic villi of the human placenta could differentiate into osteoblasts, adipocytes, and chondrocytes under proper induction conditions and that these cells should be useful for allogeneic regenerative medicine, including cartilage tissue engineering. However, similar to human mesenchymal stem cells (hMSCs), though these placental cells can be isolated easily, they are difficult to study in detail because of their limited life span in vitro. To overcome this problem, we attempted to prolong the life span of human placenta-derived mesenchymal cells (hPDMCs) by modifying hTERT and Bmi-1, and investigated whether these modified hPDMCsmore » retained their differentiation capability and multipotency. Our results indicated that the combination of hTERT and Bmi-1 was highly efficient in prolonging the life span of hPDMCs with differentiation capability to osteogenic, adipogenic, and chondrogenic cells in vitro. Clonal cell lines with directional differentiation ability were established from the immortalized parental hPDMC/hTERT + Bmi-1. Interestingly, hPDMC/Bmi-1 showed extended proliferation after long-term growth arrest and telomerase was activated in the immortal hPDMC/Bmi-1 cells. However, the differentiation potential was lost in these cells. This study reports a method to extend the life span of hPDMCs with hTERT and Bmi-1 that should become a useful tool for the study of mesenchymal stem cells.« less

2-(trimethylammonium)ethyl (R)-3-methoxy-3-oxo-2-stearamidopropyl phosphate promotes megakaryocytic differentiation of myeloid leukaemia cells and primary human CD34⁺ haematopoietic stem cells.

PubMed

Limb, Jin-Kyung; Song, Doona; Jeon, Mijeong; Han, So-Yeop; Han, Gyoonhee; Jhon, Gil-Ja; Bae, Yun Soo; Kim, Jaesang

2015-04-01

In this study we showed that 2-(trimethylammonium)ethyl (R)-3-methoxy-3-oxo-2-stearamidopropyl phosphate [(R)-TEMOSPho], a derivative of an organic chemical identified from a natural product library, promotes highly efficient differentiation of megakaryocytes. Specifically, (R)-TEMOSPho induces cell cycle arrest, cell size increase and polyploidization from K562 and HEL cells, which are used extensively to model megakaryocytic differentiation. In addition, megakaryocyte-specific cell surface markers showed a dramatic increase in expression in response to (R)-TEMOSPho treatment. Importantly, we demonstrated that such megakaryocytic differentiation can also be induced from primary human CD34(+) haematopoietic stem cells. Activation of the PI3K-AKT pathway and, to a lesser extent, the MEK-ERK pathway appears to be required for this process, as blocking with specific inhibitors interferes with the differentiation of K562 cells. A subset of (R)-TEMOSPho-treated K562 cells undergoes spontaneous apoptosis and produces platelets that are apparently functional, as they bind to fibrinogen, express P-selectin and aggregate in response to SFLLRN and AYPGFK, the activating peptides for the PAR1 and PAR4 receptors, respectively. Taken together, these results indicate that (R)-TEMOSPho will be useful for dissecting the molecular mechanisms of megakaryocytic differentiation, and that this class of compounds represents potential therapeutic reagents for thrombocytopenia. Copyright © 2012 John Wiley & Sons, Ltd.

High-performance dispersive Raman and absorption spectroscopy as tools for drug identification

NASA Astrophysics Data System (ADS)

Pawluczyk, Olga; Andrey, Sam; Nogas, Paul; Roy, Andrew; Pawluczyk, Romuald

2009-02-01

Due to increasing availability of pharmaceuticals from many sources, a need is growing to quickly and efficiently analyze substances in terms of the consistency and accuracy of their chemical composition. Differences in chemical composition occur at very low concentrations, so that highly sensitive analytical methods become crucial. Recent progress in dispersive spectroscopy with the use of 2-dimensional detector arrays, permits for signal integration along a long (up to 12 mm long) entrance slit of a spectrometer, thereby increasing signal to noise ratio and improving the ability to detect small concentration changes. This is achieved with a non-scanning, non-destructive system. Two different methods using P&P Optica high performance spectrometers were used. High performance optical dispersion Raman and high performance optical absorption spectroscopy were employed to differentiate various acetaminophen-containing drugs, such as Tylenol and other generic brands, which differ in their ingredients. A 785 nm excitation wavelength was used in Raman measurements and strong Raman signals were observed in the spectral range 300-1800 cm-1. Measurements with the absorption spectrometer were performed in the wavelength range 620-1020 nm. Both Raman and absorption techniques used transmission light spectrometers with volume phase holographic gratings and provided sufficient spectral differences, often structural, allowing for drug differentiation.

Differential programming of p53-deficient embryonic cells during rotenone block

EPA Science Inventory

Mitochondrial dysfunction has been implicated in chemical toxicities. The present study used an in vitro model to investigate the differential expression of metabolic pathways during cellular stress in p53- efficient embryonic fibroblasts compared to p53-deficient cells. These c...

Calcium: A novel and efficient inducer of differentiation of adipose-derived stem cells into neuron-like cells.

PubMed

Goudarzi, Farjam; Tayebinia, Heidar; Karimi, Jamshid; Habibitabar, Elahe; Khodadadi, Iraj

2018-06-05

This study comparatively investigated the effectiveness of calcium and other well-known inducers such as isobutylmethylxanthine (IBMX) and insulin in differentiating human adipose-derived stem cells (ADSCs) into neuronal-like cells. ADSCs were immunophenotyped and differentiated into neuron-like cells with different combinations of calcium, IBMX, and insulin. Calcium mobilization across the membrane was determined. Differentiated cells were characterized by cell cycle profiling, staining of Nissl bodies, detecting the gene expression level of markers such as neuronal nuclear antigen (NeuN), microtubule associated protein 2 (MAP2), neuron-specific enolase (NSE), doublecortin, synapsin I, glial fibrillary acidic protein (GFAP), and myelin basic protein (MBP) by quantitative real-time polymerase chain reaction (quantitative real-time polymerase chain reaction (qRT-PCR) and protein level by the immunofluorescence technique. Treatment with Ca + IBMX + Ins induced neuronal appearance and projection of neurite-like processes in the cells, accompanied with inhibition of proliferation and halt in the cell cycle. A significantly higher expression of MBP, GFAP, NeuN, NSE, synapsin 1, doublecortin, and MAP2 was detected in differentiated cells, confirming the advantages of Ca + IBMX + Ins to the other combinations of inducers. Here, we showed an efficient protocol for neuronal differentiation of ADSCs, and calcium fostered differentiation by augmenting the number of neuron-like cells and instantaneous increase in the expression of neuronal markers. © 2018 Wiley Periodicals, Inc.

APPHi: Automated Photometry Pipeline for High Cadence Large Volume Data

NASA Astrophysics Data System (ADS)

Sánchez, E.; Castro, J.; Silva, J.; Hernández, J.; Reyes, M.; Hernández, B.; Alvarez, F.; García T.

2018-04-01

APPHi (Automated Photometry Pipeline) carries out aperture and differential photometry of TAOS-II project data. It is computationally efficient and can be used also with other astronomical wide-field image data. APPHi works with large volumes of data and handles both FITS and HDF5 formats. Due the large number of stars that the software has to handle in an enormous number of frames, it is optimized to automatically find the best value for parameters to carry out the photometry, such as mask size for aperture, size of window for extraction of a single star, and the number of counts for the threshold for detecting a faint star. Although intended to work with TAOS-II data, APPHi can analyze any set of astronomical images and is a robust and versatile tool to performing stellar aperture and differential photometry.

Solving Partial Differential Equations on Overlapping Grids

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

Henshaw, W D

2008-09-22

We discuss the solution of partial differential equations (PDEs) on overlapping grids. This is a powerful technique for efficiently solving problems in complex, possibly moving, geometry. An overlapping grid consists of a set of structured grids that overlap and cover the computational domain. By allowing the grids to overlap, grids for complex geometries can be more easily constructed. The overlapping grid approach can also be used to remove coordinate singularities by, for example, covering a sphere with two or more patches. We describe the application of the overlapping grid approach to a variety of different problems. These include the solutionmore » of incompressible fluid flows with moving and deforming geometry, the solution of high-speed compressible reactive flow with rigid bodies using adaptive mesh refinement (AMR), and the solution of the time-domain Maxwell's equations of electromagnetism.« less

High Intensity Organic Light-emitting Diodes

NASA Astrophysics Data System (ADS)

Qi, Xiangfei

This thesis is dedicated to the fabrication, modeling, and characterization to achieve high efficiency organic light-emitting diodes (OLEDs) for illumination applications. Compared to conventional lighting sources, OLEDs enabled the direct conversion of electrical energy into light emission and have intrigued the world's lighting designers with the long-lasting, highly efficient illumination. We begin with a brief overview of organic technology, from basic organic semiconductor physics, to its application in optoelectronics, i.e. light-emitting diodes, photovoltaics, photodetectors and thin-film transistors. Due to the importance of phosphorescent materials, we will focus on the photophysics of metal complexes that is central to high efficiency OLED technology, followed by a transient study to examine the radiative decay dynamics in a series of phosphorescent platinum binuclear complexes. The major theme of this thesis is the design and optimization of a novel architecture where individual red, green and blue phosphorescent OLEDs are vertically stacked and electrically interconnected by the compound charge generation layers. We modeled carrier generation from the metal-oxide/doped organic interface based on a thermally assisted tunneling mechanism. The model provides insights to the optimization of a stacked OLED from both electrical and optical point of view. To realize the high intensity white lighting source, the efficient removal of heat is of a particular concern, especially in large-area devices. A fundamental transfer matrix analysis is introduced to predict the thermal properties in the devices. The analysis employs Laplace transforms to determine the response of the system to the combined effects of conduction, convection, and radiation. This perspective of constructing transmission matrices greatly facilitates the calculation of transient coupled heat transfer in a general multi-layer composite. It converts differential equations to algebraic forms, and can be expanded to study other thermal issues in more sophisticated structures.

Suppressed power saturation due to optimized optical confinement in 9xx nm high-power diode lasers that use extreme double asymmetric vertical designs

NASA Astrophysics Data System (ADS)

Kaul, T.; Erbert, G.; Maaßdorf, A.; Knigge, S.; Crump, P.

2018-03-01

Broad area lasers with novel extreme double asymmetric structure (EDAS) vertical designs featuring increased optical confinement in the quantum well, Γ, are shown to have improved temperature stability without compromising series resistance, internal efficiency or losses. Specifically, we present here vertical design considerations for the improved continuous wave (CW) performance of devices operating at 940 nm, based on systematically increasing Γ from 0.26% to 1.1%, and discuss the impact on power saturation mechanisms. The results indicate that key power saturation mechanisms at high temperatures originate in high threshold carrier densities, which arise in the quantum well at low Γ. The characteristic temperatures, T 0 and T 1, are determined under short pulse conditions and are used to clarify the thermal contribution to power limiting mechanisms. Although increased Γ reduces thermal power saturation, it is accompanied by increased optical absorption losses in the active region, which has a significant impact on the differential external quantum efficiency, {η }{{diff}}. To quantify the impact of internal optical losses contributed by the quantum well, a resonator length-dependent simulation of {η }{{diff}} is performed and compared to the experiment, which also allows the estimation of experimental values for the light absorption cross sections of electrons and holes inside the quantum well. Overall, the analysis enables vertical designs to be developed, for devices with maximized power conversion efficiency at high CW optical power and high temperatures, in a trade-off between absorption in the well and power saturation. The best balance to date is achieved in devices using EDAS designs with {{Γ }}=0.54 % , which deliver efficiencies of 50% at 14 W optical output power at an elevated junction temperature of 105 °C.

Triticale powdery mildew: population characterization and wheat gene efficiency.

PubMed

Bouguennec, Annaig; Trottet, Maxime; du Cheyron, Philippe; Lonnet, Philippe

2014-01-01

Powdery mildew has emerged on triticale in the early 2000s in many locations, probably due to a host range expansion of the wheat formae speciales, Blumeria graminis f.sp. tritici. Many triticale cultivars are highly susceptible to powdery mildew, mainly in seedling stage, revealing a probably narrow genetic basis for powdery mildew resistance genes (Pm). Moreover, as Blumeria graminis is an obligate biotrophic fungus, it is very time consuming and difficult to maintain powdery mildew isolates for a non-specialized laboratory and populations can evolve. In order to identify wheat Pm genes efficient against natural populations of powdery mildew, wheat differential hosts and triticale seedlings were inoculated below susceptible triticale crop naturally contaminated by mildew, in several locations and several years. Symptoms on seedlings were measured after approximately two weeks of incubation in favorable fungus growth conditions. According to these data, we classified the Pm genes presents in our wheat differential hosts set in 3 classes: Pm already overcame by triticale powdery mildew, Pm having variable effects and Pm still efficient against triticale mildew. Data on triticale seedlings allowed us to identify some few triticale cultivars resistant to Blumeria graminis in seedling stage. We will try to identify Pm genes present in those cultivars next year by testing them with the characterized isolates of powdery mildew from Gent University. Nevertheless, interspecific crossing of wheat, resistant to powdery mildew in seedling stage, and rye have been initiated to introduce potentially interesting genes for resistance in triticale.

An efficient algorithm for global periodic orbits generation near irregular-shaped asteroids

NASA Astrophysics Data System (ADS)

Shang, Haibin; Wu, Xiaoyu; Ren, Yuan; Shan, Jinjun

2017-07-01

Periodic orbits (POs) play an important role in understanding dynamical behaviors around natural celestial bodies. In this study, an efficient algorithm was presented to generate the global POs around irregular-shaped uniformly rotating asteroids. The algorithm was performed in three steps, namely global search, local refinement, and model continuation. First, a mascon model with a low number of particles and optimized mass distribution was constructed to remodel the exterior gravitational potential of the asteroid. Using this model, a multi-start differential evolution enhanced with a deflection strategy with strong global exploration and bypassing abilities was adopted. This algorithm can be regarded as a search engine to find multiple globally optimal regions in which potential POs were located. This was followed by applying a differential correction to locally refine global search solutions and generate the accurate POs in the mascon model in which an analytical Jacobian matrix was derived to improve convergence. Finally, the concept of numerical model continuation was introduced and used to convert the POs from the mascon model into a high-fidelity polyhedron model by sequentially correcting the initial states. The efficiency of the proposed algorithm was substantiated by computing the global POs around an elongated shoe-shaped asteroid 433 Eros. Various global POs with different topological structures in the configuration space were successfully located. Specifically, the proposed algorithm was generic and could be conveniently extended to explore periodic motions in other gravitational systems.

The utility of a classificatory decision tree approach to assist clinical differentiation of melancholic and non-melancholic depression.

PubMed

Parker, G; McCraw, S; Hadzi-Pavlovic, D

2015-07-15

Studies suggest that differentiating melancholic from non-melancholic depressive disorders is advanced by use of illness course as well as symptom variables but, in practice, potentially differentiating variables are generally positioned as having equal value. Judging that differentiating features are more likely to vary in their signal intensity, we sought to determine the number of features required to effect differentiation and their hierarchical order. The 24-item clinician-rated Sydney Melancholia Prototype Index (SMPI-CR) was completed for 364 unipolar depressed patients. The sample was divided into two cohorts according to the recruitment period. An RPART classification tree analysis identified the most discriminating SMPI items in the development sample of 197 patients, and examined the sensitivity and specificity of the diagnostic decisions, then sought to replicate findings in a validation sample of 169 patients. Independent analyses of putative SMPI items identified only seven items as required to discriminate those with clinically-diagnosed melancholic or non-melancholic depression when the conditions were examined separately. An RPART analysis considering differentiation of melancholic and non-melancholic depression in the total samples retained five of those items in the classification tree, three of which were non-symptom items, and with 92% sensitivity and 80% specificity in the development sample. This reduced item set showed 93% sensitivity and 82% specificity in the validation sample. Our clinical judgment of melancholic or non-melancholic depression may not correspond with the clinical logic employed by other clinicians. Only five SMPI items were required to derive a succinct and efficient decision tree, comprising high sensitivity and specificity in differentiating melancholic and non-melancholic depression. Current study findings provide an empirical model that could enrich clinicians׳ approach to differentiating melancholic and non-melancholic depression. Copyright © 2015 Elsevier B.V. All rights reserved.

Bessel smoothing filter for spectral-element mesh

NASA Astrophysics Data System (ADS)

Trinh, P. T.; Brossier, R.; Métivier, L.; Virieux, J.; Wellington, P.

2017-06-01

Smoothing filters are extremely important tools in seismic imaging and inversion, such as for traveltime tomography, migration and waveform inversion. For efficiency, and as they can be used a number of times during inversion, it is important that these filters can easily incorporate prior information on the geological structure of the investigated medium, through variable coherent lengths and orientation. In this study, we promote the use of the Bessel filter to achieve these purposes. Instead of considering the direct application of the filter, we demonstrate that we can rely on the equation associated with its inverse filter, which amounts to the solution of an elliptic partial differential equation. This enhances the efficiency of the filter application, and also its flexibility. We apply this strategy within a spectral-element-based elastic full waveform inversion framework. Taking advantage of this formulation, we apply the Bessel filter by solving the associated partial differential equation directly on the spectral-element mesh through the standard weak formulation. This avoids cumbersome projection operators between the spectral-element mesh and a regular Cartesian grid, or expensive explicit windowed convolution on the finite-element mesh, which is often used for applying smoothing operators. The associated linear system is solved efficiently through a parallel conjugate gradient algorithm, in which the matrix vector product is factorized and highly optimized with vectorized computation. Significant scaling behaviour is obtained when comparing this strategy with the explicit convolution method. The theoretical numerical complexity of this approach increases linearly with the coherent length, whereas a sublinear relationship is observed practically. Numerical illustrations are provided here for schematic examples, and for a more realistic elastic full waveform inversion gradient smoothing on the SEAM II benchmark model. These examples illustrate well the efficiency and flexibility of the approach proposed.

Pollen transfer efficiency and its effect on inflorescence size in deceptive pollination strategies.

PubMed

Scopece, G; Schiestl, F P; Cozzolino, S

2015-03-01

Pollination systems differ in pollen transfer efficiency, a variable that may influence the evolution of flower number. Here we apply a comparative approach to examine the link between pollen transfer efficiency and the evolution of inflorescence size in food and sexually deceptive orchids. We examined pollination performance in nine food-deceptive, and eight sexually deceptive orchids by recording pollen removal and deposition in the field. We calculated correlations between reproductive success and flower number (as a proxy for resources allocated during reproductive process), and directional selection differentials were estimated on flower number for four species. Results indicate that sexually deceptive species experience decreased pollen loss compared to food-deceptive species. Despite producing fewer flowers, sexually deceptive species attained levels of overall pollination success (through male and female function) similar to food-deceptive species. Furthermore, a positive correlation between flower number and pollination success was observed in food-deceptive species, but this correlation was not detected in sexually deceptive species. Directional selection differentials for flower number were significantly higher in food compared to sexually deceptive species. We suggest that pollination systems with more efficient pollen transfer and no correlation between pollination success and number of flowers produced, such as sexual deception, may allow the production of inflorescences with fewer flowers that permit the plant to allocate fewer resources to floral displays and, at the same time, limit transpiration. This strategy can be particularly important for ecological success in Mediterranean water-deprived habitats, and might explain the high frequency of sexually deceptive species in these specialised ecosystems. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Ultrasound -Assisted Gene Transfer to Adipose Tissue-Derived Stem/Progenitor Cells (ASCs)

NASA Astrophysics Data System (ADS)

Miyamoto, Yoshitaka; Ueno, Hitomi; Hokari, Rei; Yuan, Wenji; Kuno, Shuichi; Kakimoto, Takashi; Enosawa, Shin; Negishi, Yoichi; Yoshinaka, Kiyoshi; Matsumoto, Yoichiro; Chiba, Toshio; Hayashi, Shuji

2011-09-01

In recent years, multilineage adipose tissue-derived stem cells (ASCs) have become increasingly attractive as a promising source for cell transplantation and regenerative medicine. Particular interest has been expressed in the potential to make tissue stem cells, such as ASCs and marrow stromal cells (MSCs), differentiate by gene transfection. Gene transfection using highly efficient viral vectors such as adeno- and sendai viruses have been developed for this purpose. Sonoporation, or ultrasound (US)-assisted gene transfer, is an alternative gene manipulation technique which employs the creation of a jet stream by ultrasonic microbubble cavitation. Sonoporation using non-viral vectors is expected to be a much safer, although less efficient, tool for prospective clinical gene therapy. In this report, we assessed the efficacy of the sonoporation technique for gene transfer to ASCs. We isolated and cultured adipocyets from mouse adipose tissue. ASCs that have the potential to differentiate with transformation into adipocytes or osteoblasts were obtained. Using the US-assisted system, plasmid DNA containing beta-galactosidase (beta-Gal) and green fluorescent protein (GFP) genes were transferred to the ASCs. For this purpose, a Sonopore 4000 (NEPAGENE Co.) and a Sonazoid (Daiichi Sankyo Co.) instrument were used in combination. ASCs were subjected to US (3.1 MHz, 50% duty cycle, burst rate 2.0 Hz, intensity 1.2 W/cm2, exposure time 30 sec). We observed that the gene was more efficiently transferred with increased concentrations of plasmid DNA (5-150 μg/mL). However, further optimization of the US parameters is required, as the gene transfer efficiency was still relatively low. In conclusion, we herein demonstrate that a gene can be transferred to ASCs using our US-assisted system. In regenerative medicine, this system might resolve the current issues surrounding the use of viral vectors for gene transfer.

Differentiation in Data Analysis & Probability, PreK-Grade 2: A Content Companion for Ongoing Assessment, Grouping Students, Targeting Instruction, and Adjusting Levels of Cognitive Demand

ERIC Educational Resources Information Center

Taylor-Cox, Jennifer

2008-01-01

This book applies the author's easy but effective differentiation strategies to the data analysis and probability content standard. Taking the foundational elements of differentiation in this book, it helps you: (1) assess students' math abilities quickly and efficiently; (2) group children by need; (3) target instruction to meet every student's…

On the Solution of Elliptic Partial Differential Equations on Regions with Corners

DTIC Science & Technology

2015-07-09

In this report we investigate the solution of boundary value problems on polygonal domains for elliptic partial differential equations . We observe...that when the problems are formulated as the boundary integral equations of classical potential theory, the solutions are representable by series of...efficient numerical algorithms. The results are illustrated by a number of numerical examples. On the solution of elliptic partial differential equations on

Bioreactor cultivation enhances NTEB formation and differentiation of NTES cells into cardiomyocytes.

PubMed

Lü, Shuanghong; Liu, Sheng; He, Wenjun; Duan, Cuimi; Li, Yanmin; Liu, Zhiqiang; Zhang, Ye; Hao, Tong; Wang, Yanmeng; Li, Dexue; Wang, Changyong; Gao, Shaorong

2008-09-01

Autogenic embryonic stem cells established from somatic cell nuclear transfer (SCNT) embryos have been proposed as unlimited cell sources for cell transplantation-based treatment of many genetic and degenerative diseases, which can eliminate the immune rejection that occurs after transplantation. In the present study, pluripotent nuclear transfer ES (NTES) cell lines were successfully established from different strains of mice. One NTES cell line, NT1, with capacity of germline transmission, was used to investigate in vitro differentiation into cardiomyocytes. To optimize differentiation conditions for mass production of embryoid bodies (NTEBs) from NTES cells, a slow-turning lateral vessel (STLV) rotating bioreactor was used for culturing the NTES cells to produce NTEBs compared with a conventional static cultivation method. Our results demonstrated that the NTEBs formed in STLV bioreactor were more uniform in size, and no large necrotic centers with most of the cells in NTEBs were viable. Differentiation of the NTEBs formed in both the STLV bioreactor and static culture into cardiomyocytes was induced by ascorbic acid, and the results demonstrated that STLV-produced NTEBs differentiated into cardiomyocytes more efficiently. Taken together, our results suggested that STLV bioreactor provided a more ideal culture condition, which can facilitate the formation of better quality NTEBs and differentiation into cardiomyocytes more efficiently in vitro.

Financial performance monitoring of the technical efficiency of critical access hospitals: a data envelopment analysis and logistic regression modeling approach.

PubMed

Wilson, Asa B; Kerr, Bernard J; Bastian, Nathaniel D; Fulton, Lawrence V

2012-01-01

From 1980 to 1999, rural designated hospitals closed at a disproportionally high rate. In response to this emergent threat to healthcare access in rural settings, the Balanced Budget Act of 1997 made provisions for the creation of a new rural hospital--the critical access hospital (CAH). The conversion to CAH and the associated cost-based reimbursement scheme significantly slowed the closure rate of rural hospitals. This work investigates which methods can ensure the long-term viability of small hospitals. This article uses a two-step design to focus on a hypothesized relationship between technical efficiency of CAHs and a recently developed set of financial monitors for these entities. The goal is to identify the financial performance measures associated with efficiency. The first step uses data envelopment analysis (DEA) to differentiate efficient from inefficient facilities within a data set of 183 CAHs. Determining DEA efficiency is an a priori categorization of hospitals in the data set as efficient or inefficient. In the second step, DEA efficiency is the categorical dependent variable (efficient = 0, inefficient = 1) in the subsequent binary logistic regression (LR) model. A set of six financial monitors selected from the array of 20 measures were the LR independent variables. We use a binary LR to test the null hypothesis that recently developed CAH financial indicators had no predictive value for categorizing a CAH as efficient or inefficient, (i.e., there is no relationship between DEA efficiency and fiscal performance).

Translation elicits a growth rate-dependent, genome-wide, differential protein production in Bacillus subtilis.

PubMed

Borkowski, Olivier; Goelzer, Anne; Schaffer, Marc; Calabre, Magali; Mäder, Ulrike; Aymerich, Stéphane; Jules, Matthieu; Fromion, Vincent

2016-05-17

Complex regulatory programs control cell adaptation to environmental changes by setting condition-specific proteomes. In balanced growth, bacterial protein abundances depend on the dilution rate, transcript abundances and transcript-specific translation efficiencies. We revisited the current theory claiming the invariance of bacterial translation efficiency. By integrating genome-wide transcriptome datasets and datasets from a library of synthetic gfp-reporter fusions, we demonstrated that translation efficiencies in Bacillus subtilis decreased up to fourfold from slow to fast growth. The translation initiation regions elicited a growth rate-dependent, differential production of proteins without regulators, hence revealing a unique, hard-coded, growth rate-dependent mode of regulation. We combined model-based data analyses of transcript and protein abundances genome-wide and revealed that this global regulation is extensively used in B. subtilis We eventually developed a knowledge-based, three-step translation initiation model, experimentally challenged the model predictions and proposed that a growth rate-dependent drop in free ribosome abundance accounted for the differential protein production. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

A General Formulation for Robust and Efficient Integration of Finite Differences and Phase Unwrapping on Sparse Multidimensional Domains

NASA Astrophysics Data System (ADS)

Costantini, Mario; Malvarosa, Fabio; Minati, Federico

2010-03-01

Phase unwrapping and integration of finite differences are key problems in several technical fields. In SAR interferometry and differential and persistent scatterers interferometry digital elevation models and displacement measurements can be obtained after unambiguously determining the phase values and reconstructing the mean velocities and elevations of the observed targets, which can be performed by integrating differential estimates of these quantities (finite differences between neighboring points).In this paper we propose a general formulation for robust and efficient integration of finite differences and phase unwrapping, which includes standard techniques methods as sub-cases. The proposed approach allows obtaining more reliable and accurate solutions by exploiting redundant differential estimates (not only between nearest neighboring points) and multi-dimensional information (e.g. multi-temporal, multi-frequency, multi-baseline observations), or external data (e.g. GPS measurements). The proposed approach requires the solution of linear or quadratic programming problems, for which computationally efficient algorithms exist.The validation tests obtained on real SAR data confirm the validity of the method, which was integrated in our production chain and successfully used also in massive productions.

Efficient genome editing of differentiated renal epithelial cells.

PubMed

Hofherr, Alexis; Busch, Tilman; Huber, Nora; Nold, Andreas; Bohn, Albert; Viau, Amandine; Bienaimé, Frank; Kuehn, E Wolfgang; Arnold, Sebastian J; Köttgen, Michael

2017-02-01

Recent advances in genome editing technologies have enabled the rapid and precise manipulation of genomes, including the targeted introduction, alteration, and removal of genomic sequences. However, respective methods have been described mainly in non-differentiated or haploid cell types. Genome editing of well-differentiated renal epithelial cells has been hampered by a range of technological issues, including optimal design, efficient expression of multiple genome editing constructs, attainable mutation rates, and best screening strategies. Here, we present an easily implementable workflow for the rapid generation of targeted heterozygous and homozygous genomic sequence alterations in renal cells using transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeat (CRISPR) system. We demonstrate the versatility of established protocols by generating novel cellular models for studying autosomal dominant polycystic kidney disease (ADPKD). Furthermore, we show that cell culture-validated genetic modifications can be readily applied to mouse embryonic stem cells (mESCs) for the generation of corresponding mouse models. The described procedure for efficient genome editing can be applied to any cell type to study physiological and pathophysiological functions in the context of precisely engineered genotypes.

Hollow Fibers Structured Packings in Olefin/Paraffin Distillation: Apparatus Scale-Up and Long-Term Stability

DOE PAGES

Yang, Dali; Le, Loan; Martinez, Ronald; ...

2013-06-21

Following the conceptual demonstration of high separation efficiency and column capacity obtained in olefin/paraffin distillation using hollow fiber structured packings (HFSPs) in a bench scale (J. Membr. Sci.2006, 2007, and 2010), we scaled-up this process with a 10-fold increase in the internal flow rate and a 3-fold increase in the module length. We confirmed that the HFSPs technology gives high separation efficiency and column capacity in iso-/n-butane distillation for 18 months. We systematically investigated the effects of packing density, concentration of light component, reflux ratio, and module age on the separation efficiency and operating stability. The comprehensive characterizations using scanningmore » electron microscopy (SEM), Brunauer–Emmett–Teller (BET), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and dynamic mechanical analysis (DMA) were carried out to probe the changes in the morphological, thermal, and mechanical properties of polypropylene (PP) hollow fibers over the aging process. Our results suggest that after a long-term exposure to light hydrocarbon environments at ≤70 °C the morphological and mechanical properties of the PP polymer do not degrade significantly in a propane/propylene and iso-/n-butane environment.« less

Hopping transport in the space-charge region of p-n structures with InGaN/GaN QWs as a source of excess 1/f noise and efficiency droop in LEDs

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

Bochkareva, N. I.; Ivanov, A. M.; Klochkov, A. V.

2015-06-15

It is shown that the emission efficiency and the 1/f noise level in light-emitting diodes with InGaN/GaN quantum wells correlate with how the differential resistance of a diode varies with increasing current. Analysis of the results shows that hopping transport via defect states across the n-type part of the space-charge region results in limitation of the current by the tunneling resistance at intermediate currents and shunting of the n-type barrier at high currents. The increase in the average number of tunneling electrons suppresses the 1/f current noise at intermediate currents. The strong growth in the density of current noise atmore » high currents, S{sub J} ∝ J{sup 3}, is attributed to a decrease in the average number of tunneling electrons as the n-type barrier decreases in height and width with increasing forward bias. The tunneling-recombination leakage current along extended defects grows faster than the tunneling injection current, which leads to emission efficiency droop.« less

Optimized RNP transfection for highly efficient CRISPR/Cas9-mediated gene knockout in primary T cells.

PubMed

Seki, Akiko; Rutz, Sascha

2018-03-05

CRISPR (clustered, regularly interspaced, short palindromic repeats)/Cas9 (CRISPR-associated protein 9) has become the tool of choice for generating gene knockouts across a variety of species. The ability for efficient gene editing in primary T cells not only represents a valuable research tool to study gene function but also holds great promise for T cell-based immunotherapies, such as next-generation chimeric antigen receptor (CAR) T cells. Previous attempts to apply CRIPSR/Cas9 for gene editing in primary T cells have resulted in highly variable knockout efficiency and required T cell receptor (TCR) stimulation, thus largely precluding the study of genes involved in T cell activation or differentiation. Here, we describe an optimized approach for Cas9/RNP transfection of primary mouse and human T cells without TCR stimulation that results in near complete loss of target gene expression at the population level, mitigating the need for selection. We believe that this method will greatly extend the feasibly of target gene discovery and validation in primary T cells and simplify the gene editing process for next-generation immunotherapies. © 2018 Genentech.

RNA-Seq detection of differential gene expression in the rumen of beef steers associated with feed efficiency phenotypes

USDA-ARS?s Scientific Manuscript database

The efficient utilization of feedstuffs is an economically important trait in beef production. The rumen is important to the digestive process of steers interacting with feed, microbial populations, and volatile fatty acids indicating it may play a critical role in feed efficiency. To gain an unders...

Effect of water stress on total biomass, tuber yield, harvest index and water use efficiency in Jerusalem artichoke

USDA-ARS?s Scientific Manuscript database

The objectives of this study were to determine the effect of drought on tuber yield, total biomass, harvest index, water use efficiency of tuber yield (WUEt) and water use efficiency of biomass (WUEb), and to evaluate the differential responses of Jerusalem artichoke (JA) varieties under drought str...

Rectifying full-counting statistics in a spin Seebeck engine

NASA Astrophysics Data System (ADS)

Tang, Gaomin; Chen, Xiaobin; Ren, Jie; Wang, Jian

2018-02-01

In terms of the nonequilibrium Green's function framework, we formulate the full-counting statistics of conjugate thermal spin transport in a spin Seebeck engine, which is made by a metal-ferromagnet insulator interface driven by a temperature bias. We obtain general expressions of scaled cumulant generating functions of both heat and spin currents that hold special fluctuation symmetry relations, and demonstrate intriguing properties, such as rectification and negative differential effects of high-order fluctuations of thermal excited spin current, maximum output spin power, and efficiency. The transport and noise depend on the strongly fluctuating electron density of states at the interface. The results are relevant for designing an efficient spin Seebeck engine and can broaden our view in nonequilibrium thermodynamics and the nonlinear phenomenon in quantum transport systems.

High Temperature Performance of a SiC MESFET Based Oscillator

NASA Technical Reports Server (NTRS)

Schwartz, Zachary D.; Ponchak, George E.

2005-01-01

A hybrid, UHF-Band differential oscillator based on 10 w SiC RF Power Metal Semiconductor Field Effect Transistor (MESFET) has been designed, fabricated and characterized through 475 C. Circuit is fabricated on an alumina substrate with thin film spiral inductors, chip capacitors, chip resistors, and wire bonds for all crossovers and interconnectors. The oscillator delivers 15.7 dBm at 515 MHz into a 50 Ohm load at 125 C with a DC to RF conversion efficiency of 2,8%. After tuning the load impedance, the oscillator delivers 18.8 dBm at 610 MHz at 200 C with a DC to RF conversion efficiency of 5.8%. Finally, by tuning the load and bias conditions, the oscillator delivers 4.9 dBm at 453 MHz at 475 C.

The FLAME-slab method for electromagnetic wave scattering in aperiodic slabs

NASA Astrophysics Data System (ADS)

Mansha, Shampy; Tsukerman, Igor; Chong, Y. D.

2017-12-01

The proposed numerical method, "FLAME-slab," solves electromagnetic wave scattering problems for aperiodic slab structures by exploiting short-range regularities in these structures. The computational procedure involves special difference schemes with high accuracy even on coarse grids. These schemes are based on Trefftz approximations, utilizing functions that locally satisfy the governing differential equations, as is done in the Flexible Local Approximation Method (FLAME). Radiation boundary conditions are implemented via Fourier expansions in the air surrounding the slab. When applied to ensembles of slab structures with identical short-range features, such as amorphous or quasicrystalline lattices, the method is significantly more efficient, both in runtime and in memory consumption, than traditional approaches. This efficiency is due to the fact that the Trefftz functions need to be computed only once for the whole ensemble.

Transcriptome dynamics of human pluripotent stem cell-derived contracting cardiomyocytes using an embryoid body model with fetal bovine serum.

PubMed

Jung, Kwang Bo; Son, Ye Seul; Lee, Hana; Jung, Cho-Rok; Kim, Janghwan; Son, Mi-Young

2017-07-25

Cardiomyocyte (CM) differentiation techniques for generating adult-like mature CMs remain imperfect, and the plausible underlying mechanisms remain unclear; however, there are a number of current protocols available. Here, to explore the mechanisms controlling cardiac differentiation, we analyzed the genome-wide transcription dynamics occurring during the differentiation of human pluripotent stem cells (hPSCs) into CMs using embryoid body (EB) formation. We optimized and updated the protocol to efficiently generate contracting CMs from hPSCs by adding fetal bovine serum (FBS) as a medium supplement, which could have a significant impact on the efficiency of cardiac differentiation. To identify genes, biological processes, and pathways involved in the cardiac differentiation of hPSCs, integrative and comparative analyses of the transcriptome profiles of differentiated CMs from hPSCs and of control CMs of the adult human heart (CM-AHH) were performed using gene ontology, functional annotation clustering, and pathway analyses. Several genes commonly regulated in the differentiated CMs and CM-AHH were enriched in pathways related to cell cycle and nucleotide metabolism. Strikingly, we found that current differentiation protocols did not promote sufficient expression of genes involved in oxidative phosphorylation to differentiate CMs from hPSCs compared to the expression levels in CM-AHH. Therefore, to obtain mature CMs similar to CM-AHH, these deficient pathways in CM differentiation, such as energy-related pathways, must be augmented prior to use for in vitro and in vivo applications. This approach opens up new avenues for facilitating the utilization of hPSC-derived CMs in biomedical research, drug evaluation, and clinical applications for patients with cardiac failure.

Neural differentiation of mesenchymal stem cells influences chemotactic responses to HGF.

PubMed

Zheng, Bing; Wang, Chunyan; He, Lihong; Xu, Xiaojing; Qu, Jing; Hu, Jun; Zhang, Huanxiang

2013-01-01

Recently, mesenchymal stem cells (MSCs) have been extensively used for cell-based therapies in neuronal degenerative disease. Although much effort has been devoted to the delineation of factors involved in the migration of MSCs, the relationship between the chemotactic responses and the differentiation status of these cells remains elusive. Here, we report that MSCs in varying neural differentiation states display different chemotactic responses to hepatocyte growth factor (HGF): first, the number of chemotaxing MSCs and the optimal concentrations of HGF that induced the peak migration varied greatly; second, time-lapse video analysis showed that MSCs in certain differentiation state migrated more efficiently toward HGF; third, the phosphorylation levels of Akt, ERK1/2, SAPK/JNK, and p38MAPK were closely related to the differentiation levels of MSCs subjected to HGF; and finally, although inhibition of ERK1/2 signaling significantly attenuated HGF-stimulated transfilter migration of both undifferentiated and differentiating MSCs, abolishment of PI3K/Akt, p38MAPK, or SAPK/JNK signaling only decreased the number of migrated cells in certain differentiation state(s). Blocking of PI3K/Akt or MAPK signaling impaired the migration efficiency and/or speed, the extent of which depends on the cell differentiation states. Meanwhile, F-actin rearrangement, which is essential for MSCs chemotaxis, was induced by HGF, and the time points of cytoskeletal reorganization were different among these cells. Collectively, these results demonstrate that neural differentiation of MSCs influences their chemotactic responses to HGF: MSCs in varying differentiation states possess different migratory capacities, thereby shedding light on optimization of the therapeutic potential of MSCs to be employed for neural regeneration after injury. Copyright © 2012 Wiley Periodicals, Inc.

Selective neuronal differentiation of neural stem cells induced by nanosecond microplasma agitation.

PubMed

Xiong, Z; Zhao, S; Mao, X; Lu, X; He, G; Yang, G; Chen, M; Ishaq, M; Ostrikov, K

2014-03-01

An essential step for therapeutic and research applications of stem cells is their ability to differentiate into specific cell types. Neuronal cells are of great interest for medical treatment of neurodegenerative diseases and traumatic injuries of central nervous system (CNS), but efforts to produce these cells have been met with only modest success. In an attempt of finding new approaches, atmospheric-pressure room-temperature microplasma jets (MPJs) are shown to effectively direct in vitro differentiation of neural stem cells (NSCs) predominantly into neuronal lineage. Murine neural stem cells (C17.2-NSCs) treated with MPJs exhibit rapid proliferation and differentiation with longer neurites and cell bodies eventually forming neuronal networks. MPJs regulate ~75% of NSCs to differentiate into neurons, which is a higher efficiency compared to common protein- and growth factors-based differentiation. NSCs exposure to quantized and transient (~150 ns) micro-plasma bullets up-regulates expression of different cell lineage markers as β-Tubulin III (for neurons) and O4 (for oligodendrocytes), while the expression of GFAP (for astrocytes) remains unchanged, as evidenced by quantitative PCR, immunofluorescence microscopy and Western Blot assay. It is shown that the plasma-increased nitric oxide (NO) production is a factor in the fate choice and differentiation of NSCs followed by axonal growth. The differentiated NSC cells matured and produced mostly cholinergic and motor neuronal progeny. It is also demonstrated that exposure of primary rat NSCs to the microplasma leads to quite similar differentiation effects. This suggests that the observed effect may potentially be generic and applicable to other types of neural progenitor cells. The application of this new in vitro strategy to selectively differentiate NSCs into neurons represents a step towards reproducible and efficient production of the desired NSC derivatives. Published by Elsevier B.V.

Inhibition of TGF-β Signaling in SHED Enhances Endothelial Differentiation.

PubMed

Xu, J G; Gong, T; Wang, Y Y; Zou, T; Heng, B C; Yang, Y Q; Zhang, C F

2018-02-01

Low efficiency of deriving endothelial cells (ECs) from adult stem cells hampers their utilization in tissue engineering studies. The purpose of this study was to investigate whether suppression of transforming growth factor beta (TGF-β) signaling could enhance the differentiation efficiency of dental pulp-derived stem cells into ECs. We initially used vascular endothelial growth factor A (VEGF-A) to stimulate 2 dental pulp-derived stem cells (dental pulp stem cells and stem cells from human exfoliated deciduous teeth [SHED]) and compared their differentiation capacity into ECs. We further evaluated whether the vascular endothelial growth factor receptor I (VEGF-RI)-specific ligand placental growth factor-1 (PlGF-1) could mediate endothelial differentiation. Finally, we investigated whether the TGF-β signaling inhibitor SB-431542 could enhance the inductive effect of VEGF-A on endothelial differentiation, as well as the underlying mechanisms involved. ECs differentiated from dental pulp-derived stem cells exhibited the typical phenotypes of primary ECs, with SHED possessing a higher endothelial differentiation potential than dental pulp stem cells. VEGFR1-specific ligand-PLGF exerted a negligible effect on SHED-ECs differentiation. Compared with VEGF-A alone, the combination of VEGF-A and SB-431542 significantly enhanced the endothelial differentiation of SHED. The presence of SB-431542 inhibited the phosphorylation of Suppressor of Mothers Against Decapentaplegic 2/3 (SMAD2/3), allowing for VEGF-A-dependent phosphorylation and upregulation of VEGFR2. Our results indicate that the combination of VEGF-A and SB-431542 could enhance the differentiation of dental pulp-derived stem cells into endothelial cells, and this process is mediated through enhancement of VEGF-A-VEGFR2 signaling and concomitant inhibition of TGF-β-SMAD2/3 signaling.

Proteomics Insights into the Biomass Hydrolysis Potentials of a Hypercellulolytic Fungus Penicillium funiculosum.

PubMed

Ogunmolu, Funso Emmanuel; Kaur, Inderjeet; Gupta, Mayank; Bashir, Zeenat; Pasari, Nandita; Yazdani, Syed Shams

2015-10-02

The quest for cheaper and better enzymes needed for the efficient hydrolysis of lignocellulosic biomass has placed filamentous fungi in the limelight for bioprospecting research. In our search for efficient biomass degraders, we identified a strain of Penicillium funiculosum whose secretome demonstrates high saccharification capabilities. Our probe into the secretome of the fungus through qualitative and label-free quantitative mass spectrometry based proteomics studies revealed a high abundance of inducible CAZymes and several nonhydrolytic accessory proteins. The preferential association of these proteins and the attending differential biomass hydrolysis gives an insight into their interactions and clues about possible roles of novel hydrolytic and nonhydrolytic proteins in the synergistic deconstruction of lignocellulosic biomass. Our study thus provides the first comprehensive insight into the repertoire of proteins present in a high-performing secretome of a hypercellulolytic Penicillium funiculosum, their relative abundance in the secretome, and the interaction dynamics of the various protein groups in the secretome. The gleanings from the stoichiometry of these interactions hold a prospect as templates in the design of cost-effective synthetic cocktails for the optimal hydrolysis of biomass.

A highly linear fully integrated powerline filter for biopotential acquisition systems.

PubMed

Alzaher, Hussain A; Tasadduq, Noman; Mahnashi, Yaqub

2013-10-01

Powerline interference is one of the most dominant problems in detection and processing of biopotential signals. This work presents a new fully integrated notch filter exhibiting high linearity and low power consumption. High filter linearity is preserved utilizing active-RC approach while IC implementation is achieved through replacing passive resistors by R-2R ladders achieving area saving of approximately 120 times. The filter design is optimized for low power operation using an efficient circuit topology and an ultra-low power operational amplifier. Fully differential implementation of the proposed filter shows notch depth of 43 dB (78 dB for 4th-order) with THD of better than -70 dB while consuming about 150 nW from 1.5 V supply.

Evaluation of a Cubature Kalman Filtering-Based Phase Unwrapping Method for Differential Interferograms with High Noise in Coal Mining Areas

PubMed Central

Liu, Wanli; Bian, Zhengfu; Liu, Zhenguo; Zhang, Qiuzhao

2015-01-01

Differential interferometric synthetic aperture radar has been shown to be effective for monitoring subsidence in coal mining areas. Phase unwrapping can have a dramatic influence on the monitoring result. In this paper, a filtering-based phase unwrapping algorithm in combination with path-following is introduced to unwrap differential interferograms with high noise in mining areas. It can perform simultaneous noise filtering and phase unwrapping so that the pre-filtering steps can be omitted, thus usually retaining more details and improving the detectable deformation. For the method, the nonlinear measurement model of phase unwrapping is processed using a simplified Cubature Kalman filtering, which is an effective and efficient tool used in many nonlinear fields. Three case studies are designed to evaluate the performance of the method. In Case 1, two tests are designed to evaluate the performance of the method under different factors including the number of multi-looks and path-guiding indexes. The result demonstrates that the unwrapped results are sensitive to the number of multi-looks and that the Fisher Distance is the most suitable path-guiding index for our study. Two case studies are then designed to evaluate the feasibility of the proposed phase unwrapping method based on Cubature Kalman filtering. The results indicate that, compared with the popular Minimum Cost Flow method, the Cubature Kalman filtering-based phase unwrapping can achieve promising results without pre-filtering and is an appropriate method for coal mining areas with high noise. PMID:26153776

Transcriptome-based differentiation of closely-related Miscanthus lines.

PubMed

Chouvarine, Philippe; Cooksey, Amanda M; McCarthy, Fiona M; Ray, David A; Baldwin, Brian S; Burgess, Shane C; Peterson, Daniel G

2012-01-01

Distinguishing between individuals is critical to those conducting animal/plant breeding, food safety/quality research, diagnostic and clinical testing, and evolutionary biology studies. Classical genetic identification studies are based on marker polymorphisms, but polymorphism-based techniques are time and labor intensive and often cannot distinguish between closely related individuals. Illumina sequencing technologies provide the detailed sequence data required for rapid and efficient differentiation of related species, lines/cultivars, and individuals in a cost-effective manner. Here we describe the use of Illumina high-throughput exome sequencing, coupled with SNP mapping, as a rapid means of distinguishing between related cultivars of the lignocellulosic bioenergy crop giant miscanthus (Miscanthus × giganteus). We provide the first exome sequence database for Miscanthus species complete with Gene Ontology (GO) functional annotations. A SNP comparative analysis of rhizome-derived cDNA sequences was successfully utilized to distinguish three Miscanthus × giganteus cultivars from each other and from other Miscanthus species. Moreover, the resulting phylogenetic tree generated from SNP frequency data parallels the known breeding history of the plants examined. Some of the giant miscanthus plants exhibit considerable sequence divergence. Here we describe an analysis of Miscanthus in which high-throughput exome sequencing was utilized to differentiate between closely related genotypes despite the current lack of a reference genome sequence. We functionally annotated the exome sequences and provide resources to support Miscanthus systems biology. In addition, we demonstrate the use of the commercial high-performance cloud computing to do computational GO annotation.

Conversion of Fibroblasts to Parvalbumin Neurons by One Transcription Factor, Ascl1, and the Chemical Compound Forskolin*

PubMed Central

Shi, Zixiao; Zhang, Juan; Chen, Shuangquan; Li, Yanxin; Lei, Xuepei; Qiao, Huimin; Zhu, Qianwen; Hu, Baoyang; Zhou, Qi; Jiao, Jianwei

2016-01-01

Abnormalities in parvalbumin (PV)-expressing interneurons cause neurodevelopmental disorders such as epilepsy, autism, and schizophrenia. Unlike other types of neurons that can be efficiently differentiated from pluripotent stem cells, PV neurons were minimally generated using a conventional differentiation strategy. In this study we developed an adenovirus-based transdifferentiation strategy that incorporates an additional chemical compound for the efficient generation of induced PV (iPV) neurons. The chemical compound forskolin combined with Ascl1 induced ∼80% of mouse fibroblasts to iPV neurons. The iPV neurons generated by this procedure matured 5–7 days post infection and were characterized by electrophysiological properties and known neuronal markers, such as PV and GABA. Our studies, therefore, identified an efficient approach for generating PV neurons. PMID:27137935

Optimized optical wireless channel for indoor and intra-vehicle communications: power distribution and SNR analysis

NASA Astrophysics Data System (ADS)

Shaaban, Rana; Faruque, Saleh

2018-01-01

Light emitting diodes - LEDs are modernizing the indoor illumination and replacing current incandescent and fluorescent lamps rapidly. LEDs have multiple advantages such as extremely high energy efficient, longer lifespan, and lower heat generation. Due to the ability to switch to different light intensity at a very fast rate, LED has given rise to a unique communication technology (visible light communication - VLC) used for high speed data transmission. By studying various kinds of commonly used VLC channel analysis: diffuse and line of sight channels, we presented a simply improved indoor and intra-vehicle visible light communication transmission model. Employing optical wireless communications within the vehicle, not only enhance user mobility, but also alleviate radio frequency interference, and increase efficiency by lowering the complexity of copper cabling. Moreover, a solution to eliminate ambient noise caused by environmental conditions is examined by using optical differential receiver. The simulation results show the improved received power distribution and signal to noise ratio - SNR.

Superconducting thermoelectric generator

DOEpatents

Metzger, J.D.; El-Genk, M.S.

1994-01-01

Thermoelectricity is produced by applying a temperature differential to dissimilar electrically conducting or semiconducting materials, thereby producing a voltage that is proportional to the temperature difference. Thermoelectric generators use this effect to directly convert heat into electricity; however, presently-known generators have low efficiencies due to the production of high currents which in turn cause large resistive heating losses. Some thermoelectric generators operate at efficiencies between 4% and 7% in the 800{degrees} to 1200{degrees}C range. According to its major aspects and bradly stated, the present invention is an apparatus and method for producing electricity from heat. In particular, the invention is a thermoelectric generator that juxtaposes a superconducting material and a semiconducting material - so that the superconducting and the semiconducting materials touch - to convert heat energy into electrical energy without resistive losses in the temperature range below the critical temperature of the superconducting material. Preferably, an array of superconducting material is encased in one of several possible configurations within a second material having a high thermal conductivity, preferably a semiconductor, to form a thermoelectric generator.

Raman shifting of KrF laser radiation for tropospheric ozone measurements

NASA Technical Reports Server (NTRS)

Grant, William B.; Browell, Edward V.; Higdon, Noah S.; Ismail, Syed

1991-01-01

The differential absorption lidar (DIAL) measurement of tropospheric ozone requires use of high average power UV lasers operating at two appropriate DIAL wavelengths. Laboratory experiments have demonstrated that a KrF excimer laser can be used to generate several wavelengths with good energy conversion efficiencies by stimulated Raman shifting using hydrogen (H2) and deuterium (D2). Computer simulations for an airborne lidar have shown that these laser emissions can be used for the less than 5 percent random error, high resolution measuremment of ozone across the troposphere using the DIAL technique. In the region of strong ozone absorption, laser wavelengths of 277.0 and 291.7 nm were generated using H2 and D2, respectively. In addition, a laser wavelength at 302.0 nm was generated using two cells in series, with the first containing D2 and the second containing H2. The energy conversion efficiency for each wavelength was between 14 and 27 percent.

Impact of substrates acclimation strategy on simultaneous biodegradation of hydrogen sulfide and ammonia.

PubMed

Jiang, Xia; Luo, Yiqun; Yan, Rong; Tay, Joo Hwa

2009-12-01

Three columns were differentiated with feeding mixture of H(2)S and NH(3) (MFC), feeding NH(3) followed by H(2)S (NFC), and feeding H(2)S followed by NH(3) (SFC). Removal performance, biodegradation capacity and microbial community structures in the three columns were compared. The results show that NFC has a shorter acclimation period for the removal of NH(3) gas and nitrification than MFC. Under the high loading of H(2)S and NH(3) at 164 and 82 gm(-3) h(-1), respectively, NFC exhibited high removal efficiency of NH(3) (>95%) while the removal efficiencies were obtained at 63 and 75% in MFC and SFC, respectively. The removal of NH(3) gas in NFC was significantly attributed to nitrification (over 50%), while adsorption and chemical reaction contributed to the removal of NH(3) in MFC and SFC. The different biodegradation capacities of NH(3) could be due to the dissimilarity in the microbial population presented in each column.

Adaptive moving mesh methods for simulating one-dimensional groundwater problems with sharp moving fronts

USGS Publications Warehouse

Huang, W.; Zheng, Lingyun; Zhan, X.

2002-01-01

Accurate modelling of groundwater flow and transport with sharp moving fronts often involves high computational cost, when a fixed/uniform mesh is used. In this paper, we investigate the modelling of groundwater problems using a particular adaptive mesh method called the moving mesh partial differential equation approach. With this approach, the mesh is dynamically relocated through a partial differential equation to capture the evolving sharp fronts with a relatively small number of grid points. The mesh movement and physical system modelling are realized by solving the mesh movement and physical partial differential equations alternately. The method is applied to the modelling of a range of groundwater problems, including advection dominated chemical transport and reaction, non-linear infiltration in soil, and the coupling of density dependent flow and transport. Numerical results demonstrate that sharp moving fronts can be accurately and efficiently captured by the moving mesh approach. Also addressed are important implementation strategies, e.g. the construction of the monitor function based on the interpolation error, control of mesh concentration, and two-layer mesh movement. Copyright ?? 2002 John Wiley and Sons, Ltd.

Hyperspectral imaging coupled with chemometric analysis for non-invasive differentiation of black pens

NASA Astrophysics Data System (ADS)

Chlebda, Damian K.; Majda, Alicja; Łojewski, Tomasz; Łojewska, Joanna

2016-11-01

Differentiation of the written text can be performed with a non-invasive and non-contact tool that connects conventional imaging methods with spectroscopy. Hyperspectral imaging (HSI) is a relatively new and rapid analytical technique that can be applied in forensic science disciplines. It allows an image of the sample to be acquired, with full spectral information within every pixel. For this paper, HSI and three statistical methods (hierarchical cluster analysis, principal component analysis, and spectral angle mapper) were used to distinguish between traces of modern black gel pen inks. Non-invasiveness and high efficiency are among the unquestionable advantages of ink differentiation using HSI. It is also less time-consuming than traditional methods such as chromatography. In this study, a set of 45 modern gel pen ink marks deposited on a paper sheet were registered. The spectral characteristics embodied in every pixel were extracted from an image and analysed using statistical methods, externally and directly on the hypercube. As a result, different black gel inks deposited on paper can be distinguished and classified into several groups, in a non-invasive manner.

Fitting ordinary differential equations to short time course data.

PubMed

Brewer, Daniel; Barenco, Martino; Callard, Robin; Hubank, Michael; Stark, Jaroslav

2008-02-28

Ordinary differential equations (ODEs) are widely used to model many systems in physics, chemistry, engineering and biology. Often one wants to compare such equations with observed time course data, and use this to estimate parameters. Surprisingly, practical algorithms for doing this are relatively poorly developed, particularly in comparison with the sophistication of numerical methods for solving both initial and boundary value problems for differential equations, and for locating and analysing bifurcations. A lack of good numerical fitting methods is particularly problematic in the context of systems biology where only a handful of time points may be available. In this paper, we present a survey of existing algorithms and describe the main approaches. We also introduce and evaluate a new efficient technique for estimating ODEs linear in parameters particularly suited to situations where noise levels are high and the number of data points is low. It employs a spline-based collocation scheme and alternates linear least squares minimization steps with repeated estimates of the noise-free values of the variables. This is reminiscent of expectation-maximization methods widely used for problems with nuisance parameters or missing data.

Weak genetic differentiation in cobia, Rachycentron canadum from Indian waters as inferred from mitochondrial DNA ATPase 6 and 8 genes.

PubMed

Joy, Linu; Mohitha, C; Divya, P R; Gopalakrishnan, A; Basheer, V S; Jena, J K

2016-07-01

Cobia, Rachycentron canadum, is an economically important migratory fish distributed in tropical waters worldwide and is a candidate fish species for aquaculture practices. The genetic stock structure of R. canadum distributed along the Indian waters was identified using mitochondrial ATPase 6 and 8 genes. A total of 842 bp sequence of ATPase 6/8 genes obtained in this study revealed 15 haplotypes with mean low nucleotide diversity (π = 0.001) and high haplotype diversity (h = 0.785). AMOVA indicated the genetic differentiation of 90.47% for individuals within the population. This is well supported by co-efficient of genetic differentiation (FST) values obtained for pairwise populations that were low and non-significant with an overall value of 0.002. The parsimony network tree revealed star-like phylogeny and all the haplotypes were connected with each other by single mutational event. The findings of the present study indicated the panmixia nature of the species which can be managed as a unit stock in Indian waters.

Application of induced pluripotent stem cells to understand neurobiological basis of bipolar disorder and schizophrenia.

PubMed

Liu, Yao-Nan; Lu, Si-Yao; Yao, Jun

2017-09-01

The etiology of neuropsychiatric disorders, such as schizophrenia and bipolar disorder, usually involves complex combinations of genetic defects/variations and environmental impacts, which hindered, for a long time, research efforts based on animal models and patients' non-neuronal cells or post-mortem tissues. However, the development of human induced pluripotent stem cell (iPSC) technology by the Yamanaka group was immediately applied to establish cell research models for neuronal disorders. Since then, techniques to achieve highly efficient differentiation of different types of neural cells following iPSC modeling have made much progress. The fast-growing iPSC and neural differentiation techniques have brought valuable insights into the pathology and neurobiology of neuropsychiatric disorders. In this article, we first review the application of iPSC technology in modeling neuronal disorders and discuss the progress in the accompanying neural differentiation. Then, we summarize the progress in iPSC-based research that has been accomplished so far regarding schizophrenia and bipolar disorder. © 2017 The Authors. Psychiatry and Clinical Neurosciences © 2017 Japanese Society of Psychiatry and Neurology.

PGE2 pulsing of murine bone marrow cells reduces migration of daughter monocytes/macrophages in vitro and in vivo

PubMed Central

McGonigle, Terence A.; Dwyer, Amy R.; Greenland, Eloise L.; Scott, Naomi M.; Keane, Kevin N.; Newsholme, Philip; Goodridge, Helen S.; Zon, Leonard I.; Pixley, Fiona J.; Hart, Prue H.

2018-01-01

Monocytes/macrophages differentiating from bone marrow (BM) cells pulsed for 2 hours at 37°C with a stabilized derivative of prostaglandin E2, 16,16-dimethyl PGE2 (dmPGE2), migrated less efficiently toward a chemoattractant than monocytes/macrophages differentiated from BM cells pulsed with vehicle. To confirm that the effect on BM cells was long lasting and to replicate human BM transplantation, chimeric mice were established with donor BM cells pulsed for 2 hours with dmPGE2 before injection into marrow-ablated congenic recipient mice. After 12 weeks, when high levels (90%) of engraftment were obtained, regenerated BM-derived monocytes/macrophages differentiating in vitro or in vivo migrated inefficiently toward the chemokines colony-stimulating factor-1 (CSF-1) and chemokine (C-C motif) ligand 2 (CCL2) or thioglycollate, respectively. Our results reveal long-lasting changes to progenitor cells of monocytes/macrophages by a 2-hour dmPGE2 pulse that, in turn, limits the migration of their daughter cells to chemoattractants and inflammatory mediators. PMID:28822771

Essential mechanisms of differential activation of eosinophils by IL-3 compared to GM-CSF and IL-5

PubMed Central

Esnault, Stephane; Kelly, Elizabeth A.

2017-01-01

There is compelling evidence that the eosinophils bring negative biological outcomes in several diseases, including eosinophilic asthma and hypereosinophilic syndromes. Eosinophils produce and store a broad range of toxic proteins and other mediators that enhance the inflammatory response and lead to tissue damage. For instance, in asthma, there is a close relationship between increased lung eosinophilia, asthma exacerbation, and loss of lung function. The use of an anti-IL-5 therapy in severe eosinophilic asthmatic patients is efficient to reduce exacerbations. However, anti-IL-5-treated patients still display a relatively high amount of functional lung tissue eosinophils, indicating that supplemental therapies are required to damper the eosinophil functions. Our recent published works, suggest that compared to IL-5, IL-3 can more strongly and differentially affect eosinophil functions. In this review, we will summarize our and other investigations that have compared the effects of the three β-chain receptor cytokines (IL-5, GM-CSF and IL-3) on eosinophil biology. We will focus on how IL-3 differentially activates eosinophils compared to IL-5 or GM-CSF. PMID:28605348

Differential Electrochemical Conductance Imaging at the Nanoscale.

PubMed

López-Martínez, Montserrat; Artés, Juan Manuel; Sarasso, Veronica; Carminati, Marco; Díez-Pérez, Ismael; Sanz, Fausto; Gorostiza, Pau

2017-09-01

Electron transfer in proteins is essential in crucial biological processes. Although the fundamental aspects of biological electron transfer are well characterized, currently there are no experimental tools to determine the atomic-scale electronic pathways in redox proteins, and thus to fully understand their outstanding efficiency and environmental adaptability. This knowledge is also required to design and optimize biomolecular electronic devices. In order to measure the local conductance of an electrode surface immersed in an electrolyte, this study builds upon the current-potential spectroscopic capacity of electrochemical scanning tunneling microscopy, by adding an alternating current modulation technique. With this setup, spatially resolved, differential electrochemical conductance images under bipotentiostatic control are recorded. Differential electrochemical conductance imaging allows visualizing the reversible oxidation of an iron electrode in borate buffer and individual azurin proteins immobilized on atomically flat gold surfaces. In particular, this method reveals submolecular regions with high conductance within the protein. The direct observation of nanoscale conduction pathways in redox proteins and complexes enables important advances in biochemistry and bionanotechnology. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An efficient numerical scheme for the study of equal width equation

NASA Astrophysics Data System (ADS)

Ghafoor, Abdul; Haq, Sirajul

2018-06-01

In this work a new numerical scheme is proposed in which Haar wavelet method is coupled with finite difference scheme for the solution of a nonlinear partial differential equation. The scheme transforms the partial differential equation to a system of algebraic equations which can be solved easily. The technique is applied to equal width equation in order to study the behaviour of one, two, three solitary waves, undular bore and soliton collision. For efficiency and accuracy of the scheme, L2 and L∞ norms and invariants are computed. The results obtained are compared with already existing results in literature.

Nanochelating based nanocomplex, GFc7, improves quality and quantity of human mesenchymal stem cells during in vitro expansion.

PubMed

Hafizi, Maryam; Hajarizadeh, Atena; Atashi, Amir; Kalanaky, Somayeh; Fakharzadeh, Saideh; Masoumi, Zahra; Nazaran, Mohammad Hassan; Soleimani, Masoud

2015-11-23

Human mesenchymal stem cells (hMSCs) have been approved for therapeutic applications. Despite the advances in this field, in vitro approaches are still required to improve the essential indices that would pave the way to a bright horizon for an efficient transplantation in the future. Nanotechnology could help to improve these approaches. Studies signified the important role of iron in stem cell metabolism and efficiency of copper chelation application for stem cell expansion For the first time, based on novel Nanochelating technology, we design an iron containing copper chelator nano complex, GFc7 and examined on hMSCs during in vitro expansion. In this study, the hMSCs were isolated, characterized and expanded in vitro in two media (with or without GFc7). Then proliferation, cell viability, cell cycle analysis, surface markers, HLADR, pluripotency genes expression, homing and antioxidative defense at genes and protein expression were investigated. Also we analyzed the spontaneous differentiation and examined osteogenic and lipogenic differentiation. GFc7 affected the expression of key genes, improving both the stemness and fitness of the cells in a precise and balanced manner. We observed significant increases in cell proliferation, enhanced expression of pluripotency genes and homing markers, improved antioxidative defense, repression of genes involved in spontaneous differentiation and exposing the hMSCs to differentiation medium indicated that pretreatment with GFc7 increased the quality and rate of differentiation. Thus, GFc7 appears to be a potential new supplement for cell culture medium for increasing the efficiency of transplantation.

Colonization of collagen scaffolds by adipocytes derived from mesenchymal stem cells of the common marmoset monkey

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

Bernemann, Inga, E-mail: bernemann@imp.uni-hannover.de; Mueller, Thomas; Blasczyk, Rainer

Highlights: {yields} Marmoset bone marrow-derived MSCs differentiate in suspension into adipogenic, osteogenic and chondrogenic lineages. {yields} Marmoset MSCs integrate in collagen type I scaffolds and differentiate excellently into adipogenic cells. {yields} Common marmoset monkey is a suitable model for soft tissue engineering in human regenerative medicine. -- Abstract: In regenerative medicine, human cell replacement therapy offers great potential, especially by cell types differentiated from immunologically and ethically unproblematic mesenchymal stem cells (MSCs). In terms of an appropriate carrier material, collagen scaffolds with homogeneous pore size of 65 {mu}m were optimal for cell seeding and cultivating. However, before clinical application andmore » transplantation of MSC-derived cells in scaffolds, the safety and efficiency, but also possible interference in differentiation due to the material must be preclinically tested. The common marmoset monkey (Callithrix jacchus) is a preferable non-human primate animal model for this aim due to its genetic and physiological similarities to the human. Marmoset bone marrow-derived MSCs were successfully isolated, cultured and differentiated in suspension into adipogenic, osteogenic and chondrogenic lineages by defined factors. The differentiation capability could be determined by FACS. Specific marker genes for all three cell types could be detected by RT-PCR. Furthermore, MSCs seeded on collagen I scaffolds differentiated in adipogenic lineage showed after 28 days of differentiation high cell viability and homogenous distribution on the material which was validated by calcein AM and EthD staining. As proof of adipogenic cells, the intracellular lipid vesicles in the cells were stained with Oil Red O. The generation of fat vacuoles was visibly extensive distinguishable and furthermore determined on the molecular level by expression of specific marker genes. The results of the study proved both the differential potential of marmoset MSCs in adipogenic, osteogenic and chondrogenic lineages and the suitability of collagen scaffolds as carrier material undisturbing differentiation of primate mesenchymal stem cells.« less

High-contrast differentiation resolution 3D imaging of rodent brain by X-ray computed microtomography

NASA Astrophysics Data System (ADS)

Zikmund, T.; Novotná, M.; Kavková, M.; Tesařová, M.; Kaucká, M.; Szarowská, B.; Adameyko, I.; Hrubá, E.; Buchtová, M.; Dražanová, E.; Starčuk, Z.; Kaiser, J.

2018-02-01

The biomedically focused brain research is largely performed on laboratory mice considering a high homology between the human and mouse genomes. A brain has an intricate and highly complex geometrical structure that is hard to display and analyse using only 2D methods. Applying some fast and efficient methods of brain visualization in 3D will be crucial for the neurobiology in the future. A post-mortem analysis of experimental animals' brains usually involves techniques such as magnetic resonance and computed tomography. These techniques are employed to visualize abnormalities in the brains' morphology or reparation processes. The X-ray computed microtomography (micro CT) plays an important role in the 3D imaging of internal structures of a large variety of soft and hard tissues. This non-destructive technique is applied in biological studies because the lab-based CT devices enable to obtain a several-micrometer resolution. However, this technique is always used along with some visualization methods, which are based on the tissue staining and thus differentiate soft tissues in biological samples. Here, a modified chemical contrasting protocol of tissues for a micro CT usage is introduced as the best tool for ex vivo 3D imaging of a post-mortem mouse brain. This way, the micro CT provides a high spatial resolution of the brain microscopic anatomy together with a high tissue differentiation contrast enabling to identify more anatomical details in the brain. As the micro CT allows a consequent reconstruction of the brain structures into a coherent 3D model, some small morphological changes can be given into context of their mutual spatial relationships.

Visual versus mechanised leucocyte differential counts: costing and evaluation of traditional and Hemalog D methods.

PubMed

Hudson, M J; Green, A E

1980-11-01

Visual differential counts were examined for efficiency, cost effectiveness, and staff acceptability within our laboratory. A comparison with the Hemalog D system was attempted. The advantages and disadvantages of each system are enumerated and discussed in the context of a large general hospital.

Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant

PubMed Central

Bourion, Virginie

2014-01-01

To complement N2 fixation through symbiosis, legumes can efficiently acquire soil mineral N through adapted root architecture. However, root architecture adaptation to mineral N availability has been little studied in legumes. Therefore, this study investigated the effect of nitrate availability on root architecture in Medicago truncatula and assessed the N-uptake potential of a new highly branched root mutant, TR185. The effects of varying nitrate supply on both root architecture and N uptake were characterized in the mutant and in the wild type. Surprisingly, the root architecture of the mutant was not modified by variation in nitrate supply. Moreover, despite its highly branched root architecture, TR185 had a permanently N-starved phenotype. A transcriptome analysis was performed to identify genes differentially expressed between the two genotypes. This analysis revealed differential responses related to the nitrate acquisition pathway and confirmed that N starvation occurred in TR185. Changes in amino acid content and expression of genes involved in the phenylpropanoid pathway were associated with differences in root architecture between the mutant and the wild type. PMID:24706718

Assessment of the performance of a compact concentric spectrometer system for Atmospheric Differential Optical Absorption Spectroscopy

NASA Astrophysics Data System (ADS)

Whyte, C.; Leigh, R. J.; Lobb, D.; Williams, T.; Remedios, J. J.; Cutter, M.; Monks, P. S.

2009-12-01

A breadboard demonstrator of a novel UV/VIS grating spectrometer has been developed based upon a concentric arrangement of a spherical meniscus lens, concave spherical mirror and curved diffraction grating suitable for a range of atmospheric remote sensing applications from the ground or space. The spectrometer is compact and provides high optical efficiency and performance benefits over traditional instruments. The concentric design is capable of handling high relative apertures, owing to spherical aberration and comma being near zero at all surfaces. The design also provides correction for transverse chromatic aberration and distortion, in addition to correcting for the distortion called "smile", the curvature of the slit image formed at each wavelength. These properties render this design capable of superior spectral and spatial performance with size and weight budgets significantly lower than standard configurations. This form of spectrometer design offers the potential for exceptionally compact instrument for differential optical absorption spectroscopy (DOAS) applications from LEO, GEO, HAP or ground-based platforms. The breadboard demonstrator has been shown to offer high throughput and a stable Gaussian line shape with a spectral range from 300 to 450 nm at 0.5 nm resolution, suitable for a number of typical DOAS applications.

High-resolution imaging of cellular processes across textured surfaces using an indexed-matched elastomer.

PubMed

Ravasio, Andrea; Vaishnavi, Sree; Ladoux, Benoit; Viasnoff, Virgile

2015-03-01

Understanding and controlling how cells interact with the microenvironment has emerged as a prominent field in bioengineering, stem cell research and in the development of the next generation of in vitro assays as well as organs on a chip. Changing the local rheology or the nanotextured surface of substrates has proved an efficient approach to improve cell lineage differentiation, to control cell migration properties and to understand environmental sensing processes. However, introducing substrate surface textures often alters the ability to image cells with high precision, compromising our understanding of molecular mechanisms at stake in environmental sensing. In this paper, we demonstrate how nano/microstructured surfaces can be molded from an elastomeric material with a refractive index matched to the cell culture medium. Once made biocompatible, contrast imaging (differential interference contrast, phase contrast) and high-resolution fluorescence imaging of subcellular structures can be implemented through the textured surface using an inverted microscope. Simultaneous traction force measurements by micropost deflection were also performed, demonstrating the potential of our approach to study cell-environment interactions, sensing processes and cellular force generation with unprecedented resolution. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Symmetric and arbitrarily high-order Birkhoff-Hermite time integrators and their long-time behaviour for solving nonlinear Klein-Gordon equations

NASA Astrophysics Data System (ADS)

Liu, Changying; Iserles, Arieh; Wu, Xinyuan

2018-03-01

The Klein-Gordon equation with nonlinear potential occurs in a wide range of application areas in science and engineering. Its computation represents a major challenge. The main theme of this paper is the construction of symmetric and arbitrarily high-order time integrators for the nonlinear Klein-Gordon equation by integrating Birkhoff-Hermite interpolation polynomials. To this end, under the assumption of periodic boundary conditions, we begin with the formulation of the nonlinear Klein-Gordon equation as an abstract second-order ordinary differential equation (ODE) and its operator-variation-of-constants formula. We then derive a symmetric and arbitrarily high-order Birkhoff-Hermite time integration formula for the nonlinear abstract ODE. Accordingly, the stability, convergence and long-time behaviour are rigorously analysed once the spatial differential operator is approximated by an appropriate positive semi-definite matrix, subject to suitable temporal and spatial smoothness. A remarkable characteristic of this new approach is that the requirement of temporal smoothness is reduced compared with the traditional numerical methods for PDEs in the literature. Numerical results demonstrate the advantage and efficiency of our time integrators in comparison with the existing numerical approaches.

Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant.

PubMed

Bourion, Virginie; Martin, Chantal; de Larambergue, Henri; Jacquin, Françoise; Aubert, Grégoire; Martin-Magniette, Marie-Laure; Balzergue, Sandrine; Lescure, Geoffroy; Citerne, Sylvie; Lepetit, Marc; Munier-Jolain, Nathalie; Salon, Christophe; Duc, Gérard

2014-06-01

To complement N2 fixation through symbiosis, legumes can efficiently acquire soil mineral N through adapted root architecture. However, root architecture adaptation to mineral N availability has been little studied in legumes. Therefore, this study investigated the effect of nitrate availability on root architecture in Medicago truncatula and assessed the N-uptake potential of a new highly branched root mutant, TR185. The effects of varying nitrate supply on both root architecture and N uptake were characterized in the mutant and in the wild type. Surprisingly, the root architecture of the mutant was not modified by variation in nitrate supply. Moreover, despite its highly branched root architecture, TR185 had a permanently N-starved phenotype. A transcriptome analysis was performed to identify genes differentially expressed between the two genotypes. This analysis revealed differential responses related to the nitrate acquisition pathway and confirmed that N starvation occurred in TR185. Changes in amino acid content and expression of genes involved in the phenylpropanoid pathway were associated with differences in root architecture between the mutant and the wild type. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Linear Back-Drive Differentials

NASA Technical Reports Server (NTRS)

Waydo, Peter

2003-01-01

Linear back-drive differentials have been proposed as alternatives to conventional gear differentials for applications in which there is only limited rotational motion (e.g., oscillation). The finite nature of the rotation makes it possible to optimize a linear back-drive differential in ways that would not be possible for gear differentials or other differentials that are required to be capable of unlimited rotation. As a result, relative to gear differentials, linear back-drive differentials could be more compact and less massive, could contain fewer complex parts, and could be less sensitive to variations in the viscosities of lubricants. Linear back-drive differentials would operate according to established principles of power ball screws and linear-motion drives, but would utilize these principles in an innovative way. One major characteristic of such mechanisms that would be exploited in linear back-drive differentials is the possibility of designing them to drive or back-drive with similar efficiency and energy input: in other words, such a mechanism can be designed so that a rotating screw can drive a nut linearly or the linear motion of the nut can cause the screw to rotate. A linear back-drive differential (see figure) would include two collinear shafts connected to two parts that are intended to engage in limited opposing rotations. The linear back-drive differential would also include a nut that would be free to translate along its axis but not to rotate. The inner surface of the nut would be right-hand threaded at one end and left-hand threaded at the opposite end to engage corresponding right- and left-handed threads on the shafts. A rotation and torque introduced into the system via one shaft would drive the nut in linear motion. The nut, in turn, would back-drive the other shaft, creating a reaction torque. Balls would reduce friction, making it possible for the shaft/nut coupling on each side to operate with 90 percent efficiency.

Program for solution of ordinary differential equations

NASA Technical Reports Server (NTRS)

Sloate, H.

1973-01-01

A program for the solution of linear and nonlinear first order ordinary differential equations is described and user instructions are included. The program contains a new integration algorithm for the solution of initial value problems which is particularly efficient for the solution of differential equations with a wide range of eigenvalues. The program in its present form handles up to ten state variables, but expansion to handle up to fifty state variables is being investigated.

The sequence of the CA-SP1 junction accounts for the differential sensitivity of HIV-1 and SIV to the small molecule maturation inhibitor 3-O-{3',3'-dimethylsuccinyl}-betulinic acid.

PubMed

Zhou, Jing; Chen, Chin Ho; Aiken, Christopher

2004-06-29

Despite the effectiveness of currently available antiretroviral therapies in the treatment of HIV-1 infection, a continuing need exists for novel compounds that can be used in combination with existing drugs to slow the emergence of drug-resistant viruses. We previously reported that the small molecule 3-O-{3',3'-dimethylsuccinyl}-betulinic acid (DSB) specifically inhibits HIV-1 replication by delaying the processing of the CA-SP1 junction in Pr55Gag. By contrast, SIVmac239 replicates efficiently in the presence of high concentrations of DSB. To determine whether sequence differences in the CA-SP1 junction can fully account for the differential sensitivity of HIV-1 and SIV to DSB, we engineered mutations in this region of two viruses and tested their sensitivity to DSB in replication assays using activated human primary CD4+ T cells. Substitution of the P2 and P1 residues of HIV-1 by the corresponding amino acids of SIV resulted in strong resistance to DSB, but the mutant virus replicated with reduced efficiency. Conversely, replication of an SIV mutant containing three amino acid substitutions in the CA-SP1 cleavage site was highly sensitive to DSB, and the mutations resulted in delayed cleavage of the CA-SP1 junction in the presence of the drug. These results demonstrate that the CA-SP1 junction in Pr55Gag represents the primary viral target of DSB. They further suggest that the therapeutic application of DSB will be accompanied by emergence of mutant viruses that are highly resistant to the drug but which exhibit reduced fitness relative to wild type HIV-1.

Performance evaluation of the Abbott CELL-DYN Ruby and the Sysmex XT-2000i haematology analysers.

PubMed

Leers, M P G; Goertz, H; Feller, A; Hoffmann, J J M L

2011-02-01

Two mid-range haematology analysers (Abbott CELL-DYN Ruby and Sysmex XT-2000i) were evaluated to determine their analytical performance and workflow efficiency in the haematology laboratory. In total 418 samples were processed for determining equivalence of complete blood count (CBC) measurements, and 100 for reticulocyte comparison. Blood smears served for assessing the agreement of the differential counts. Inter-instrument agreement for most parameters was good although small numbers of discrepancies were observed. Systematic biases were found for mean cell volume, reticulocytes, platelets and mean platelet volume. CELL-DYN Ruby WBC differentials were obtained with all samples while the XT-2000i suppressed differentials partially or completely in 13 samples (3.1%). WBC subpopulation counts were otherwise in good agreement with no major outliers. Following first-pass CBC/differential analysis, 88 (21%) of XT-2000i samples required further analyser processing compared to 18 (4.3%) for the CELL-DYN Ruby. Smear referrals for suspected WBC/nucleated red blood cells and platelet abnormalities were indicated for 106 (25.4%) and 95 (22.7%) of the XT-2000i and CELL-DYN Ruby samples respectively. Flagging efficiencies for both analysers were found to be similar. The Sysmex XT-2000i and Abbott CELL-DYN Ruby analysers have broadly comparable analytical performance, but the CELL-DYN Ruby showed superior first-pass efficiency. © 2010 Blackwell Publishing Ltd.

Mapping by admixture linkage disequilibrium in human populations: Limits and guidelines

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

Stephens, J.C.; Briscoe, D.; O`Brien, S.J.

1994-10-01

Certain human hereditary conditions, notably those with low penetrance and those which require an environmental event such as infectious disease exposure, are difficult to localize in pedigree analysis, because of uncertainty in the phenotype of an affected patient`s relatives. An approach to locating these genes in human cohort studies would be to use association analysis, which depends on linkage disequilibrium of flanking polymorphic DNA markers. In theory, a high degree of linkage disequilibrium between genes separated by 10-20 cM will be generated and persist in populations that have a history of recent (3-20 generations ago) admixture between genetically differentiated racialmore » groups, such as has occurred in African Americans and Hispanic populations. We have conducted analytic and computer simulations to quantify the effect of genetic, genomic, and population parameters that affect the amount and ascertainment of linkage disequilibrium in populations with a history of genetic admixture. Our goal is to thoroughly explore the ranges of all relevant parameters or factors (e.g., sample size and degree of genetic differentiation between populations) that may be involved in gene localization studies, in hopes of prescribing guidelines for an efficient mapping strategy. The results provide reasonable limits on sample size (200-300 patients), marker number (200-300 in 20-cM intervals), and allele differentiation (loci with allele frequency difference of {ge}.3 between admixed parent populations) to produce an efficient approach (>95% ascertainment) for locating genes not easily tracked in human pedigrees. 321 refs., 8 figs., 7 tabs.« less

A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus).

PubMed

Ferchaud, Anne-Laure; Pedersen, Susanne H; Bekkevold, Dorte; Jian, Jianbo; Niu, Yongchao; Hansen, Michael M

2014-10-06

The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In particular, differential adaptation to freshwater and marine environments has led to high differentiation between freshwater and marine stickleback populations at the phenotypic trait of lateral plate morphology and the underlying candidate gene Ectodysplacin (EDA). Many studies have focused on this trait and candidate gene, although other genes involved in marine-freshwater adaptation may be equally important. In order to develop a resource for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background. RAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional selection in freshwater vs. marine environments, whereas 26 SNPs were assumed to be neutral. Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new. We have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback. The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA).

LOCAL ORTHOGONAL CUTTING METHOD FOR COMPUTING MEDIAL CURVES AND ITS BIOMEDICAL APPLICATIONS

PubMed Central

Einstein, Daniel R.; Dyedov, Vladimir

2010-01-01

Medial curves have a wide range of applications in geometric modeling and analysis (such as shape matching) and biomedical engineering (such as morphometry and computer assisted surgery). The computation of medial curves poses significant challenges, both in terms of theoretical analysis and practical efficiency and reliability. In this paper, we propose a definition and analysis of medial curves and also describe an efficient and robust method called local orthogonal cutting (LOC) for computing medial curves. Our approach is based on three key concepts: a local orthogonal decomposition of objects into substructures, a differential geometry concept called the interior center of curvature (ICC), and integrated stability and consistency tests. These concepts lend themselves to robust numerical techniques and result in an algorithm that is efficient and noise resistant. We illustrate the effectiveness and robustness of our approach with some highly complex, large-scale, noisy biomedical geometries derived from medical images, including lung airways and blood vessels. We also present comparisons of our method with some existing methods. PMID:20628546

The Wnt/β-catenin signaling pathway tips the balance between apoptosis and reprograming of cell fusion hybrids.

PubMed

Lluis, Frederic; Pedone, Elisa; Pepe, Stefano; Cosma, Maria Pia

2010-11-01

Cell-cell fusion contributes to cell differentiation and developmental processes. We have previously showed that activation of Wnt/β-catenin enhances somatic cell reprograming after polyethylene glycol (PEG)-mediated fusion. Here, we show that neural stem cells and ESCs can fuse spontaneously in cocultures, although with very low efficiency (about 2%), as the hybrids undergo apoptosis. In contrast, when Wnt/β-catenin signaling is activated in ESCs and leads to accumulation of low amounts of β-catenin in the nucleus, activated ESCs can reprogram somatic cells with very high efficiency after spontaneous fusion. Furthermore, we also show that different levels of β-catenin accumulation in the ESC nuclei can modulate cell proliferation, although in our experimental setting, cell proliferation does not modulate the reprograming efficiency per se. Overall, the present study provides evidence that spontaneous fusion occurs, while the survival of the reprogramed clones is strictly dependent on induction of a Wnt-mediated reprograming pathway. Copyright © 2010 AlphaMed Press.

Efficient transduction of equine adipose-derived mesenchymal stem cells by VSV-G pseudotyped lentiviral vectors.

PubMed

Petersen, Gayle F; Hilbert, Bryan; Trope, Gareth; Kalle, Wouter; Strappe, Padraig

2014-12-01

Equine adipose-derived mesenchymal stem cells (EADMSC) provide a unique cell-based approach for treatment of a variety of equine musculoskeletal injuries, via regeneration of diseased or damaged tissue, or the secretion of immunomodulatory molecules. These capabilities can be further enhanced by genetic modification using lentiviral vectors, which provide a safe and efficient method of gene delivery. We investigated the suitability of lentiviral vector technology for gene delivery into EADMSC, using GFP expressing lentiviral vectors pseudotyped with the G glycoprotein from the vesicular stomatitis virus (V-GFP) or, for the first time, the baculovirus gp64 envelope protein (G-GFP). In this study, we produced similarly high titre V-GFP and G-GFP lentiviral vectors. Flow cytometric analysis showed efficient transduction using V-GFP; however G-GFP exhibited a poor ability to transduce EADMSC. Transduction resulted in sustained GFP expression over four passages, with minimal effects on cell viability and doubling time, and an unaltered chondrogenic differentiation potential. Copyright © 2014 Elsevier Ltd. All rights reserved.

New second order Mumford-Shah model based on Γ-convergence approximation for image processing

NASA Astrophysics Data System (ADS)

Duan, Jinming; Lu, Wenqi; Pan, Zhenkuan; Bai, Li

2016-05-01

In this paper, a second order variational model named the Mumford-Shah total generalized variation (MSTGV) is proposed for simultaneously image denoising and segmentation, which combines the original Γ-convergence approximated Mumford-Shah model with the second order total generalized variation (TGV). For image denoising, the proposed MSTGV can eliminate both the staircase artefact associated with the first order total variation and the edge blurring effect associated with the quadratic H1 regularization or the second order bounded Hessian regularization. For image segmentation, the MSTGV can obtain clear and continuous boundaries of objects in the image. To improve computational efficiency, the implementation of the MSTGV does not directly solve its high order nonlinear partial differential equations and instead exploits the efficient split Bregman algorithm. The algorithm benefits from the fast Fourier transform, analytical generalized soft thresholding equation, and Gauss-Seidel iteration. Extensive experiments are conducted to demonstrate the effectiveness and efficiency of the proposed model.

Sustained attentional and disattentional abilities: differences between low and highly hypnotizable persons.

PubMed

Crawford, H J; Brown, A M; Moon, C E

1993-11-01

Relations between sustained attentional and disattentional abilities and hypnotic susceptibility (Harvard Group Scale of Hypnotic Susceptibility: Form A; Stanford Hypnotic Susceptibility Scale: Form C) were examined in 38 low (0-3) and 39 highly (10-12) hypnotizable college students. Highs showed greater sustained attention on Necker cube and autokinetic movement tasks and self-reported greater absorption (Tellegen Absorption Scale) and extremely focused attentional (Differential Attentional Processes Inventory) styles. Hypnotizability was unrelated to dichotic selective attention (A. Karlin, 1979) and random number generation (C. Graham & F. J. Evans, 1977) tasks. Discriminant analysis correctly classified 74% of the lows and 69% of the highs. Results support H. J. Crawford and J. H. Gruzelier's (1992) neuropsychophysiological model of hypnosis that proposes that highly hypnotizable persons have a more efficient far frontolimbic sustained attentional and disattentional system.

Basic mechanisms governing solar-cell efficiency

NASA Technical Reports Server (NTRS)

Lindholm, F. A.; Neugroschel, A.; Sah, C. T.

1976-01-01

The efficiency of a solar cell depends on the material parameters appearing in the set of differential equations that describe the transport, recombination, and generation of electrons and holes. This paper describes the many basic mechanisms occurring in semiconductors that can control these material parameters.

Intraspecific Variation in Wood Anatomical, Hydraulic, and Foliar Traits in Ten European Beech Provenances Differing in Growth Yield

PubMed Central

Hajek, Peter; Kurjak, Daniel; von Wühlisch, Georg; Delzon, Sylvain; Schuldt, Bernhard

2016-01-01

In angiosperms, many studies have described the inter-specific variability of hydraulic-related traits and little is known at the intra-specific level. This information is however mandatory to assess the adaptive capacities of tree populations in the context of increasing drought frequency and severity. Ten 20-year old European beech (Fagus sylvatica L.) provenances representing the entire distribution range throughout Europe and differing significantly in aboveground biomass increment (ABI) by a factor of up to four were investigated for branch wood anatomical, hydraulic, and foliar traits in a provenance trial located in Northern Europe. We quantified to which extend xylem hydraulic and leaf traits are under genetic control and tested whether the xylem hydraulic properties (hydraulic efficiency and safety) trades off with yield and wood anatomical and leaf traits. Our results showed that only three out of 22 investigated ecophysiological traits showed significant genetic differentiations between provenances, namely vessel density (VD), the xylem pressure causing 88% loss of hydraulic conductance and mean leaf size. Depending of the ecophysiological traits measured, genetic differentiation between populations explained 0–14% of total phenotypic variation, while intra-population variability was higher than inter-population variability. Most wood anatomical traits and some foliar traits were additionally related to the climate of provenance origin. The lumen to sapwood area ratio, vessel diameter, theoretical specific conductivity and theoretical leaf-specific conductivity as well as the C:N-ratio increased with climatic aridity at the place of origin while the carbon isotope signature (δ13C) decreased. Contrary to our assumption, none of the wood anatomical traits were related to embolism resistance but were strong determinants of hydraulic efficiency. Although ABI was associated with both VD and δ13C, both hydraulic efficiency and embolism resistance were unrelated, disproving the assumed trade-off between hydraulic efficiency and safety. European beech seems to compensate increasing water stress with growing size mainly by adjusting vessel number and not vessel diameter. In conclusion, European beech has a high potential capacity to cope with climate change due to the high degree of intra-population genetic variability. PMID:27379112

Intraspecific Variation in Wood Anatomical, Hydraulic, and Foliar Traits in Ten European Beech Provenances Differing in Growth Yield.

PubMed

Hajek, Peter; Kurjak, Daniel; von Wühlisch, Georg; Delzon, Sylvain; Schuldt, Bernhard

2016-01-01

In angiosperms, many studies have described the inter-specific variability of hydraulic-related traits and little is known at the intra-specific level. This information is however mandatory to assess the adaptive capacities of tree populations in the context of increasing drought frequency and severity. Ten 20-year old European beech (Fagus sylvatica L.) provenances representing the entire distribution range throughout Europe and differing significantly in aboveground biomass increment (ABI) by a factor of up to four were investigated for branch wood anatomical, hydraulic, and foliar traits in a provenance trial located in Northern Europe. We quantified to which extend xylem hydraulic and leaf traits are under genetic control and tested whether the xylem hydraulic properties (hydraulic efficiency and safety) trades off with yield and wood anatomical and leaf traits. Our results showed that only three out of 22 investigated ecophysiological traits showed significant genetic differentiations between provenances, namely vessel density (VD), the xylem pressure causing 88% loss of hydraulic conductance and mean leaf size. Depending of the ecophysiological traits measured, genetic differentiation between populations explained 0-14% of total phenotypic variation, while intra-population variability was higher than inter-population variability. Most wood anatomical traits and some foliar traits were additionally related to the climate of provenance origin. The lumen to sapwood area ratio, vessel diameter, theoretical specific conductivity and theoretical leaf-specific conductivity as well as the C:N-ratio increased with climatic aridity at the place of origin while the carbon isotope signature (δ(13)C) decreased. Contrary to our assumption, none of the wood anatomical traits were related to embolism resistance but were strong determinants of hydraulic efficiency. Although ABI was associated with both VD and δ(13)C, both hydraulic efficiency and embolism resistance were unrelated, disproving the assumed trade-off between hydraulic efficiency and safety. European beech seems to compensate increasing water stress with growing size mainly by adjusting vessel number and not vessel diameter. In conclusion, European beech has a high potential capacity to cope with climate change due to the high degree of intra-population genetic variability.

Technical Desiderata for the Integration of Genomic Data into Electronic Health Records

PubMed Central

Masys, Daniel R.; Jarvik, Gail P.; Abernethy, Neil F.; Anderson, Nicholas R.; Papanicolaou, George J.; Paltoo, Dina N.; Hoffman, Mark A.; Kohane, Isaac S.; Levy, Howard P.

2012-01-01

The era of “Personalized Medicine,” guided by individual molecular variation in DNA, RNA, expressed proteins and other forms of high volume molecular data brings new requirements and challenges to the design and implementation of Electronic Health Records (EHRs). In this article we describe the characteristics of biomolecular data that differentiate it from other classes of data commonly found in EHRs, enumerate a set of technical desiderata for its management in healthcare settings, and offer a candidate technical approach to its compact and efficient representation in operational systems. PMID:22223081

A systematic and efficient method to compute multi-loop master integrals

NASA Astrophysics Data System (ADS)

Liu, Xiao; Ma, Yan-Qing; Wang, Chen-Yu

2018-04-01

We propose a novel method to compute multi-loop master integrals by constructing and numerically solving a system of ordinary differential equations, with almost trivial boundary conditions. Thus it can be systematically applied to problems with arbitrary kinematic configurations. Numerical tests show that our method can not only achieve results with high precision, but also be much faster than the only existing systematic method sector decomposition. As a by product, we find a new strategy to compute scalar one-loop integrals without reducing them to master integrals.

Through the looking glass: Basics and principles of reflectance confocal microscopy.

PubMed

Que, Syril Keena T; Fraga-Braghiroli, Naiara; Grant-Kels, Jane M; Rabinovitz, Harold S; Oliviero, Margaret; Scope, Alon

2015-08-01

Reflectance confocal microscopy (RCM) offers high-resolution, noninvasive skin imaging and can help avoid obtaining unnecessary biopsy specimens. It can also increase efficiency in the surgical setting by helping to delineate tumor margins. Diagnostic criteria and several RCM algorithms have been published for the differentiation of benign and malignant neoplasms. We provide an overview of the basic principles of RCM, characteristic RCM features of normal skin and cutaneous neoplasms, and the limitations and future directions of RCM. Copyright © 2015 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

Idas, a Novel Phylogenetically Conserved Geminin-related Protein, Binds to Geminin and Is Required for Cell Cycle Progression*

PubMed Central

Pefani, Dafni-Eleutheria; Dimaki, Maria; Spella, Magda; Karantzelis, Nickolas; Mitsiki, Eirini; Kyrousi, Christina; Symeonidou, Ioanna-Eleni; Perrakis, Anastassis; Taraviras, Stavros; Lygerou, Zoi

2011-01-01

Development and homeostasis of multicellular organisms relies on an intricate balance between cell proliferation and differentiation. Geminin regulates the cell cycle by directly binding and inhibiting the DNA replication licensing factor Cdt1. Geminin also interacts with transcriptional regulators of differentiation and chromatin remodelling factors, and its balanced interactions are implicated in proliferation-differentiation decisions during development. Here, we describe Idas (Idas being a cousin of the Gemini in Ancient Greek Mythology), a previously uncharacterised coiled-coil protein related to Geminin. We show that human Idas localizes to the nucleus, forms a complex with Geminin both in cells and in vitro through coiled-coil mediated interactions, and can change Geminin subcellular localization. Idas does not associate with Cdt1 and prevents Geminin from binding to Cdt1 in vitro. Idas depletion from cells affects cell cycle progression; cells accumulate in S phase and are unable to efficiently progress to mitosis. Idas protein levels decrease in anaphase, whereas its overexpression causes mitotic defects. During development, we show that Idas exhibits high level expression in the choroid plexus and the cortical hem of the mouse telencephalon. Our data highlight Idas as a novel Geminin binding partner, implicated in cell cycle progression, and a putative regulator of proliferation-differentiation decisions during development. PMID:21543332

Idas, a novel phylogenetically conserved geminin-related protein, binds to geminin and is required for cell cycle progression.

PubMed

Pefani, Dafni-Eleutheria; Dimaki, Maria; Spella, Magda; Karantzelis, Nickolas; Mitsiki, Eirini; Kyrousi, Christina; Symeonidou, Ioanna-Eleni; Perrakis, Anastassis; Taraviras, Stavros; Lygerou, Zoi

2011-07-01

Development and homeostasis of multicellular organisms relies on an intricate balance between cell proliferation and differentiation. Geminin regulates the cell cycle by directly binding and inhibiting the DNA replication licensing factor Cdt1. Geminin also interacts with transcriptional regulators of differentiation and chromatin remodelling factors, and its balanced interactions are implicated in proliferation-differentiation decisions during development. Here, we describe Idas (Idas being a cousin of the Gemini in Ancient Greek Mythology), a previously uncharacterised coiled-coil protein related to Geminin. We show that human Idas localizes to the nucleus, forms a complex with Geminin both in cells and in vitro through coiled-coil mediated interactions, and can change Geminin subcellular localization. Idas does not associate with Cdt1 and prevents Geminin from binding to Cdt1 in vitro. Idas depletion from cells affects cell cycle progression; cells accumulate in S phase and are unable to efficiently progress to mitosis. Idas protein levels decrease in anaphase, whereas its overexpression causes mitotic defects. During development, we show that Idas exhibits high level expression in the choroid plexus and the cortical hem of the mouse telencephalon. Our data highlight Idas as a novel Geminin binding partner, implicated in cell cycle progression, and a putative regulator of proliferation-differentiation decisions during development.

Role of the Lymphotoxin/LIGHT System in the Development and Maintenance of Reticular Networks and Vasculature in Lymphoid Tissues

PubMed Central

Lu, Theresa T.; Browning, Jeffrey L.

2014-01-01

Lymphoid organs are meeting zones where lymphocytes come together and encounter antigens present in the blood and lymph or as delivered by cells migrating from the draining tissue bed. The exquisite efficiency of this process relies heavily on highly specialized anatomy to direct and position the various players. Gated entry and exit control access to these theaters and reticular networks and associated chemokines guide cells into the proper sections. Lymphoid tissues are remarkably plastic, being able to expand dramatically and then involute upon resolution of the danger. All of the reticular scaffolds and vascular and lymphatic components adapt accordingly. As such, the lymph node (LN) is a wonderful example of a physiologic remodeling process and is potentially a guide to study such elements in pathological settings such as fibrosis, chronic infection, and tumor metastasis. The lymphotoxin/LIGHT axis delivers critical differentiation signals that direct and hone differentiation of both reticular networks and the vasculature. Considerable progress has been made recently in understanding the mesenchymal differentiation pathways leading to these specialized networks and in the remodeling that occurs in reactive LNs. In this article, we will review some new advances in the area in terms of developmental, differentiation, and maintenance events mediated by this axis. PMID:24575096

Compact, highly efficient, single-frequency 25W, 2051nm Tm fiber-based MOPA for CO2 trace-gas laser space transmitter

NASA Astrophysics Data System (ADS)

Engin, Doruk; Chuang, Ti; Litvinovitch, Slava; Storm, Mark

2017-08-01

Fibertek has developed and demonstrated an ideal high-power; low-risk; low-size, weight, and power (SWaP) 2051 nm laser design meeting the lidar requirements for satellite-based global measurement of carbon dioxide (CO2). The laser design provides a path to space for either a coherent lidar approach being developed by NASA Jet Propulsion Laboratory (JPL)1,2 or an Integrated Path Differential Lidar (IPDA) approach developed by Harris Corp using radio frequency (RF) modulation and being flown as part of a NASA Earth Venture Suborbital Mission—NASA's Atmospheric Carbon and Transport - America.3,4 The thulium (Tm) fiber laser amplifies a <500 kHz linewidth distributed feedback (DFB) laser up to 25 W average power in a polarization maintaining (PM) fiber. The design manages and suppresses all deleterious non-linear effects that can cause linewidth broadening or amplified spontaneous emission (ASE) and meets all lidar requirements. We believe the core laser components, architecture, and design margins can support a coherent or IPDA lidar 10-year space mission. With follow-on funding Fibertek can adapt an existing space-based Technology Readiness Level 6 (TRL-6), 20 W erbium fiber laser package for this Tm design and enable a near-term space mission with an electrical-to-optical (e-o) efficiency of <20%. A cladding-pumped PM Tm fiber-based amplifier optimized for high efficiency and high-power operation at 2051 nm is presented. The two-stage amplifier has been demonstrated to achieve 25 W average power and <16 dB polarization extinction ratio (PER) out of a single-mode PM fiber using a <500 kHz linewidth JPL DFB laser5-7 and 43 dB gain. The power amplifier's optical conversion efficiency is 53%. An internal efficiency of 58% is calculated after correcting for passive losses. The two-stage amplifier sustains its highly efficient operation for a temperature range of 5-40°C. The absence of stimulated Brillouin scattering (SBS) for the narrow linewidth amplification shows promise for further power scaling.

Histone h1 depletion impairs embryonic stem cell differentiation.

PubMed

Zhang, Yunzhe; Cooke, Marissa; Panjwani, Shiraj; Cao, Kaixiang; Krauth, Beth; Ho, Po-Yi; Medrzycki, Magdalena; Berhe, Dawit T; Pan, Chenyi; McDevitt, Todd C; Fan, Yuhong

2012-01-01

Pluripotent embryonic stem cells (ESCs) are known to possess a relatively open chromatin structure; yet, despite efforts to characterize the chromatin signatures of ESCs, the role of chromatin compaction in stem cell fate and function remains elusive. Linker histone H1 is important for higher-order chromatin folding and is essential for mammalian embryogenesis. To investigate the role of H1 and chromatin compaction in stem cell pluripotency and differentiation, we examine the differentiation of embryonic stem cells that are depleted of multiple H1 subtypes. H1c/H1d/H1e triple null ESCs are more resistant to spontaneous differentiation in adherent monolayer culture upon removal of leukemia inhibitory factor. Similarly, the majority of the triple-H1 null embryoid bodies (EBs) lack morphological structures representing the three germ layers and retain gene expression signatures characteristic of undifferentiated ESCs. Furthermore, upon neural differentiation of EBs, triple-H1 null cell cultures are deficient in neurite outgrowth and lack efficient activation of neural markers. Finally, we discover that triple-H1 null embryos and EBs fail to fully repress the expression of the pluripotency genes in comparison with wild-type controls and that H1 depletion impairs DNA methylation and changes of histone marks at promoter regions necessary for efficiently silencing pluripotency gene Oct4 during stem cell differentiation and embryogenesis. In summary, we demonstrate that H1 plays a critical role in pluripotent stem cell differentiation, and our results suggest that H1 and chromatin compaction may mediate pluripotent stem cell differentiation through epigenetic repression of the pluripotency genes.

Increased reprogramming of human fetal hepatocytes compared with adult hepatocytes in feeder-free conditions.

PubMed

Hansel, Marc C; Gramignoli, Roberto; Blake, William; Davila, Julio; Skvorak, Kristen; Dorko, Kenneth; Tahan, Veysel; Lee, Brian R; Tafaleng, Edgar; Guzman-Lepe, Jorge; Soto-Gutierrez, Alejandro; Fox, Ira J; Strom, Stephen C

2014-01-01

Hepatocyte transplantation has been used to treat liver disease. The availability of cells for these procedures is quite limited. Human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) may be a useful source of hepatocytes for basic research and transplantation if efficient and effective differentiation protocols were developed and problems with tumorigenicity could be overcome. Recent evidence suggests that the cell of origin may affect hiPSC differentiation. Thus, hiPSCs generated from hepatocytes may differentiate back to hepatocytes more efficiently than hiPSCs from other cell types. We examined the efficiency of reprogramming adult and fetal human hepatocytes. The present studies report the generation of 40 hiPSC lines from primary human hepatocytes under feeder-free conditions. Of these, 37 hiPSC lines were generated from fetal hepatocytes, 2 hiPSC lines from normal hepatocytes, and 1 hiPSC line from hepatocytes of a patient with Crigler-Najjar syndrome, type 1. All lines were confirmed reprogrammed and expressed markers of pluripotency by gene expression, flow cytometry, immunocytochemistry, and teratoma formation. Fetal hepatocytes were reprogrammed at a frequency over 50-fold higher than adult hepatocytes. Adult hepatocytes were only reprogrammed with six factors, while fetal hepatocytes could be reprogrammed with three (OCT4, SOX2, NANOG) or four factors (OCT4, SOX2, NANOG, LIN28 or OCT4, SOX2, KLF4, C-MYC). The increased reprogramming efficiency of fetal cells was not due to increased transduction efficiency or vector toxicity. These studies confirm that hiPSCs can be generated from adult and fetal hepatocytes including those with genetic diseases. Fetal hepatocytes reprogram much more efficiently than adult hepatocytes, although both could serve as useful sources of hiPSC-derived hepatocytes for basic research or transplantation.

Induction of hepatocyte-like cells from mouse embryonic stem cells by lentivirus-mediated constitutive expression of Foxa2/Hnf4a.

PubMed

Liu, Tao; Zhang, Shichang; Xiang, Dedong; Wang, Yingjie

2013-11-01

Hepatocytes can be generated from embryonic stem cells (ESCs) using inducers such as chemical compounds and cytokines, but issues related to low differentiation efficiencies remain to be resolved. Recent work has shown that overexpression of lineage-specific transcription factors can directly cause cells phenotypic changes, including differentiation, trans-differentiation, and de-differentiation. We hypothesized that lentivirus-mediated constitutive expression of forkhead box A2 (Foxa2) and hepatocyte nuclear factor 4 alpha (Hnf4a) could promote inducing mouse ESCs to hepatocyte-likes cells. First, ESC lines that stably expressed Foxa2, Hnf4a, or Foxa2/Hnf4a were constructed via lentiviral expression vectors. Second, observations of cell morphology changes were made during the cell culture process, followed by experiments examining teratoma formation. Then, the effects of constitutive expression of Foxa2 and Hnf4a on hepatic differentiation and maturation were determined by measuring the marker gene expression levels of Albumin, α-fetoprotein, Cytokeratin18, and α1-antitrypsin. The results indicate that constitutive expression of Foxa2 and Hnf4a does not affect ESCs culture, teratoma formation, or the expression levels of the specific hepatocyte genes under autonomous differentiation. However, with some assistance from inducing factors, Foxa2 significantly increased the hepatic differentiation of ESCs, whereas the expression of Hnf4a alone or Foxa2/Hnf4a could not. Differentiated CCE-Foxa2 cells were more superior in expressing several liver-specific markers and protein, storing glycogen than differentiated CCE cells. Therefore, our method employing the transduction of Foxa2 would be a valuable tool for the efficient generation of functional hepatocytes derived from ESCs. © 2013 Wiley Periodicals, Inc.

Two stages of enteropathogenic Escherichia coli intestinal pathogenicity are up and down-regulated by the epithelial cell differentiation.

PubMed

Gabastou, J M; Kernéis, S; Bernet-Camard, M F; Barbat, A; Coconnier, M H; Kaper, J B; Servin, A L

1995-09-01

Pathogens and eucaryotic cells are active partners during the process of pathogenicity. To gain access to enterocytes and to cross the epithelial membrane, many enterovirulent microorganisms interact with the brush border membrane-associated components as receptors. Recent reports provide evidence that intestinal cell differentiation plays a role in microbial pathogenesis. Human enteropathogenic Escherichia coli (EPEC) develop their pathogenicity upon infecting enterocytes. To determine if intestinal epithelial cell differentiation influences EPEC pathogenicity, we examined the infection of human intestinal epithelial cells by JPN 15 (pMAR7) [EAF+ eae+] EPEC strain as a function of the cell differentiation. The human embryonic intestinal INT407 cells, the human colonic T84 cells, the human undifferentiated HT-29 cells (HT-29 Std) and two enterocytic cell lines, HT-29 glc-/+ and Caco-2 cells, were used as cellular models. Cells were infected apically with the EPEC strain and the cell-association and cell-entry were examined by quantitative determination using metabolically radiolabeled bacteria, as well as by light, scanning and transmission electron microscopy. [EAF+ eae+] EPEC bacteria efficiently colonized the cultured human intestinal cells. Diffuse bacterial adhesion occurred to undifferentiated HT-29 Std and INT407 cells, whereas characteristic EPEC cell clusters were observed on fully differentiated enterocytic HT-29 glc-/+ cells and on colonic crypt T84 cells. As shown using the Caco-2 cell line, which spontaneously differentiates in culture, the formation of EPEC clusters increased as a function of the epithelial cell differentiation. In contrast, efficient cell-entry of [EAF+ eae+] EPEC bacteria occurred in recently differentiated Caco-2 cells and decreased when the cells were fully differentiated.(ABSTRACT TRUNCATED AT 250 WORDS)